Load data
corpus_md<-create_corpus_dataset(f_corp_meta,jarprepro)
dfu<-(read.csv(f_rousage,stringsAsFactors = FALSE))
dfu$AX<-apply(dfu[c("AX")],1,base64)
df<-unique(dfu)
df_sample<-read.csv(f_onts,stringsAsFactors = FALSE)
#df_ad_raw<-read_csvs_tdl(f_impactad)
nrow(df)
## [1] 870713
#nrow(df_ad_raw)
Preprocess RO usage dataset
df$O<-gsub("http://purl.obolibrary.org/obo/","", df$ONT)
df$O<-gsub(".owl$","", df$O)
df$O<-gsub(".obo$","", df$O)
df$O<-gsub("^ontoneo/","", df$O)
df$O<-gsub("http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus","NCITNCBO", df$O)
df$O<-gsub("http://www.ebi.ac.uk/swo/","", df$O)
df$O<-gsub("http://semanticscience.org/ontology/","", df$O)
df$O<-gsub("http://anobase.vectorbase.org/mirnao/","", df$O)
df$O<-gsub("agro-edit","agro", df$O)
df$O<-gsub("caro/caro","caro", df$O)
df$O<-gsub("^mfmo$","feed", df$O)
df$O<-gsub("^ico$","ico_merged", df$O)
df$O<-gsub("^ido$","ido-merged", df$O)
df$O<-gsub("^ncro$","ncro-all-in-one", df$O)
df$O<-gsub("^obcs$","obcs_merged_inferred", df$O)
df$O<-gsub("^obib$","obib_merged_inferred", df$O)
df$O<-gsub("^omiabis$","omiabis_merged", df$O)
df$O<-gsub("^opl$","opl_inferred", df$O)
df$O<-gsub("^pco_merged$","pco_merged_inferred", df$O)
df$O<-gsub("^bcgo$","bcgo_merged_inferred", df$O)
df$O<-gsub("^DINTO$","DINTO_1.2", df$O)
df$O<-gsub("^swo$","swo_merged", df$O)
df$O<-gsub("^ogg$","ogg-merged", df$O)
df$TEMP_ANN<-ifelse(df$TEMP_ANN==""&df$RO_REL=="depends on","Dom:X-Ran:X~Time:Same~Rig:Yes-Nec:No",df$TEMP_ANN)
df$TEMP_ANN_ALL<-paste(df$TEMP_ANN,df$TEMP_INF_ANN,sep="~")
df$CAT<-ifelse(grepl("Dom:C.*Ran:C",df$TEMP_ANN_ALL),"CC",ifelse(grepl("(Dom:C.*Ran:O)|(Dom:O.*Ran:C)",df$TEMP_ANN_ALL),"OC-CO",ifelse(grepl("Dom:O.*Ran:O",df$TEMP_ANN_ALL),"OO","OT")))
df$containsnecno<-grepl("Nec:No",df$TEMP_ANN_ALL)
kable(plyr::count(df$MATCH),row.names = FALSE)
| exact |
362326 |
| smart |
508387 |
# removing broken records (that are neither exact nor smart matches)
df_broken<-(df[!(df$MATCH %in% c("exact","smart")),])
df<-(df[(df$MATCH %in% c("exact","smart")),])
# Excluding exact matches
df_ex<-(df[(df$MATCH %in% c("exact")),])
df<-(df[(df$MATCH %in% c("smart")),])
o_smart<-unique(df$ONT)
o_exact<-unique(df_ex$ONT)
# ontologies with smart matches:
length(o_smart)
## [1] 98
# ontologies with exact matches:
length(o_exact)
## [1] 68
length(o_exact)/length(o_smart)
## [1] 0.6938776
length(unique(df_ex$AX))/length(unique(df$AX))
## [1] 0.7018598
print("Broken")
## [1] "Broken"
nrow(df_broken)
## [1] 0
print("Excluded Exact matches (redundant)")
## [1] "Excluded Exact matches (redundant)"
nrow(df_ex)
## [1] 362326
print("Remaining Smart matches")
## [1] "Remaining Smart matches"
nrow(df)
## [1] 508387
# Variable with number of all ontologies in dataset
ct_o<-length(unique(df$O))
Dataset characteristics
d0<-unique(df[c("O","ONT_TOTAL_AX","AX")])
## Percentage of axioms with temporal annotations across ontologies
ct_ov_o<-plyr::count(d0[c("O","ONT_TOTAL_AX")])
ct_ov_o$pc<-round((ct_ov_o$freq/ct_ov_o$ONT_TOTAL_AX)*100,2)
summary(ct_ov_o$pc)
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.040 5.485 18.005 25.784 39.005 98.510
ct_ov_o<-ct_ov_o[order(-ct_ov_o$pc),]
kable(ct_ov_o,row.names = FALSE)
| flopo |
23504 |
23154 |
98.51 |
| emap |
21723 |
21196 |
97.57 |
| wbls |
1424 |
1334 |
93.68 |
| xao |
5887 |
4373 |
74.28 |
| zfa |
11750 |
8619 |
73.35 |
| tgma |
2733 |
1952 |
71.42 |
| tads |
948 |
663 |
69.94 |
| oba |
36448 |
24245 |
66.52 |
| mmusdv |
307 |
196 |
63.84 |
| ddanat |
347 |
221 |
63.69 |
| hsapdv |
698 |
442 |
63.32 |
| zfs |
148 |
92 |
62.16 |
| fbdv |
719 |
437 |
60.78 |
| fbbt |
33282 |
19997 |
60.08 |
| spd |
840 |
458 |
54.52 |
| clo |
117057 |
61416 |
52.47 |
| ma |
4104 |
1975 |
48.12 |
| cl |
7976 |
3784 |
47.44 |
| olatdv |
91 |
42 |
46.15 |
| wbbt |
15187 |
7002 |
46.11 |
| uberon |
53169 |
24218 |
45.55 |
| pdumdv |
42 |
19 |
45.24 |
| fypo |
33040 |
14080 |
42.62 |
| ehdaa2 |
13369 |
5394 |
40.35 |
| cvdo |
580 |
229 |
39.48 |
| bto |
6884 |
2587 |
37.58 |
| mp |
22776 |
8516 |
37.39 |
| po |
3152 |
1053 |
33.41 |
| opl_inferred |
886 |
292 |
32.96 |
| emapa |
21772 |
6877 |
31.59 |
| dpo |
1265 |
393 |
31.07 |
| exo |
101 |
31 |
30.69 |
| mro |
3098 |
920 |
29.70 |
| go |
106492 |
31414 |
29.50 |
| ceph |
604 |
178 |
29.47 |
| aeo |
366 |
101 |
27.60 |
| bspo |
473 |
130 |
27.48 |
| feed |
353 |
97 |
27.48 |
| hp |
21326 |
5719 |
26.82 |
| ovae |
4701 |
1173 |
24.95 |
| idomal |
3468 |
846 |
24.39 |
| so-xp |
3096 |
747 |
24.13 |
| obi |
6316 |
1461 |
23.13 |
| hao |
10171 |
2274 |
22.36 |
| caro |
163 |
36 |
22.09 |
| fao |
116 |
25 |
21.55 |
| cteno |
999 |
202 |
20.22 |
| bcgo_merged_inferred |
4514 |
886 |
19.63 |
| sibo |
1106 |
205 |
18.54 |
| to |
6406 |
1119 |
17.47 |
| obib_merged_inferred |
1291 |
216 |
16.73 |
| chebi |
224955 |
36582 |
16.26 |
| omiabis_merged |
990 |
153 |
15.45 |
| poro |
1211 |
186 |
15.36 |
| dideo |
442 |
65 |
14.71 |
| ido-merged |
1064 |
150 |
14.10 |
| fbcv |
2836 |
399 |
14.07 |
| stato |
1876 |
264 |
14.07 |
| agro |
986 |
135 |
13.69 |
| ontoneo |
430 |
58 |
13.49 |
| envo |
9896 |
1238 |
12.51 |
| ico_merged |
705 |
86 |
12.20 |
| cheminf |
485 |
56 |
11.55 |
| MicrO |
5441 |
623 |
11.45 |
| DINTO_1.2 |
173859 |
19400 |
11.16 |
| bco |
304 |
32 |
10.53 |
| mirnao |
764 |
79 |
10.34 |
| oostt |
175 |
18 |
10.29 |
| omp |
1998 |
203 |
10.16 |
| rex |
730 |
62 |
8.49 |
| xco |
607 |
49 |
8.07 |
| obcs_merged_inferred |
1438 |
99 |
6.88 |
| ero |
4893 |
322 |
6.58 |
| NCITNCBO |
281421 |
14411 |
5.12 |
| iao |
383 |
19 |
4.96 |
| rxno |
1328 |
58 |
4.37 |
| pw |
3253 |
136 |
4.18 |
| swo_merged |
7683 |
320 |
4.17 |
| ms |
2949 |
114 |
3.87 |
| ogsf-merged |
1056 |
36 |
3.41 |
| fix |
1684 |
51 |
3.03 |
| chmo |
3417 |
91 |
2.66 |
| mi |
1424 |
33 |
2.32 |
| mod |
3581 |
82 |
2.29 |
| aero |
1101 |
23 |
2.09 |
| miro |
4457 |
79 |
1.77 |
| MFOEM |
289 |
5 |
1.73 |
| vario |
405 |
4 |
0.99 |
| pato |
2384 |
15 |
0.63 |
| mop |
3809 |
20 |
0.53 |
| cdao |
421 |
2 |
0.48 |
| genepio |
3148 |
14 |
0.44 |
| pco_merged_inferred |
2600 |
11 |
0.42 |
| mpath |
941 |
3 |
0.32 |
| cmo |
3299 |
8 |
0.24 |
| ncro-all-in-one |
5471 |
7 |
0.13 |
| rs |
5922 |
7 |
0.12 |
| ogg-merged |
70116 |
28 |
0.04 |
## Distribution of ontologies
options(scipen=1000)
ov_o_size<-unique(d0[c("O","ONT_TOTAL_AX")])
summary(ov_o_size$ONT_TOTAL_AX)
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 42.0 708.5 2191.0 14958.1 6217.5 281421.0
#ggplot(ov_o_size,aes(ONT_TOTAL_AX)) + geom_histogram(bins = 10) + scale_x_log10()
ct_cat<-plyr::count(df$CAT)
kable(ct_cat,row.names = FALSE)
| CC |
253334 |
| OC-CO |
29694 |
| OO |
35071 |
| OT |
190288 |
### The impact of smart matching (difference of top ten relation by coverage)
ds<-unique(df[c("O","AX","RO_REL","CAT")])
de<-unique(df_ex[c("O","AX","RO_REL","CAT")])
coverage_rel_wosmart<-compute_coverage_rel(de[c("O","RO_REL","CAT")],ct_o)
coverage_rel<-compute_coverage_rel(ds[c("O","RO_REL","CAT")],ct_o)
top10<-head(coverage_rel[order(-coverage_rel$coverage),],10)
top10e<-coverage_rel_wosmart[coverage_rel_wosmart$x %in% top10$x,]
top10e$source<-"exact"
top10$source<-"smart"
top<-merge(top10,top10e,all = TRUE)
top$CAT<-NULL
top$freq<-NULL
top<-reshape(top,direction = "wide",timevar = "source",idvar = "x")
names(top)<-c("Relation","Exact","Smart")
top$pdiff<-round(((top$Smart-top$Exact)/top$Exact)*100,2)
top<-top[order(-top$Smart),]
kable(top,row.names = FALSE)
| part of |
52.04 |
79.59 |
52.94 |
| has part |
40.82 |
48.98 |
19.99 |
| inheres in |
24.49 |
29.59 |
20.82 |
| has participant |
17.35 |
27.55 |
58.79 |
| has role |
16.33 |
26.53 |
62.46 |
| realizes |
21.43 |
24.49 |
14.28 |
| located in |
18.37 |
21.43 |
16.66 |
| has quality |
12.24 |
20.41 |
66.75 |
| bearer of |
15.31 |
19.39 |
26.65 |
| develops from |
16.33 |
19.39 |
18.74 |
print(xtable(top,digits=c(0,0,2,2,2)),include.rownames=FALSE,file="coverage_rel_exact_v_smart.tex")
## Histogram of smart matches over ontology size
#### y axis = number of ontologies, x axis: % of (axioms that use RO relations) / (total axioms)
ct_o_smart<-plyr::count(unique(ds[c("O","AX")])[c("O")])
ct_o_smart<-merge(ct_o_smart,ov_o_size,by="O")
ct_o_smart$rat<-ct_o_smart$freq/ct_o_smart$ONT_TOTAL_AX
p<-ggplot(ct_o_smart,aes(rat)) + geom_histogram() + xlab("% of axioms with smart matches") + ylab("Number of ontologies")
theme_tdl(p)
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
ggsave("hist_matches_d_ontsize.jpg",width = 3,height = 4,units="in")
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
#### y axis = number of ontologies, x axis: number of DIFFERENT ro relations used in ontology
ct_o_ro<-plyr::count(unique(ds[c("O","RO_REL")])[c("O")])
ct_o_ro$pc<-100*(ct_o_ro$freq/nr_ro_rel)
p<-ggplot(ct_o_ro,aes(freq)) + geom_histogram() + xlab("Nr. of RO relations used") + ylab("Number of ontologies")
theme_tdl(p)
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
ggsave("hist_ro_rel_ont.jpg",width = 3,height = 4,units="in")
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
### Check for duplicates
xx<-plyr::count(dfu[!(names(dfu) %in% c("AX"))])
yy<-xx[xx$freq>1,]
### Number of exact duplicate records in raw dataset
nrow(yy)
## [1] 4
head(yy)
## ONT_TOTAL_AX RO_REL OBO_REL
## 93370 117057 part of part_of
## 93371 117057 part of part_of
## 189473 117057 derives from derives from
## 189474 117057 derives from derives from
## TEMP_INF_ANN
## 93370
## 93371
## 189473 Time:Diff~Dom:C-Ran:IC~Ran:Changed~Dom:C-Ran:C~Dom:Changed~Dom:IC-Ran:C
## 189474 Time:Diff~Dom:C-Ran:IC~Ran:Changed~Dom:C-Ran:C~Dom:Changed~Dom:IC-Ran:C
## ONT
## 93370 http://purl.obolibrary.org/obo/clo.owl
## 93371 http://purl.obolibrary.org/obo/clo.owl
## 189473 http://purl.obolibrary.org/obo/clo.owl
## 189474 http://purl.obolibrary.org/obo/clo.owl
## RO_REL_IRI RO_REL_HC OBO_REL_HC
## 93370 http://purl.obolibrary.org/obo/BFO_0000050 -978027865 -978027865
## 93371 http://purl.obolibrary.org/obo/BFO_0000050 -978027865 -978027865
## 189473 http://purl.obolibrary.org/obo/RO_0001000 1643394301 1643394301
## 189474 http://purl.obolibrary.org/obo/RO_0001000 1643394301 1643394301
## MATCH AX_HC OBO_REL_IRI
## 93370 exact 1812853289 http://purl.obolibrary.org/obo/BFO_0000050
## 93371 smart 1812853289 http://purl.obolibrary.org/obo/BFO_0000050
## 189473 exact 1812853289 http://purl.obolibrary.org/obo/RO_0001000
## 189474 smart 1812853289 http://purl.obolibrary.org/obo/RO_0001000
## TEMP_ANN X freq
## 93370 Dom:X-Ran:X~Time:Same~Rig:Yes-Nec:No~TI:AHFAT NA 2
## 93371 Dom:X-Ran:X~Time:Same~Rig:Yes-Nec:No~TI:AHFAT NA 2
## 189473 Dom:IC-Ran:IC~Time:Past~Dom:Birth~Ran:Death NA 2
## 189474 Dom:IC-Ran:IC~Time:Past~Dom:Birth~Ran:Death NA 2
Example MIRNAO
unique(ct_ov_o[ct_ov_o$O=="mirnao",c("O","ONT_TOTAL_AX","freq","pc")])
## O ONT_TOTAL_AX freq pc
## 50 mirnao 764 79 10.34
ct_different_rorels <-plyr::count(ds[ds$O=="mirnao","RO_REL"])
nrow(ct_different_rorels)
## [1] 8
ct_different_rorels
## x freq
## 1 adjacent to 1
## 2 derives from 41
## 3 has part 1
## 4 has participant 1
## 5 has role 1
## 6 part of 30
## 7 preceded by 1
## 8 regulates 3
summary(ct_o_ro$freq)
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 1.000 2.000 4.500 8.306 11.000 78.000
summary(ct_o_ro$pc)
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.250 0.500 1.125 2.077 2.750 19.500
(ct_o_ro[ct_o_ro$freq>20,])
## O freq pc
## 4 bcgo_merged_inferred 23 5.75
## 26 envo 35 8.75
## 30 fbbt 30 7.50
## 36 fypo 21 5.25
## 63 obi 25 6.25
## 70 ontoneo 21 5.25
## 73 ovae 51 12.75
## 91 uberon 78 19.50
Coverage: Relation
coverage_rel<-compute_coverage_rel(df[c("O","RO_REL","CAT")],ct_o)
d_coverage_rel<-preparePlotRanksDf(coverage_rel,"x","coverage")
plotRanks(coverage_rel,"x","coverage",xlab="Relation",ylab="Coverage",ncol=1)
ggsave("coverage_rel.jpg",width = 3,height = 4,units="in")
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
top10<-head(coverage_rel[order(-coverage_rel$coverage),],10)
top10relcov<-top10$x
all<-coverage_rel[order(coverage_rel$CAT,-coverage_rel$coverage),]
print(xtable(all,digits=c(0,0,2,2,2)),include.rownames=FALSE,file="coverage_rel.tex")
print(xtable(top10,digits=c(0,0,2,2,2)),include.rownames=FALSE,file="coverage_rel_top10.tex")
# Summary stats over ALL temporal features
summary(all$coverage)
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 1.020 1.020 2.040 5.728 6.120 79.590
sd(all$coverage)
## [1] 9.375772
# Summary stats BY DOMAIN RANGE over ALL temporal features
ddply(all,~CAT,summarise,mean=mean(coverage),median=median(coverage),sd=sd(coverage), min=min(coverage),max=max(coverage))
## CAT mean median sd min max
## 1 CC 4.413980 2.04 5.801800 1.02 29.59
## 2 OC-CO 6.844583 3.06 7.538174 1.02 27.55
## 3 OO 5.555000 3.06 5.482081 1.02 18.37
## 4 OT 26.734000 2.04 35.949403 1.02 79.59
kable(all,row.names = FALSE)
| inheres in |
29 |
29.59 |
CC |
| has role |
26 |
26.53 |
CC |
| located in |
21 |
21.43 |
CC |
| has quality |
20 |
20.41 |
CC |
| bearer of |
19 |
19.39 |
CC |
| develops from |
19 |
19.39 |
CC |
| derives from |
16 |
16.33 |
CC |
| adjacent to |
15 |
15.31 |
CC |
| concretizes |
15 |
15.31 |
CC |
| has function |
10 |
10.20 |
CC |
| has member |
10 |
10.20 |
CC |
| towards |
10 |
10.20 |
CC |
| overlaps |
9 |
9.18 |
CC |
| continuous with |
8 |
8.16 |
CC |
| composed primarily of |
7 |
7.14 |
CC |
| has component |
7 |
7.14 |
CC |
| location of |
7 |
7.14 |
CC |
| member of |
7 |
7.14 |
CC |
| surrounded by |
7 |
7.14 |
CC |
| function of |
6 |
6.12 |
CC |
| is concretized as |
6 |
6.12 |
CC |
| produces |
6 |
6.12 |
CC |
| role of |
6 |
6.12 |
CC |
| surrounds |
6 |
6.12 |
CC |
| attached to |
5 |
5.10 |
CC |
| inheres in part of |
5 |
5.10 |
CC |
| connected to |
4 |
4.08 |
CC |
| connects |
4 |
4.08 |
CC |
| has developmental contribution from |
4 |
4.08 |
CC |
| innervates |
4 |
4.08 |
CC |
| produced by |
4 |
4.08 |
CC |
| bounding layer of |
3 |
3.06 |
CC |
| contains |
3 |
3.06 |
CC |
| develops into |
3 |
3.06 |
CC |
| directly develops from |
3 |
3.06 |
CC |
| has potential to develop into |
3 |
3.06 |
CC |
| innervated_by |
3 |
3.06 |
CC |
| conduit for |
2 |
2.04 |
CC |
| contributes to morphology of |
2 |
2.04 |
CC |
| developmentally induced by |
2 |
2.04 |
CC |
| developmentally replaces |
2 |
2.04 |
CC |
| develops in |
2 |
2.04 |
CC |
| has 2D boundary |
2 |
2.04 |
CC |
| has habitat |
2 |
2.04 |
CC |
| has modifier |
2 |
2.04 |
CC |
| has plasma membrane part |
2 |
2.04 |
CC |
| has potential to developmentally contribute to |
2 |
2.04 |
CC |
| has skeleton |
2 |
2.04 |
CC |
| has soma location |
2 |
2.04 |
CC |
| has synaptic terminal in |
2 |
2.04 |
CC |
| immediate transformation of |
2 |
2.04 |
CC |
| interacts with |
2 |
2.04 |
CC |
| luminal space of |
2 |
2.04 |
CC |
| quality of |
2 |
2.04 |
CC |
| skeleton of |
2 |
2.04 |
CC |
| supplies |
2 |
2.04 |
CC |
| synapsed by |
2 |
2.04 |
CC |
| synapsed to |
2 |
2.04 |
CC |
| transformation of |
2 |
2.04 |
CC |
| tributary of |
2 |
2.04 |
CC |
| attached to part of |
1 |
1.02 |
CC |
| branching part of |
1 |
1.02 |
CC |
| child nucleus of |
1 |
1.02 |
CC |
| child nucleus of in hermaphrodite |
1 |
1.02 |
CC |
| child nucleus of in male |
1 |
1.02 |
CC |
| confers advantage in |
1 |
1.02 |
CC |
| contained in |
1 |
1.02 |
CC |
| determined by |
1 |
1.02 |
CC |
| determined by part of |
1 |
1.02 |
CC |
| develops from part of |
1 |
1.02 |
CC |
| distributary of |
1 |
1.02 |
CC |
| drains |
1 |
1.02 |
CC |
| electrically_synapsed_to |
1 |
1.02 |
CC |
| expresses |
1 |
1.02 |
CC |
| fasciculates with |
1 |
1.02 |
CC |
| gene product of |
1 |
1.02 |
CC |
| has disposition |
1 |
1.02 |
CC |
| has fused element |
1 |
1.02 |
CC |
| has host |
1 |
1.02 |
CC |
| has muscle antagonist |
1 |
1.02 |
CC |
| has muscle insertion |
1 |
1.02 |
CC |
| has muscle origin |
1 |
1.02 |
CC |
| has postsynaptic terminal in |
1 |
1.02 |
CC |
| has presynaptic terminal in |
1 |
1.02 |
CC |
| has synaptic terminal of |
1 |
1.02 |
CC |
| has vector |
1 |
1.02 |
CC |
| in homology relationship with |
1 |
1.02 |
CC |
| lumen of |
1 |
1.02 |
CC |
| molecularly interacts with |
1 |
1.02 |
CC |
| partially overlaps |
1 |
1.02 |
CC |
| serially homologous to |
1 |
1.02 |
CC |
| spatially disjoint from |
1 |
1.02 |
CC |
| synapsed_via_type_Ib_bouton_to |
1 |
1.02 |
CC |
| synapsed_via_type_II_bouton_to |
1 |
1.02 |
CC |
| synapsed_via_type_III_bouton_to |
1 |
1.02 |
CC |
| synapsed_via_type_Is_bouton_to |
1 |
1.02 |
CC |
| transcribed from |
1 |
1.02 |
CC |
| transcribed to |
1 |
1.02 |
CC |
| has participant |
27 |
27.55 |
OC-CO |
| realizes |
24 |
24.49 |
OC-CO |
| realized in |
17 |
17.35 |
OC-CO |
| participates in |
15 |
15.31 |
OC-CO |
| occurs in |
14 |
14.29 |
OC-CO |
| capable of |
10 |
10.20 |
OC-CO |
| has output |
8 |
8.16 |
OC-CO |
| output of |
6 |
6.12 |
OC-CO |
| has input |
5 |
5.10 |
OC-CO |
| existence starts during |
4 |
4.08 |
OC-CO |
| existence starts during or after |
4 |
4.08 |
OC-CO |
| capable of part of |
3 |
3.06 |
OC-CO |
| existence ends during |
3 |
3.06 |
OC-CO |
| existence ends during or before |
3 |
3.06 |
OC-CO |
| existence starts and ends during |
3 |
3.06 |
OC-CO |
| actively participates in |
2 |
2.04 |
OC-CO |
| existence ends with |
2 |
2.04 |
OC-CO |
| existence starts with |
2 |
2.04 |
OC-CO |
| formed as result of |
2 |
2.04 |
OC-CO |
| has active participant |
2 |
2.04 |
OC-CO |
| results in formation of |
2 |
2.04 |
OC-CO |
| contains process |
1 |
1.02 |
OC-CO |
| functionally related to |
1 |
1.02 |
OC-CO |
| has intermediate |
1 |
1.02 |
OC-CO |
| preceded by |
18 |
18.37 |
OO |
| immediately preceded by |
15 |
15.31 |
OO |
| precedes |
15 |
15.31 |
OO |
| regulates |
10 |
10.20 |
OO |
| negatively regulates |
6 |
6.12 |
OO |
| starts |
6 |
6.12 |
OO |
| ends during |
4 |
4.08 |
OO |
| positively regulates |
4 |
4.08 |
OO |
| ends |
3 |
3.06 |
OO |
| happens during |
3 |
3.06 |
OO |
| obsolete preceded by |
3 |
3.06 |
OO |
| ends with |
2 |
2.04 |
OO |
| immediately precedes |
2 |
2.04 |
OO |
| starts during |
2 |
2.04 |
OO |
| starts with |
2 |
2.04 |
OO |
| causally downstream of |
1 |
1.02 |
OO |
| causally upstream of or within |
1 |
1.02 |
OO |
| simultaneous with |
1 |
1.02 |
OO |
| part of |
78 |
79.59 |
OT |
| has part |
48 |
48.98 |
OT |
| in taxon |
2 |
2.04 |
OT |
| only in taxon |
2 |
2.04 |
OT |
| depends on |
1 |
1.02 |
OT |
kable(top10,row.names = FALSE)
| part of |
78 |
79.59 |
OT |
| has part |
48 |
48.98 |
OT |
| inheres in |
29 |
29.59 |
CC |
| has participant |
27 |
27.55 |
OC-CO |
| has role |
26 |
26.53 |
CC |
| realizes |
24 |
24.49 |
OC-CO |
| located in |
21 |
21.43 |
CC |
| has quality |
20 |
20.41 |
CC |
| bearer of |
19 |
19.39 |
CC |
| develops from |
19 |
19.39 |
CC |
Coverage: Temporal Annotation
coverage_ann<-compute_coverage_ann(df[df$TEMP_ANN!="",c("O","TEMP_ANN","CAT")],ct_o)
coverage_ann$ann_id<-paste("A",1:nrow(coverage_ann),sep="")
plotRanks(coverage_ann,"ann_id","coverage",xlab="Annotation",ylab="Coverage")
ggsave("coverage_ann.jpg",width = 3,height = 2.5,units="in")
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
top10<-head(coverage_ann[order(-coverage_ann$coverage),],10)
top10anncov<-top10$x
all<-coverage_ann[order(coverage_ann$CAT,-coverage_ann$coverage),]
# Summary stats over ALL temporal features
summary(all$coverage)
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 1.020 2.040 4.080 9.168 14.290 85.710
sd(all$coverage)
## [1] 12.71982
# Summary stats BY DOMAIN RANGE over ALL temporal features
ddply(all,~CAT,summarise,mean=mean(coverage),median=median(coverage),sd=sd(coverage), min=min(coverage),max=max(coverage))
## CAT mean median sd min max
## 1 CC 8.832187 4.08 9.949514 1.02 34.69
## 2 OC-CO 8.216316 4.08 8.089142 1.02 27.55
## 3 OO 6.777857 3.57 6.387612 1.02 21.43
## 4 OT 29.930000 3.06 48.317664 1.02 85.71
kable(all,row.names = FALSE)
| Dom:IC-Ran:ICTime:SameRig:Yes-Nec:No~TI:AHFAT |
34 |
34.69 |
CC |
A32 |
| Dom:IC-Ran:SDCTime:SameRig:Yes-Nec:No |
34 |
34.69 |
CC |
A38 |
| Dom:SDC-Ran:ICTime:SameRig:Yes-Nec:No~TI:AHFAT |
29 |
29.59 |
CC |
A63 |
| Dom:C-Ran:CTime:SameRig:Yes-Nec:No~TI:AHFAT |
19 |
19.39 |
CC |
A2 |
| Dom:IC-Ran:ICTime:PastIdentity:Same-Nec:No~Dom:Birth-Nec:No |
19 |
19.39 |
CC |
A26 |
| Dom:IC-Ran:SDCTime:SameRig:Yes-Nec:No~TI:AHFAT |
19 |
19.39 |
CC |
A39 |
| Dom:IC-Ran:ICTime:PastDom:Birth~Ran:Death |
17 |
17.35 |
CC |
A23 |
| Dom:SDC-Ran:GDCTime:SameRig:Yes-Nec:No |
15 |
15.31 |
CC |
A61 |
| Dom:IC-Ran:ICTime:SameRig:Yes-Nec:No |
14 |
14.29 |
CC |
A31 |
| Dom:SDC-Ran:C~Time:Same |
10 |
10.20 |
CC |
A60 |
| Dom:SDC-Ran:ICTime:SameRig:Yes-Nec:No |
9 |
9.18 |
CC |
A62 |
| Dom:GDC-Ran:SDCTime:SameRig:Yes-Nec:No |
6 |
6.12 |
CC |
A14 |
| Dom:IC-Ran:ICTime:FutureRan:Birth |
6 |
6.12 |
CC |
A20 |
| Dom:IC-Ran:IC~Time:Same |
5 |
5.10 |
CC |
A29 |
| Dom:IC-Ran:ICTime:SameRig:Yes~TI:AHFAT |
5 |
5.10 |
CC |
A33 |
| Dom:IC-Ran:IC~Time:Past |
4 |
4.08 |
CC |
A21 |
| Dom:IC-Ran:ICTime:PastDom:Birth |
4 |
4.08 |
CC |
A22 |
| Dom:IC-Ran:ICTime:SameRig:Yes |
4 |
4.08 |
CC |
A30 |
| Dom:IC-Ran:ICTime:FutureIdentity:Same-Nec:No~Dom:Birth-Nec:No |
3 |
3.06 |
CC |
A18 |
| Dom:IC-Ran:ICTime:FutureIdentity:Same-Nec:No~Ran:Birth-Nec:No |
3 |
3.06 |
CC |
A19 |
| Dom:IC-Ran:CTime:SameRig:Yes-Nec:No~TI:AHFAT |
2 |
2.04 |
CC |
A17 |
| Dom:IC-Ran:ICTime:PastDom:Changed |
2 |
2.04 |
CC |
A24 |
| Dom:IC-Ran:ICTime:PastDom:ChangedRan:ChangedDom:Birth-Nec:No~Ran:Death-Nec:No |
2 |
2.04 |
CC |
A25 |
| Dom:IC-Ran:ICTime:PastIdentity:Same~Dom:Changed |
2 |
2.04 |
CC |
A27 |
| Dom:IC-Ran:ICTime:PastImmediateIdentity:Same~Dom:Changed |
2 |
2.04 |
CC |
A28 |
| Dom:SDC-Ran:SDCTime:SameRig:Yes-Nec:No |
2 |
2.04 |
CC |
A65 |
| Dom:C-Ran:C~Time:Same |
1 |
1.02 |
CC |
A1 |
| Dom:C-Ran:ICTime:SameRig:Yes-Nec:No~TI:AHFAT |
1 |
1.02 |
CC |
A3 |
| Dom:GDC-Ran:GDCTime:FutureRan:Birth |
1 |
1.02 |
CC |
A12 |
| Dom:GDC-Ran:GDCTime:PastDom:Birth |
1 |
1.02 |
CC |
A13 |
| Dom:IC-Ran:CTime:PastDom:Birth |
1 |
1.02 |
CC |
A15 |
| Dom:IC-Ran:C~Time:Same |
1 |
1.02 |
CC |
A16 |
| Dom:P-Ran:CTime:SameRig:Yes-Nec:No |
27 |
27.55 |
OC-CO |
A57 |
| Dom:P-Ran:SDCTime:SameRig:Yes-Nec:No |
24 |
24.49 |
OC-CO |
A59 |
| Dom:SDC-Ran:PTime:SameRig:Yes-Nec:No |
17 |
17.35 |
OC-CO |
A64 |
| Dom:C-Ran:PTime:SameRig:Yes-Nec:No |
16 |
16.33 |
OC-CO |
A11 |
| Dom:O-Ran:ICTime:SameRig:Yes |
14 |
14.29 |
OC-CO |
A40 |
| Dom:IC-Ran:P~Time:Future |
10 |
10.20 |
OC-CO |
A35 |
| Dom:P-Ran:CTime:SameRan:Birth |
9 |
9.18 |
OC-CO |
A54 |
| Dom:C-Ran:P~Time:Same |
6 |
6.12 |
OC-CO |
A9 |
| Dom:P-Ran:CTime:SameRan:Changed |
5 |
5.10 |
OC-CO |
A55 |
| Dom:C-Ran:OTime:Same/PastDom:Birth |
4 |
4.08 |
OC-CO |
A5 |
| Dom:C-Ran:OTime:SameDom:Birth |
4 |
4.08 |
OC-CO |
A6 |
| Dom:C-Ran:OTime:Same/FutureDom:Death |
3 |
3.06 |
OC-CO |
A4 |
| Dom:C-Ran:OTime:SameRig:YesDom:BirthDom:Death |
3 |
3.06 |
OC-CO |
A7 |
| Dom:C-Ran:OTime:SameRig:Yes~Dom:Death |
3 |
3.06 |
OC-CO |
A8 |
| Dom:IC-Ran:P~Time:Same |
3 |
3.06 |
OC-CO |
A36 |
| Dom:C-Ran:PTime:SameDom:Birth |
2 |
2.04 |
OC-CO |
A10 |
| Dom:IC-Ran:OTime:SameRig:Yes-Nec:No |
1 |
1.02 |
OC-CO |
A34 |
| Dom:IC-Ran:PTime:SameRig:Yes |
1 |
1.02 |
OC-CO |
A37 |
| Dom:P-Ran:CTime:SameRig:Yes |
1 |
1.02 |
OC-CO |
A56 |
| Dom:O-Ran:O~Time:BeforeInverse |
21 |
21.43 |
OO |
A43 |
| Dom:O-Ran:O~Time:Before |
15 |
15.31 |
OO |
A41 |
| Dom:O-Ran:O~Time:MeetsInverse |
15 |
15.31 |
OO |
A51 |
| Dom:P-Ran:P~Time:Before/During |
10 |
10.20 |
OO |
A58 |
| Dom:O-Ran:O~Time:Before/During |
7 |
7.14 |
OO |
A42 |
| Dom:O-Ran:O~Time:Starts |
6 |
6.12 |
OO |
A52 |
| Dom:O-Ran:O~Time:During/Overlaps |
4 |
4.08 |
OO |
A45 |
| Dom:O-Ran:O~Time:During |
3 |
3.06 |
OO |
A44 |
| Dom:O-Ran:O~Time:Finishes |
3 |
3.06 |
OO |
A47 |
| Dom:O-Ran:O~Time:During/OverlapsInverse |
2 |
2.04 |
OO |
A46 |
| Dom:O-Ran:O~Time:FinishesInverse |
2 |
2.04 |
OO |
A48 |
| Dom:O-Ran:O~Time:Meets |
2 |
2.04 |
OO |
A50 |
| Dom:O-Ran:O~Time:StartsInverse |
2 |
2.04 |
OO |
A53 |
| Dom:O-Ran:O~Time:IsEqualTo |
1 |
1.02 |
OO |
A49 |
| Dom:X-Ran:XTime:SameRig:Yes-Nec:No~TI:AHFAT |
84 |
85.71 |
OT |
A68 |
| Dom:X-Ran:IC~Time:Same |
3 |
3.06 |
OT |
A66 |
| Dom:X-Ran:XTime:SameRig:Yes-Nec:No |
1 |
1.02 |
OT |
A67 |
kable(top10,row.names = FALSE)
| Dom:X-Ran:XTime:SameRig:Yes-Nec:No~TI:AHFAT |
84 |
85.71 |
OT |
A68 |
| Dom:IC-Ran:ICTime:SameRig:Yes-Nec:No~TI:AHFAT |
34 |
34.69 |
CC |
A32 |
| Dom:IC-Ran:SDCTime:SameRig:Yes-Nec:No |
34 |
34.69 |
CC |
A38 |
| Dom:SDC-Ran:ICTime:SameRig:Yes-Nec:No~TI:AHFAT |
29 |
29.59 |
CC |
A63 |
| Dom:P-Ran:CTime:SameRig:Yes-Nec:No |
27 |
27.55 |
OC-CO |
A57 |
| Dom:P-Ran:SDCTime:SameRig:Yes-Nec:No |
24 |
24.49 |
OC-CO |
A59 |
| Dom:O-Ran:O~Time:BeforeInverse |
21 |
21.43 |
OO |
A43 |
| Dom:C-Ran:CTime:SameRig:Yes-Nec:No~TI:AHFAT |
19 |
19.39 |
CC |
A2 |
| Dom:IC-Ran:ICTime:PastIdentity:Same-Nec:No~Dom:Birth-Nec:No |
19 |
19.39 |
CC |
A26 |
| Dom:IC-Ran:SDCTime:SameRig:Yes-Nec:No~TI:AHFAT |
19 |
19.39 |
CC |
A39 |
coverage_ann_xt<-coverage_ann
coverage_ann_xt$x<-NULL
print(xtable(all[,c("ann_id","freq","coverage","CAT")],digits=c(0,0,2,2,2)),include.rownames=FALSE,file="coverage_ann.tex")
print(xtable(top10[,c("ann_id","freq","coverage","CAT")],digits=c(0,0,2,2,2)),include.rownames=FALSE,file="coverage_ann_top10.tex")
Coverage: Temporal Attributes
coverage_feat<-compute_coverage_feat(df[c("O","TEMP_ANN_ALL","CAT")],ct_o)
## Warning in "\"\"": attributes are not identical across measure variables;
## they will be dropped
plotRanks(coverage_feat,"x","coverage",xlab="Temporal Feature",ylab="Coverage",ncol = 1)
ggsave("coverage_feat.jpg",width = 3,height = 4,units="in")
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
top10<-head(coverage_feat[order(-coverage_feat$coverage),],10)
top10attcov<-top10$x
all<-coverage_feat[order(coverage_feat$CAT,-coverage_feat$coverage),]
# Summary stats over ALL temporal features
summary(all$coverage)
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 1.02 5.10 15.31 23.45 36.73 85.71
sd(all$coverage)
## [1] 23.22989
# Summary stats BY DOMAIN RANGE over ALL temporal features
ddply(all,~CAT,summarise,mean=mean(coverage),median=median(coverage),sd=sd(coverage), min=min(coverage),max=max(coverage))
## CAT mean median sd min max
## 1 CC 25.31258 19.39 21.22622 1.02 69.39
## 2 OC-CO 18.90095 13.27 14.03151 3.06 46.94
## 3 OO 11.54375 5.10 13.33598 1.02 41.84
## 4 OT 69.18000 85.71 36.96220 3.06 85.71
kable(all,row.names = FALSE)
| CC-Dom:C-Ran:C |
68 |
69.39 |
CC |
| CC-Dom:IC-Ran:C |
62 |
63.27 |
CC |
| CC-Time:Same |
60 |
61.22 |
CC |
| CC-Rig:Yes-Nec:No |
59 |
60.20 |
CC |
| CC-TI:AHFAT |
53 |
54.08 |
CC |
| CC-Dom:C-Ran:IC |
46 |
46.94 |
CC |
| CC-Dom:IC-Ran:IC |
46 |
46.94 |
CC |
| CC-Dom:IC-Ran:SDC |
38 |
38.78 |
CC |
| CC-Time:Diff |
37 |
37.76 |
CC |
| CC-Time:Past |
36 |
36.73 |
CC |
| CC-Dom:SDC-Ran:C |
34 |
34.69 |
CC |
| CC-Dom:SDC-Ran:IC |
30 |
30.61 |
CC |
| CC-Dom:Birth |
22 |
22.45 |
CC |
| CC-Dom:Changed |
22 |
22.45 |
CC |
| CC-Ran:Changed |
22 |
22.45 |
CC |
| CC-Dom:Birth-Nec:No |
19 |
19.39 |
CC |
| CC-Dom:Changed-Nec:No |
19 |
19.39 |
CC |
| CC-Identity:Same-Nec:No |
19 |
19.39 |
CC |
| CC-Ran:Death |
17 |
17.35 |
CC |
| CC-Dom:SDC-Ran:GDC |
15 |
15.31 |
CC |
| CC-Time:Future |
9 |
9.18 |
CC |
| CC-Ran:Birth |
7 |
7.14 |
CC |
| CC-Dom:GDC-Ran:SDC |
6 |
6.12 |
CC |
| CC-Rig:Yes |
6 |
6.12 |
CC |
| CC-Ran:Changed-Nec:No |
5 |
5.10 |
CC |
| CC-Ran:Birth-Nec:No |
3 |
3.06 |
CC |
| CC-Dom:SDC-Ran:SDC |
2 |
2.04 |
CC |
| CC-Identity:Same |
2 |
2.04 |
CC |
| CC-Ran:Death-Nec:No |
2 |
2.04 |
CC |
| CC-Time:PastImmediate |
2 |
2.04 |
CC |
| CC-Dom:GDC-Ran:GDC |
1 |
1.02 |
CC |
| OC-CO-Time:Same |
46 |
46.94 |
OC-CO |
| OC-CO-Dom:O-Ran:C |
42 |
42.86 |
OC-CO |
| OC-CO-Dom:P-Ran:C |
37 |
37.76 |
OC-CO |
| OC-CO-Rig:Yes-Nec:No |
36 |
36.73 |
OC-CO |
| OC-CO-Dom:C-Ran:O |
34 |
34.69 |
OC-CO |
| OC-CO-Dom:C-Ran:P |
33 |
33.67 |
OC-CO |
| OC-CO-Dom:P-Ran:SDC |
24 |
24.49 |
OC-CO |
| OC-CO-Rig:Yes |
18 |
18.37 |
OC-CO |
| OC-CO-Dom:SDC-Ran:P |
17 |
17.35 |
OC-CO |
| OC-CO-Dom:O-Ran:IC |
14 |
14.29 |
OC-CO |
| OC-CO-Time:Diff |
13 |
13.27 |
OC-CO |
| OC-CO-Dom:IC-Ran:O |
11 |
11.22 |
OC-CO |
| OC-CO-Dom:IC-Ran:P |
11 |
11.22 |
OC-CO |
| OC-CO-Time:Future |
10 |
10.20 |
OC-CO |
| OC-CO-Ran:Birth |
9 |
9.18 |
OC-CO |
| OC-CO-Ran:Changed |
9 |
9.18 |
OC-CO |
| OC-CO-Dom:Birth |
7 |
7.14 |
OC-CO |
| OC-CO-Dom:Changed |
7 |
7.14 |
OC-CO |
| OC-CO-Dom:Death |
4 |
4.08 |
OC-CO |
| OC-CO-Time:Same/Past |
4 |
4.08 |
OC-CO |
| OC-CO-Time:Same/Future |
3 |
3.06 |
OC-CO |
| OO-Dom:O-Ran:O |
41 |
41.84 |
OO |
| OO-Time:All |
41 |
41.84 |
OO |
| OO-Time:BeforeInverse |
21 |
21.43 |
OO |
| OO-Time:Before |
15 |
15.31 |
OO |
| OO-Time:MeetsInverse |
15 |
15.31 |
OO |
| OO-Time:Before/During |
13 |
13.27 |
OO |
| OO-Dom:P-Ran:P |
10 |
10.20 |
OO |
| OO-Time:Starts |
6 |
6.12 |
OO |
| OO-Time:During/Overlaps |
4 |
4.08 |
OO |
| OO-Time:During |
3 |
3.06 |
OO |
| OO-Time:Finishes |
3 |
3.06 |
OO |
| OO-Time:During/OverlapsInverse |
2 |
2.04 |
OO |
| OO-Time:FinishesInverse |
2 |
2.04 |
OO |
| OO-Time:Meets |
2 |
2.04 |
OO |
| OO-Time:StartsInverse |
2 |
2.04 |
OO |
| OO-Time:IsEqualTo |
1 |
1.02 |
OO |
| OT-Dom:X-Ran:X |
84 |
85.71 |
OT |
| OT-Rig:Yes-Nec:No |
84 |
85.71 |
OT |
| OT-TI:AHFAT |
84 |
85.71 |
OT |
| OT-Time:Same |
84 |
85.71 |
OT |
| OT-Dom:X-Ran:IC |
3 |
3.06 |
OT |
kable(top10,row.names = FALSE)
| OT-Dom:X-Ran:X |
84 |
85.71 |
OT |
| OT-Rig:Yes-Nec:No |
84 |
85.71 |
OT |
| OT-TI:AHFAT |
84 |
85.71 |
OT |
| OT-Time:Same |
84 |
85.71 |
OT |
| CC-Dom:C-Ran:C |
68 |
69.39 |
CC |
| CC-Dom:IC-Ran:C |
62 |
63.27 |
CC |
| CC-Time:Same |
60 |
61.22 |
CC |
| CC-Rig:Yes-Nec:No |
59 |
60.20 |
CC |
| CC-TI:AHFAT |
53 |
54.08 |
CC |
| CC-Dom:C-Ran:IC |
46 |
46.94 |
CC |
print(xtable(all,digits=c(0,0,2,2,2)),include.rownames=FALSE,file="coverage_att.tex")
print(xtable(top10,digits=c(0,0,2,2,2)),include.rownames=FALSE,file="coverage_att_top10.tex")
Impact: Relations
impact_rel<-compute_impact_rel(df[c("O","CAT","ONT_TOTAL_AX","RO_REL")])
plotRanks(impact_rel,"RO_REL","impact",xlab="Relation",ylab="Impact (Basic)",ncol=1)
ggsave("impact_rel.jpg",width = 3,height = 4,units="in")
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
top10<-head(impact_rel[order(-impact_rel$impact),],10)
top10relim<-top10$RO_REL
all<-impact_rel[order(impact_rel$CAT,-impact_rel$impact),]
# Summary stats over ALL temporal features
summary(all$impact)
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.000000 0.002347 0.014796 0.225384 0.115408 11.518980
sd(all$impact)
## [1] 1.027628
# Summary stats BY DOMAIN RANGE over ALL temporal features
ddply(all,~CAT,summarise,mean=mean(impact),median=median(impact),sd=sd(impact), min=min(impact),max=max(impact))
## CAT mean median sd min max
## 1 CC 0.1060933 0.007959184 0.3140803 0.0000000000 2.066224
## 2 OC-CO 0.1267007 0.027295918 0.1550766 0.0001020408 0.560102
## 3 OO 0.2440986 0.065459184 0.5318933 0.0000000000 2.239592
## 4 OT 2.9697755 0.276224490 4.9457643 0.0047959184 11.518980
kable(all,row.names = FALSE)
| inheres in |
2.0662245 |
CC |
| has quality |
1.5213265 |
CC |
| bearer of |
1.3021429 |
CC |
| develops from |
0.9943878 |
CC |
| has modifier |
0.6513265 |
CC |
| derives from |
0.5711224 |
CC |
| has role |
0.5301020 |
CC |
| overlaps |
0.3409184 |
CC |
| has component |
0.2064286 |
CC |
| attached to |
0.1939796 |
CC |
| concretizes |
0.1577551 |
CC |
| has function |
0.1474490 |
CC |
| towards |
0.1320408 |
CC |
| has member |
0.1308163 |
CC |
| has plasma membrane part |
0.1286735 |
CC |
| child nucleus of |
0.1255102 |
CC |
| inheres in part of |
0.1227551 |
CC |
| located in |
0.1154082 |
CC |
| composed primarily of |
0.0916327 |
CC |
| innervated_by |
0.0760204 |
CC |
| directly develops from |
0.0478571 |
CC |
| adjacent to |
0.0475510 |
CC |
| continuous with |
0.0446939 |
CC |
| has postsynaptic terminal in |
0.0381633 |
CC |
| gene product of |
0.0372449 |
CC |
| has presynaptic terminal in |
0.0353061 |
CC |
| child nucleus of in male |
0.0347959 |
CC |
| has disposition |
0.0278571 |
CC |
| has synaptic terminal in |
0.0259184 |
CC |
| child nucleus of in hermaphrodite |
0.0255102 |
CC |
| interacts with |
0.0225510 |
CC |
| is concretized as |
0.0220408 |
CC |
| surrounds |
0.0218367 |
CC |
| role of |
0.0206122 |
CC |
| has soma location |
0.0201020 |
CC |
| connected to |
0.0200000 |
CC |
| fasciculates with |
0.0181633 |
CC |
| has potential to develop into |
0.0172449 |
CC |
| expresses |
0.0169388 |
CC |
| contributes to morphology of |
0.0166327 |
CC |
| has developmental contribution from |
0.0161224 |
CC |
| produces |
0.0159184 |
CC |
| connects |
0.0147959 |
CC |
| synapsed by |
0.0116327 |
CC |
| quality of |
0.0100000 |
CC |
| member of |
0.0098980 |
CC |
| location of |
0.0095918 |
CC |
| synapsed to |
0.0095918 |
CC |
| has host |
0.0080612 |
CC |
| surrounded by |
0.0078571 |
CC |
| innervates |
0.0074490 |
CC |
| has skeleton |
0.0071429 |
CC |
| skeleton of |
0.0069388 |
CC |
| immediate transformation of |
0.0068367 |
CC |
| spatially disjoint from |
0.0058163 |
CC |
| in homology relationship with |
0.0051020 |
CC |
| develops into |
0.0050000 |
CC |
| function of |
0.0048980 |
CC |
| has muscle insertion |
0.0047959 |
CC |
| has vector |
0.0045918 |
CC |
| transcribed to |
0.0045918 |
CC |
| branching part of |
0.0044898 |
CC |
| has muscle origin |
0.0044898 |
CC |
| has potential to developmentally contribute to |
0.0036735 |
CC |
| produced by |
0.0036735 |
CC |
| luminal space of |
0.0034694 |
CC |
| synapsed_via_type_Ib_bouton_to |
0.0033673 |
CC |
| bounding layer of |
0.0031633 |
CC |
| develops in |
0.0028571 |
CC |
| contains |
0.0026531 |
CC |
| supplies |
0.0026531 |
CC |
| tributary of |
0.0020408 |
CC |
| determined by |
0.0019388 |
CC |
| molecularly interacts with |
0.0017347 |
CC |
| conduit for |
0.0016327 |
CC |
| drains |
0.0014286 |
CC |
| has synaptic terminal of |
0.0014286 |
CC |
| developmentally induced by |
0.0013265 |
CC |
| transformation of |
0.0011224 |
CC |
| has fused element |
0.0010204 |
CC |
| has muscle antagonist |
0.0009184 |
CC |
| determined by part of |
0.0006122 |
CC |
| developmentally replaces |
0.0006122 |
CC |
| electrically_synapsed_to |
0.0006122 |
CC |
| transcribed from |
0.0006122 |
CC |
| has habitat |
0.0005102 |
CC |
| distributary of |
0.0002041 |
CC |
| has 2D boundary |
0.0002041 |
CC |
| synapsed_via_type_II_bouton_to |
0.0002041 |
CC |
| synapsed_via_type_Is_bouton_to |
0.0002041 |
CC |
| attached to part of |
0.0001020 |
CC |
| confers advantage in |
0.0001020 |
CC |
| develops from part of |
0.0001020 |
CC |
| partially overlaps |
0.0001020 |
CC |
| serially homologous to |
0.0001020 |
CC |
| synapsed_via_type_III_bouton_to |
0.0001020 |
CC |
| contained in |
0.0000000 |
CC |
| lumen of |
0.0000000 |
CC |
| has participant |
0.5601020 |
OC-CO |
| realized in |
0.3850000 |
OC-CO |
| participates in |
0.2664286 |
OC-CO |
| existence ends during |
0.2630612 |
OC-CO |
| existence starts during or after |
0.2605102 |
OC-CO |
| existence starts during |
0.2604082 |
OC-CO |
| existence ends during or before |
0.2587755 |
OC-CO |
| realizes |
0.2330612 |
OC-CO |
| occurs in |
0.2279592 |
OC-CO |
| capable of |
0.1451020 |
OC-CO |
| has output |
0.0626531 |
OC-CO |
| has input |
0.0291837 |
OC-CO |
| output of |
0.0254082 |
OC-CO |
| existence starts and ends during |
0.0218367 |
OC-CO |
| formed as result of |
0.0171429 |
OC-CO |
| has active participant |
0.0054082 |
OC-CO |
| capable of part of |
0.0051020 |
OC-CO |
| actively participates in |
0.0042857 |
OC-CO |
| results in formation of |
0.0036735 |
OC-CO |
| has intermediate |
0.0023469 |
OC-CO |
| existence ends with |
0.0012245 |
OC-CO |
| existence starts with |
0.0012245 |
OC-CO |
| contains process |
0.0008163 |
OC-CO |
| functionally related to |
0.0001020 |
OC-CO |
| immediately preceded by |
2.2395918 |
OO |
| preceded by |
0.5603061 |
OO |
| ends during |
0.4964286 |
OO |
| starts during |
0.4964286 |
OO |
| regulates |
0.1565306 |
OO |
| happens during |
0.1162245 |
OO |
| negatively regulates |
0.0829592 |
OO |
| precedes |
0.0717347 |
OO |
| positively regulates |
0.0710204 |
OO |
| obsolete preceded by |
0.0598980 |
OO |
| immediately precedes |
0.0233673 |
OO |
| causally downstream of |
0.0115306 |
OO |
| starts |
0.0068367 |
OO |
| ends |
0.0003061 |
OO |
| ends with |
0.0002041 |
OO |
| simultaneous with |
0.0002041 |
OO |
| starts with |
0.0002041 |
OO |
| causally upstream of or within |
0.0000000 |
OO |
| part of |
11.5189796 |
OT |
| has part |
3.0292857 |
OT |
| in taxon |
0.2762245 |
OT |
| only in taxon |
0.0195918 |
OT |
| depends on |
0.0047959 |
OT |
kable(top10,row.names = FALSE)
| part of |
11.5189796 |
OT |
| has part |
3.0292857 |
OT |
| immediately preceded by |
2.2395918 |
OO |
| inheres in |
2.0662245 |
CC |
| has quality |
1.5213265 |
CC |
| bearer of |
1.3021429 |
CC |
| develops from |
0.9943878 |
CC |
| has modifier |
0.6513265 |
CC |
| derives from |
0.5711224 |
CC |
| preceded by |
0.5603061 |
OO |
print(xtable(all,digits=c(3)),include.rownames=FALSE,file="impact_rel.tex")
print(xtable(top10,digits=c(2)),include.rownames=FALSE,file="impact_rel_top10.tex")
Impact: Annotations
impact_anno<-compute_impact_anno(df[c("O","CAT","ONT_TOTAL_AX","TEMP_ANN")])
impact_anno<-merge(impact_anno,unique(coverage_ann[,c("x","ann_id")]),by.x = "TEMP_ANN",by.y = "x")
plotRanks(impact_anno,"ann_id","impact",xlab="Annotation",ylab="Impact (Basic)")
ggsave("impact_anno.jpg",width = 3,height = 2.5,units="in")
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
top10<-head(impact_anno[order(-impact_anno$impact),],10)
top10annim<-top10$TEMP_ANN
all<-impact_anno[order(impact_anno$CAT,-impact_anno$impact),]
# Summary stats over ALL temporal features
summary(all$impact)
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.000102 0.005077 0.036480 0.480609 0.277041 14.548673
sd(all$impact)
## [1] 1.801924
# Summary stats BY DOMAIN RANGE over ALL temporal features
ddply(all,~CAT,summarise,mean=mean(impact),median=median(impact),sd=sd(impact), min=min(impact),max=max(impact))
## CAT mean median sd min max
## 1 CC 0.3249235 0.02397959 0.6010122 0.0002040816 2.2267347
## 2 OC-CO 0.1600430 0.14510204 0.1601661 0.0001020408 0.5654082
## 3 OO 0.3138484 0.09397959 0.5946116 0.0002040816 2.2395918
## 4 OT 4.9497279 0.29571429 8.3142032 0.0047959184 14.5486735
kable(all,row.names = FALSE)
| Dom:IC-Ran:SDCTime:SameRig:Yes-Nec:No |
2.2267347 |
CC |
A38 |
| Dom:SDC-Ran:ICTime:SameRig:Yes-Nec:No~TI:AHFAT |
2.1889796 |
CC |
A63 |
| Dom:IC-Ran:SDCTime:SameRig:Yes-Nec:No~TI:AHFAT |
1.3021429 |
CC |
A39 |
| Dom:IC-Ran:ICTime:PastIdentity:Same-Nec:No~Dom:Birth-Nec:No |
1.0425510 |
CC |
A26 |
| Dom:IC-Ran:ICTime:SameRig:Yes-Nec:No~TI:AHFAT |
0.8132653 |
CC |
A32 |
| Dom:IC-Ran:ICTime:PastDom:Birth~Ran:Death |
0.7569388 |
CC |
A23 |
| Dom:SDC-Ran:SDCTime:SameRig:Yes-Nec:No |
0.6513265 |
CC |
A65 |
| Dom:C-Ran:CTime:SameRig:Yes-Nec:No~TI:AHFAT |
0.4816327 |
CC |
A2 |
| Dom:IC-Ran:ICTime:SameRig:Yes-Nec:No |
0.3142857 |
CC |
A31 |
| Dom:SDC-Ran:GDCTime:SameRig:Yes-Nec:No |
0.1577551 |
CC |
A61 |
| Dom:SDC-Ran:C~Time:Same |
0.1320408 |
CC |
A60 |
| Dom:IC-Ran:ICTime:SameRig:Yes |
0.0780612 |
CC |
A30 |
| Dom:IC-Ran:CTime:PastDom:Birth |
0.0372449 |
CC |
A15 |
| Dom:SDC-Ran:ICTime:SameRig:Yes-Nec:No |
0.0357143 |
CC |
A62 |
| Dom:IC-Ran:IC~Time:Same |
0.0260204 |
CC |
A29 |
| Dom:IC-Ran:CTime:SameRig:Yes-Nec:No~TI:AHFAT |
0.0259184 |
CC |
A17 |
| Dom:GDC-Ran:SDCTime:SameRig:Yes-Nec:No |
0.0220408 |
CC |
A14 |
| Dom:IC-Ran:ICTime:FutureIdentity:Same-Nec:No~Dom:Birth-Nec:No |
0.0172449 |
CC |
A18 |
| Dom:IC-Ran:C~Time:Same |
0.0169388 |
CC |
A16 |
| Dom:IC-Ran:IC~Time:Past |
0.0161224 |
CC |
A21 |
| Dom:IC-Ran:ICTime:FutureRan:Birth |
0.0159184 |
CC |
A20 |
| Dom:IC-Ran:ICTime:SameRig:Yes~TI:AHFAT |
0.0132653 |
CC |
A33 |
| Dom:IC-Ran:ICTime:PastImmediateIdentity:Same~Dom:Changed |
0.0068367 |
CC |
A28 |
| Dom:IC-Ran:ICTime:FutureIdentity:Same-Nec:No~Ran:Birth-Nec:No |
0.0050000 |
CC |
A19 |
| Dom:GDC-Ran:GDCTime:FutureRan:Birth |
0.0045918 |
CC |
A12 |
| Dom:IC-Ran:ICTime:PastDom:Birth |
0.0036735 |
CC |
A22 |
| Dom:C-Ran:ICTime:SameRig:Yes-Nec:No~TI:AHFAT |
0.0014286 |
CC |
A3 |
| Dom:IC-Ran:ICTime:PastDom:Changed |
0.0013265 |
CC |
A24 |
| Dom:IC-Ran:ICTime:PastIdentity:Same~Dom:Changed |
0.0011224 |
CC |
A27 |
| Dom:GDC-Ran:GDCTime:PastDom:Birth |
0.0006122 |
CC |
A13 |
| Dom:IC-Ran:ICTime:PastDom:ChangedRan:ChangedDom:Birth-Nec:No~Ran:Death-Nec:No |
0.0006122 |
CC |
A25 |
| Dom:C-Ran:C~Time:Same |
0.0002041 |
CC |
A1 |
| Dom:P-Ran:CTime:SameRig:Yes-Nec:No |
0.5654082 |
OC-CO |
A57 |
| Dom:SDC-Ran:PTime:SameRig:Yes-Nec:No |
0.3850000 |
OC-CO |
A64 |
| Dom:C-Ran:PTime:SameRig:Yes-Nec:No |
0.2708163 |
OC-CO |
A11 |
| Dom:C-Ran:OTime:SameRig:Yes~Dom:Death |
0.2642857 |
OC-CO |
A8 |
| Dom:C-Ran:OTime:SameDom:Birth |
0.2616327 |
OC-CO |
A6 |
| Dom:C-Ran:OTime:Same/PastDom:Birth |
0.2605102 |
OC-CO |
A5 |
| Dom:C-Ran:OTime:Same/FutureDom:Death |
0.2587755 |
OC-CO |
A4 |
| Dom:P-Ran:SDCTime:SameRig:Yes-Nec:No |
0.2330612 |
OC-CO |
A59 |
| Dom:O-Ran:ICTime:SameRig:Yes |
0.2279592 |
OC-CO |
A40 |
| Dom:IC-Ran:P~Time:Future |
0.1451020 |
OC-CO |
A35 |
| Dom:P-Ran:CTime:SameRan:Birth |
0.0663265 |
OC-CO |
A54 |
| Dom:P-Ran:CTime:SameRan:Changed |
0.0291837 |
OC-CO |
A55 |
| Dom:C-Ran:P~Time:Same |
0.0254082 |
OC-CO |
A9 |
| Dom:C-Ran:OTime:SameRig:YesDom:BirthDom:Death |
0.0218367 |
OC-CO |
A7 |
| Dom:C-Ran:PTime:SameDom:Birth |
0.0171429 |
OC-CO |
A10 |
| Dom:IC-Ran:P~Time:Same |
0.0051020 |
OC-CO |
A36 |
| Dom:P-Ran:CTime:SameRig:Yes |
0.0023469 |
OC-CO |
A56 |
| Dom:IC-Ran:PTime:SameRig:Yes |
0.0008163 |
OC-CO |
A37 |
| Dom:IC-Ran:OTime:SameRig:Yes-Nec:No |
0.0001020 |
OC-CO |
A34 |
| Dom:O-Ran:O~Time:MeetsInverse |
2.2395918 |
OO |
A51 |
| Dom:O-Ran:O~Time:BeforeInverse |
0.6318367 |
OO |
A43 |
| Dom:O-Ran:O~Time:During/Overlaps |
0.4964286 |
OO |
A45 |
| Dom:O-Ran:O~Time:During/OverlapsInverse |
0.4964286 |
OO |
A46 |
| Dom:P-Ran:P~Time:Before/During |
0.1565306 |
OO |
A58 |
| Dom:O-Ran:O~Time:Before/During |
0.1539796 |
OO |
A42 |
| Dom:O-Ran:O~Time:During |
0.1162245 |
OO |
A44 |
| Dom:O-Ran:O~Time:Before |
0.0717347 |
OO |
A41 |
| Dom:O-Ran:O~Time:Meets |
0.0233673 |
OO |
A50 |
| Dom:O-Ran:O~Time:Starts |
0.0068367 |
OO |
A52 |
| Dom:O-Ran:O~Time:Finishes |
0.0003061 |
OO |
A47 |
| Dom:O-Ran:O~Time:FinishesInverse |
0.0002041 |
OO |
A48 |
| Dom:O-Ran:O~Time:IsEqualTo |
0.0002041 |
OO |
A49 |
| Dom:O-Ran:O~Time:StartsInverse |
0.0002041 |
OO |
A53 |
| Dom:X-Ran:XTime:SameRig:Yes-Nec:No~TI:AHFAT |
14.5486735 |
OT |
A68 |
| Dom:X-Ran:IC~Time:Same |
0.2957143 |
OT |
A66 |
| Dom:X-Ran:XTime:SameRig:Yes-Nec:No |
0.0047959 |
OT |
A67 |
kable(top10,row.names = FALSE)
| Dom:X-Ran:XTime:SameRig:Yes-Nec:No~TI:AHFAT |
14.5486735 |
OT |
A68 |
| Dom:O-Ran:O~Time:MeetsInverse |
2.2395918 |
OO |
A51 |
| Dom:IC-Ran:SDCTime:SameRig:Yes-Nec:No |
2.2267347 |
CC |
A38 |
| Dom:SDC-Ran:ICTime:SameRig:Yes-Nec:No~TI:AHFAT |
2.1889796 |
CC |
A63 |
| Dom:IC-Ran:SDCTime:SameRig:Yes-Nec:No~TI:AHFAT |
1.3021429 |
CC |
A39 |
| Dom:IC-Ran:ICTime:PastIdentity:Same-Nec:No~Dom:Birth-Nec:No |
1.0425510 |
CC |
A26 |
| Dom:IC-Ran:ICTime:SameRig:Yes-Nec:No~TI:AHFAT |
0.8132653 |
CC |
A32 |
| Dom:IC-Ran:ICTime:PastDom:Birth~Ran:Death |
0.7569388 |
CC |
A23 |
| Dom:SDC-Ran:SDCTime:SameRig:Yes-Nec:No |
0.6513265 |
CC |
A65 |
| Dom:O-Ran:O~Time:BeforeInverse |
0.6318367 |
OO |
A43 |
impact_anno_x<-merge(impact_anno,unique(coverage_ann[,c("x","ann_id")]),by.x = "TEMP_ANN",by.y = "x")
print(xtable(all[,c("ann_id","impact","CAT")],digits=c(3)),include.rownames=FALSE,file="impact_ann.tex")
print(xtable(top10[,c("ann_id","impact","CAT")],digits=c(2)),include.rownames=FALSE,file="impact_ann_top10.tex")
Impact: Attributes
impact_feat<-compute_impact_feat(df[c("O","CAT","ONT_TOTAL_AX","TEMP_ANN_ALL")])
## Warning in "\"\"": attributes are not identical across measure variables;
## they will be dropped
plotRanks(impact_feat,"TEMP_FEAT","impact",xlab="Temporal Feature",ylab="Impact (Basic)",ncol = 1)
ggsave("impact_feat.jpg",width = 3,height = 4,units="in")
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
top10<-head(impact_feat[order(-impact_feat$impact),],10)
top10attim<-top10$TEMP_FEAT
all<-impact_feat[order(impact_feat$CAT,-impact_feat$impact),]
# Summary stats over ALL temporal features
summary(all$impact)
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.000204 0.095510 0.560918 2.068777 1.916020 14.849286
sd(all$impact)
## [1] 3.692601
# Summary stats BY DOMAIN RANGE over ALL temporal features
ddply(all,~CAT,summarise,mean=mean(impact),median=median(impact),sd=sd(impact), min=min(impact),max=max(impact))
## CAT mean median sd min max
## 1 CC 2.0942363 0.8082653 2.8314447 0.0006122449 10.397653
## 2 OC-CO 0.6648299 0.5172449 0.6285685 0.0663265306 2.375918
## 3 OO 0.8335842 0.1363776 1.4952231 0.0002040816 4.393469
## 4 OT 11.7601224 14.5534694 6.4100931 0.2957142857 14.849286
kable(all,row.names = FALSE)
| CC-Dom:C-Ran:C |
10.3976531 |
CC |
| CC-Time:Same |
8.4880612 |
CC |
| CC-Rig:Yes-Nec:No |
8.2214286 |
CC |
| CC-Dom:IC-Ran:C |
6.7211224 |
CC |
| CC-TI:AHFAT |
4.8268367 |
CC |
| CC-Dom:IC-Ran:SDC |
3.5289796 |
CC |
| CC-Dom:SDC-Ran:C |
3.1658163 |
CC |
| CC-Dom:C-Ran:IC |
3.1136735 |
CC |
| CC-Dom:IC-Ran:IC |
3.1123469 |
CC |
| CC-Dom:SDC-Ran:IC |
2.2246939 |
CC |
| CC-Time:Diff |
1.9096939 |
CC |
| CC-Time:Past |
1.8668367 |
CC |
| CC-Identity:Same-Nec:No |
1.0647959 |
CC |
| CC-Dom:Birth-Nec:No |
1.0603061 |
CC |
| CC-Dom:Changed-Nec:No |
1.0603061 |
CC |
| CC-Dom:Changed |
0.8082653 |
CC |
| CC-Dom:Birth |
0.7984694 |
CC |
| CC-Ran:Changed |
0.7780612 |
CC |
| CC-Ran:Death |
0.7569388 |
CC |
| CC-Dom:SDC-Ran:SDC |
0.6513265 |
CC |
| CC-Dom:SDC-Ran:GDC |
0.1577551 |
CC |
| CC-Rig:Yes |
0.0913265 |
CC |
| CC-Time:Future |
0.0427551 |
CC |
| CC-Dom:GDC-Ran:SDC |
0.0220408 |
CC |
| CC-Ran:Birth |
0.0205102 |
CC |
| CC-Identity:Same |
0.0079592 |
CC |
| CC-Time:PastImmediate |
0.0068367 |
CC |
| CC-Ran:Changed-Nec:No |
0.0056122 |
CC |
| CC-Dom:GDC-Ran:GDC |
0.0053061 |
CC |
| CC-Ran:Birth-Nec:No |
0.0050000 |
CC |
| CC-Ran:Death-Nec:No |
0.0006122 |
CC |
| OC-CO-Time:Same |
2.3759184 |
OC-CO |
| OC-CO-Dom:C-Ran:O |
1.9160204 |
OC-CO |
| OC-CO-Rig:Yes-Nec:No |
1.4540816 |
OC-CO |
| OC-CO-Dom:O-Ran:C |
1.1243878 |
OC-CO |
| OC-CO-Dom:Changed |
1.0838776 |
OC-CO |
| OC-CO-Dom:P-Ran:C |
0.8963265 |
OC-CO |
| OC-CO-Dom:C-Ran:P |
0.8491837 |
OC-CO |
| OC-CO-Time:Diff |
0.6643878 |
OC-CO |
| OC-CO-Dom:Birth |
0.5609184 |
OC-CO |
| OC-CO-Dom:Death |
0.5447959 |
OC-CO |
| OC-CO-Rig:Yes |
0.5172449 |
OC-CO |
| OC-CO-Dom:SDC-Ran:P |
0.3850000 |
OC-CO |
| OC-CO-Time:Same/Past |
0.2605102 |
OC-CO |
| OC-CO-Time:Same/Future |
0.2587755 |
OC-CO |
| OC-CO-Dom:P-Ran:SDC |
0.2330612 |
OC-CO |
| OC-CO-Dom:O-Ran:IC |
0.2279592 |
OC-CO |
| OC-CO-Dom:IC-Ran:O |
0.1510204 |
OC-CO |
| OC-CO-Dom:IC-Ran:P |
0.1510204 |
OC-CO |
| OC-CO-Time:Future |
0.1451020 |
OC-CO |
| OC-CO-Ran:Changed |
0.0955102 |
OC-CO |
| OC-CO-Ran:Birth |
0.0663265 |
OC-CO |
| OO-Dom:O-Ran:O |
4.3934694 |
OO |
| OO-Time:All |
4.3934694 |
OO |
| OO-Time:MeetsInverse |
2.2395918 |
OO |
| OO-Time:BeforeInverse |
0.6318367 |
OO |
| OO-Time:During/Overlaps |
0.4964286 |
OO |
| OO-Time:During/OverlapsInverse |
0.4964286 |
OO |
| OO-Time:Before/During |
0.3105102 |
OO |
| OO-Dom:P-Ran:P |
0.1565306 |
OO |
| OO-Time:During |
0.1162245 |
OO |
| OO-Time:Before |
0.0717347 |
OO |
| OO-Time:Meets |
0.0233673 |
OO |
| OO-Time:Starts |
0.0068367 |
OO |
| OO-Time:Finishes |
0.0003061 |
OO |
| OO-Time:FinishesInverse |
0.0002041 |
OO |
| OO-Time:IsEqualTo |
0.0002041 |
OO |
| OO-Time:StartsInverse |
0.0002041 |
OO |
| OT-Time:Same |
14.8492857 |
OT |
| OT-Dom:X-Ran:X |
14.5534694 |
OT |
| OT-Rig:Yes-Nec:No |
14.5534694 |
OT |
| OT-TI:AHFAT |
14.5486735 |
OT |
| OT-Dom:X-Ran:IC |
0.2957143 |
OT |
kable(top10,row.names = FALSE)
| OT-Time:Same |
14.849286 |
OT |
| OT-Dom:X-Ran:X |
14.553469 |
OT |
| OT-Rig:Yes-Nec:No |
14.553469 |
OT |
| OT-TI:AHFAT |
14.548673 |
OT |
| CC-Dom:C-Ran:C |
10.397653 |
CC |
| CC-Time:Same |
8.488061 |
CC |
| CC-Rig:Yes-Nec:No |
8.221429 |
CC |
| CC-Dom:IC-Ran:C |
6.721122 |
CC |
| CC-TI:AHFAT |
4.826837 |
CC |
| OO-Dom:O-Ran:O |
4.393469 |
OO |
#write.csv(impact_feat,file="impact_feat.csv")
#print(xtable(impact_feat[order(impact_feat$CAT,-impact_feat$impact),],digits=c(0,0,2,2)),include.rownames=FALSE)
print(xtable(all[,],digits=c(3)),include.rownames=FALSE,file="impact_att.tex")
print(xtable(top10[,],digits=c(2)),include.rownames=FALSE,file="impact_att_top10.tex")
Correlation: Coverage and Impact
plotCovImRel(coverage_rel,impact_rel,"RO_REL",top10relcov,top10relim)
## Warning in "\"\"": Transformation introduced infinite values in continuous
## x-axis
ggsave("cor_rel_imp_cov.jpg",width = 3,height = 4,units="in")
## Warning in "\"\"": Transformation introduced infinite values in continuous
## x-axis
plotCovImRel(coverage_ann,impact_anno,"TEMP_ANN",top10anncov,top10annim)
ggsave("cor_ann_imp_cov.jpg",width = 3,height = 4,units="in")
plotCovImRel(coverage_feat,impact_feat,"TEMP_FEAT",top10attcov,top10attim)
ggsave("cor_feat_imp_cov.jpg",width = 3,height = 4,units="in")
rel<-merge(coverage_rel[,c("x","coverage","CAT")],impact_rel[,c("RO_REL","impact","CAT")],by.x=c("x","CAT"),by.y=c("RO_REL","CAT"))
ann<-merge(coverage_ann[,c("ann_id","coverage","CAT")],impact_anno[,c("ann_id","impact","CAT")],by=c("ann_id","CAT"))
att<-merge(coverage_feat[,c("x","coverage","CAT")],impact_feat[,c("TEMP_FEAT","impact","CAT")],by.x=c("x","CAT"),by.y=c("TEMP_FEAT","CAT"))
# Actual correlations of impact and coverage for temporal features
cor(rel$coverage,rel$impact,method="pearson")
## [1] 0.8307543
cor(ann$coverage,ann$impact,method="pearson")
## [1] 0.8428761
cor(att$coverage,att$impact,method="pearson")
## [1] 0.9068331
cordf <- function(xx) {
return(data.frame(COR = cor(xx$coverage, xx$impact,method="pearson")))
}
asis_output("Correlations by group")
Correlations by group
ddply(rel, .(CAT), cordf)
## CAT COR
## 1 CC 0.7639252
## 2 OC-CO 0.7629174
## 3 OO 0.5516688
## 4 OT 0.9404088
ddply(ann, .(CAT), cordf)
## CAT COR
## 1 CC 0.8484335
## 2 OC-CO 0.7248845
## 3 OO 0.5129402
## 4 OT 0.9999935
ddply(att, .(CAT), cordf)
## CAT COR
## 1 CC 0.9207927
## 2 OC-CO 0.7612683
## 3 OO 0.9087527
## 4 OT 0.9997981
Requirements analysis pre-processing
## Warning in "\"\"": attributes are not identical across measure variables;
## they will be dropped
Annotation: Importance
| A68 |
1.0000000 |
14.5486735 |
1.0000000 |
85.71 |
1.0000000 |
| A38 |
0.2753079 |
2.2267347 |
0.1530482 |
34.69 |
0.3975676 |
| A63 |
0.2439005 |
2.1889796 |
0.1504531 |
29.59 |
0.3373480 |
| A32 |
0.2267303 |
0.8132653 |
0.0558930 |
34.69 |
0.3975676 |
| A57 |
0.1760583 |
0.5654082 |
0.0388565 |
27.55 |
0.3132601 |
| A51 |
0.1613325 |
2.2395918 |
0.1539319 |
15.31 |
0.1687330 |
| A39 |
0.1532024 |
1.3021429 |
0.0894961 |
19.39 |
0.2169087 |
| A59 |
0.1465704 |
0.2330612 |
0.0160125 |
24.49 |
0.2771284 |
| A26 |
0.1442809 |
1.0425510 |
0.0716530 |
19.39 |
0.2169087 |
| A43 |
0.1422095 |
0.6318367 |
0.0434225 |
21.43 |
0.2409966 |
| A2 |
0.1250034 |
0.4816327 |
0.0330981 |
19.39 |
0.2169087 |
| A23 |
0.1224211 |
0.7569388 |
0.0520214 |
17.35 |
0.1928209 |
| A64 |
0.1096385 |
0.3850000 |
0.0264561 |
17.35 |
0.1928209 |
| A11 |
0.0996923 |
0.2708163 |
0.0186076 |
16.33 |
0.1807770 |
| A61 |
0.0897847 |
0.1577551 |
0.0108363 |
15.31 |
0.1687330 |
| A31 |
0.0891423 |
0.3142857 |
0.0215955 |
14.29 |
0.1566891 |
| A41 |
0.0868284 |
0.0717347 |
0.0049237 |
15.31 |
0.1687330 |
| A40 |
0.0861755 |
0.2279592 |
0.0156618 |
14.29 |
0.1566891 |
| A58 |
0.0595737 |
0.1565306 |
0.0107522 |
10.20 |
0.1083953 |
| A35 |
0.0591810 |
0.1451020 |
0.0099666 |
10.20 |
0.1083953 |
| A60 |
0.0587321 |
0.1320408 |
0.0090688 |
10.20 |
0.1083953 |
| A54 |
0.0504517 |
0.0663265 |
0.0045520 |
9.18 |
0.0963514 |
| A62 |
0.0493996 |
0.0357143 |
0.0024478 |
9.18 |
0.0963514 |
| A42 |
0.0414202 |
0.1539796 |
0.0105768 |
7.14 |
0.0722635 |
| A45 |
0.0351235 |
0.4964286 |
0.0341151 |
4.08 |
0.0361318 |
| A9 |
0.0309795 |
0.0254082 |
0.0017394 |
6.12 |
0.0602196 |
| A14 |
0.0308638 |
0.0220408 |
0.0015080 |
6.12 |
0.0602196 |
| A20 |
0.0306534 |
0.0159184 |
0.0010871 |
6.12 |
0.0602196 |
| A52 |
0.0303413 |
0.0068367 |
0.0004629 |
6.12 |
0.0602196 |
| A65 |
0.0284030 |
0.6513265 |
0.0447621 |
2.04 |
0.0120439 |
| A6 |
0.0270541 |
0.2616327 |
0.0179764 |
4.08 |
0.0361318 |
| A5 |
0.0270155 |
0.2605102 |
0.0178992 |
4.08 |
0.0361318 |
| A55 |
0.0250873 |
0.0291837 |
0.0019989 |
5.10 |
0.0481757 |
| A29 |
0.0249786 |
0.0260204 |
0.0017815 |
5.10 |
0.0481757 |
| A33 |
0.0245402 |
0.0132653 |
0.0009048 |
5.10 |
0.0481757 |
| A46 |
0.0230795 |
0.4964286 |
0.0341151 |
2.04 |
0.0120439 |
| A66 |
0.0222034 |
0.2957143 |
0.0203190 |
3.06 |
0.0240878 |
| A8 |
0.0211233 |
0.2642857 |
0.0181587 |
3.06 |
0.0240878 |
| A4 |
0.0209339 |
0.2587755 |
0.0177800 |
3.06 |
0.0240878 |
| A30 |
0.0207452 |
0.0780612 |
0.0053585 |
4.08 |
0.0361318 |
| A21 |
0.0186165 |
0.0161224 |
0.0011012 |
4.08 |
0.0361318 |
| A22 |
0.0181886 |
0.0036735 |
0.0002455 |
4.08 |
0.0361318 |
| A44 |
0.0160348 |
0.1162245 |
0.0079817 |
3.06 |
0.0240878 |
| A7 |
0.0127909 |
0.0218367 |
0.0014939 |
3.06 |
0.0240878 |
| A18 |
0.0126331 |
0.0172449 |
0.0011783 |
3.06 |
0.0240878 |
| A36 |
0.0122158 |
0.0051020 |
0.0003437 |
3.06 |
0.0240878 |
| A19 |
0.0122123 |
0.0050000 |
0.0003367 |
3.06 |
0.0240878 |
| A47 |
0.0120509 |
0.0003061 |
0.0000140 |
3.06 |
0.0240878 |
| A17 |
0.0069092 |
0.0259184 |
0.0017745 |
2.04 |
0.0120439 |
| A50 |
0.0068215 |
0.0233673 |
0.0015991 |
2.04 |
0.0120439 |
| A10 |
0.0066076 |
0.0171429 |
0.0011713 |
2.04 |
0.0120439 |
| A28 |
0.0062534 |
0.0068367 |
0.0004629 |
2.04 |
0.0120439 |
| A24 |
0.0060640 |
0.0013265 |
0.0000842 |
2.04 |
0.0120439 |
| A27 |
0.0060570 |
0.0011224 |
0.0000701 |
2.04 |
0.0120439 |
| A25 |
0.0060395 |
0.0006122 |
0.0000351 |
2.04 |
0.0120439 |
| A48 |
0.0060255 |
0.0002041 |
0.0000070 |
2.04 |
0.0120439 |
| A53 |
0.0060255 |
0.0002041 |
0.0000070 |
2.04 |
0.0120439 |
| A15 |
0.0012765 |
0.0372449 |
0.0025530 |
1.02 |
0.0000000 |
| A16 |
0.0005786 |
0.0169388 |
0.0011573 |
1.02 |
0.0000000 |
| A67 |
0.0001613 |
0.0047959 |
0.0003226 |
1.02 |
0.0000000 |
| A12 |
0.0001543 |
0.0045918 |
0.0003086 |
1.02 |
0.0000000 |
| A56 |
0.0000772 |
0.0023469 |
0.0001543 |
1.02 |
0.0000000 |
| A3 |
0.0000456 |
0.0014286 |
0.0000912 |
1.02 |
0.0000000 |
| A37 |
0.0000245 |
0.0008163 |
0.0000491 |
1.02 |
0.0000000 |
| A13 |
0.0000175 |
0.0006122 |
0.0000351 |
1.02 |
0.0000000 |
| A1 |
0.0000035 |
0.0002041 |
0.0000070 |
1.02 |
0.0000000 |
| A49 |
0.0000035 |
0.0002041 |
0.0000070 |
1.02 |
0.0000000 |
| A34 |
0.0000000 |
0.0001020 |
0.0000000 |
1.02 |
0.0000000 |
Requirements Analysis
asis_output("## Requirments Overview")
Requirments Overview
languages$ID<-as.numeric(gsub("R","",languages$LID))
languages<-languages[order(languages$ID),]
kable(languages,row.names = FALSE)
| R1 |
A1, A2, A9, A10, A11, A20, A23, A29, A30, A31, A32, A35, A38, A40, A43, A47, A54, A55, A57, A58, A60, A63, A68 |
1 |
| R2 |
A2, A63 |
2 |
| R3 |
A2, A26, A30, A31, A32, A33, A68 |
3 |
| R4 |
A2, A4, A5, A6, A8, A21, A26, A32, A45, A46, A68 |
4 |
| R5 |
A2 |
5 |
| R6 |
A2, A9, A23, A32, A38, A40, A41, A42, A43, A44, A45, A54, A58, A60, A63, A68 |
6 |
| R7 |
A2, A14, A32, A38, A39, A43, A51, A52, A57, A59, A61, A62, A63, A64, A68 |
7 |
| R8 |
A2, A11, A23, A32, A38, A39, A57, A59, A63, A64, A68 |
8 |
| R9 |
A2, A3, A16, A17, A26, A30, A31, A32, A33, A35, A36, A40, A58, A63, A68 |
9 |
| R10 |
A2, A4, A5, A6, A7, A8, A9, A11, A18, A20, A21, A22, A24, A25, A26, A27, A28, A29, A30, A31, A32, A33, A34, A35, A36, A37, A38, A41, A42, A43, A47, A48, A49, A51, A52, A53, A58, A66, A68 |
10 |
| R11 |
A2, A38, A41, A43, A50, A51, A58, A60, A63, A68 |
11 |
| R12 |
A2, A12, A13, A23, A32, A38, A68 |
12 |
| R13 |
A2, A11, A14, A23, A32, A38, A39, A52, A57, A59, A61, A62, A63, A64, A68 |
13 |
| R14 |
A2, A11, A38, A39, A57, A59, A61, A63, A68 |
14 |
| R15 |
A2, A5, A7, A21, A26, A31, A32, A33, A36, A51, A68 |
15 |
| R16 |
A2, A32, A51, A63 |
16 |
| R17 |
A2, A41, A43, A50, A51, A58, A60, A63, A68 |
17 |
| R18 |
A2, A11, A14, A23, A31, A32, A38, A39, A40, A43, A51, A52, A57, A59, A61, A62, A63, A64, A68 |
18 |
| R19 |
A2, A4, A5, A6, A7, A8, A18, A20, A21, A22, A24, A25, A26, A27, A28, A29, A31, A32, A38, A40, A41, A43, A47, A48, A51, A52, A53, A57, A59, A61, A64, A68 |
19 |
| R20 |
A6, A22, A35, A40, A42, A60, A63, A65, A68 |
20 |
| R21 |
A9, A38, A41, A54, A55, A57, A68 |
21 |
| R22 |
A9, A14, A38, A39, A40, A54, A55, A59, A61, A63, A64, A68 |
22 |
| R23 |
A9, A23, A32, A38, A39, A54, A55, A57, A59, A61, A63, A64, A68 |
23 |
| R24 |
A10, A26, A29, A31, A32, A35, A38, A39, A40, A57, A59, A62, A64, A68 |
24 |
| R25 |
A11, A38, A39, A41, A43, A44, A59, A68 |
25 |
| R26 |
A11, A20, A32, A35, A38, A40, A42, A54, A59, A63, A64, A68 |
26 |
| R27 |
A11, A14, A18, A19, A23, A26, A32, A35, A38, A39, A51, A57, A59, A61, A62, A63, A64, A68 |
27 |
| R28 |
A11, A26, A32, A41, A43, A57, A68 |
28 |
| R29 |
A11, A17, A19, A20, A26, A32, A33, A35, A39, A68 |
29 |
| R30 |
A11, A39, A43, A57, A59, A61, A62, A63, A64, A68 |
30 |
| R31 |
A11, A31, A32, A38, A57, A68 |
31 |
| R32 |
A11, A38, A39, A42, A43, A57, A59, A61, A63, A64, A68 |
32 |
| R33 |
A11, A31, A38, A40, A41, A43, A52, A57, A59, A60, A61, A62, A63, A67, A68 |
33 |
| R34 |
A11, A23, A41, A57 |
34 |
| R35 |
A14, A23, A32, A38, A39, A41, A43, A57, A59, A61, A62, A63, A64, A68 |
35 |
| R36 |
A15, A66, A68 |
36 |
| R37 |
A19, A26, A43, A45, A46, A68 |
37 |
| R38 |
A20, A22, A26, A32, A35, A54, A68 |
38 |
| R39 |
A23, A32, A38, A43, A57, A58, A68 |
39 |
| R40 |
A23, A32, A41, A43, A68 |
40 |
| R41 |
A23, A32, A38, A39, A41, A57, A59, A61, A62, A63, A64, A68 |
41 |
| R42 |
A23, A32 |
42 |
| R43 |
A23, A26, A68 |
43 |
| R44 |
A23, A32, A38, A59, A61, A63, A64, A68 |
44 |
| R45 |
A23, A38, A39, A57, A59, A63, A68 |
45 |
| R46 |
A26, A68 |
46 |
| R47 |
A26, A29, A31, A32, A35, A66, A68 |
47 |
| R48 |
A26, A31, A32, A68 |
48 |
| R49 |
A31, A68 |
49 |
| R50 |
A32, A39, A68 |
50 |
| R51 |
A32, A68 |
51 |
| R52 |
A32, A38, A41, A59 |
52 |
| R53 |
A32, A58, A68 |
53 |
| R54 |
A38, A41, A57 |
54 |
| R55 |
A38, A42, A58, A60, A63, A68 |
55 |
| R56 |
A38, A57, A63, A64 |
56 |
| R57 |
A38, A59 |
57 |
| R58 |
A38, A68 |
58 |
| R59 |
A38, A39, A60, A68 |
59 |
| R60 |
A38, A40, A43, A60, A63, A65, A68 |
60 |
| R61 |
A39, A57, A61, A68 |
61 |
| R62 |
A40, A63, A68 |
62 |
| R63 |
A40, A59, A64 |
63 |
| R64 |
A40, A42, A44, A45, A58, A68 |
64 |
| R65 |
A43, A51, A68 |
65 |
| R66 |
A43 |
66 |
| R67 |
A51, A68 |
67 |
| R68 |
A51 |
68 |
| R69 |
A54 |
69 |
| R70 |
A54, A55, A57, A68 |
70 |
| R71 |
A56, A57, A59, A68 |
71 |
| R72 |
A57, A59 |
72 |
| R73 |
A60, A68 |
73 |
| R74 |
A63, A68 |
74 |
| R75 |
A68 |
75 |
#print(xtable(languages,digits=c(0,0,2)),include.rownames=FALSE)
print(xtable(languages[c("LID","L")],digits=c(0,0,2)),include.rownames=FALSE,file="languages.tex")
asis_output("## Annotations Overview")
Annotations Overview
kable(annotations,row.names = FALSE)
| A1 |
Dom:C-Ran:C~Time:Same |
|
| A2 |
Dom:C-Ran:CTime:SameRig:Yes-Nec:No~TI:AHFAT |
|
| A3 |
Dom:C-Ran:ICTime:SameRig:Yes-Nec:No~TI:AHFAT |
Dom:C-Ran:C |
| A4 |
Dom:C-Ran:OTime:Same/FutureDom:Death |
Time:Diff~Dom:Changed |
| A5 |
Dom:C-Ran:OTime:Same/PastDom:Birth |
Time:Diff~Dom:Changed |
| A6 |
Dom:C-Ran:OTime:SameDom:Birth |
Dom:Changed |
| A7 |
Dom:C-Ran:OTime:SameRig:YesDom:BirthDom:Death |
Dom:Changed |
| A8 |
Dom:C-Ran:OTime:SameRig:Yes~Dom:Death |
Dom:Changed |
| A9 |
Dom:C-Ran:P~Time:Same |
Dom:C-Ran:O |
| A10 |
Dom:C-Ran:PTime:SameDom:Birth |
Dom:C-Ran:O~Dom:Changed |
| A11 |
Dom:C-Ran:PTime:SameRig:Yes-Nec:No |
Dom:C-Ran:O |
| A12 |
Dom:GDC-Ran:GDCTime:FutureRan:Birth |
Time:DiffRan:ChangedDom:C-Ran:C |
| A13 |
Dom:GDC-Ran:GDCTime:PastDom:Birth |
Time:DiffDom:C-Ran:CDom:Changed |
| A14 |
Dom:GDC-Ran:SDCTime:SameRig:Yes-Nec:No |
Dom:C-Ran:C |
| A15 |
Dom:IC-Ran:CTime:PastDom:Birth |
Time:DiffDom:ChangedDom:C-Ran:C |
| A16 |
Dom:IC-Ran:C~Time:Same |
Dom:C-Ran:C |
| A17 |
Dom:IC-Ran:CTime:SameRig:Yes-Nec:No~TI:AHFAT |
Dom:C-Ran:C |
| A18 |
Dom:IC-Ran:ICTime:FutureIdentity:Same-Nec:No~Dom:Birth-Nec:No |
Time:DiffDom:Changed-Nec:NoDom:C-Ran:ICDom:C-Ran:CDom:IC-Ran:C |
| A19 |
Dom:IC-Ran:ICTime:FutureIdentity:Same-Nec:No~Ran:Birth-Nec:No |
Time:DiffRan:Changed-Nec:NoDom:C-Ran:ICDom:C-Ran:CDom:IC-Ran:C |
| A20 |
Dom:IC-Ran:ICTime:FutureRan:Birth |
Time:DiffDom:C-Ran:ICRan:ChangedDom:C-Ran:CDom:IC-Ran:C |
| A21 |
Dom:IC-Ran:IC~Time:Past |
Time:DiffDom:C-Ran:ICDom:C-Ran:C~Dom:IC-Ran:C |
| A22 |
Dom:IC-Ran:ICTime:PastDom:Birth |
Time:DiffDom:C-Ran:ICDom:C-Ran:CDom:ChangedDom:IC-Ran:C |
| A23 |
Dom:IC-Ran:ICTime:PastDom:Birth~Ran:Death |
Time:DiffDom:C-Ran:ICRan:ChangedDom:C-Ran:CDom:Changed~Dom:IC-Ran:C |
| A24 |
Dom:IC-Ran:ICTime:PastDom:Changed |
Time:DiffDom:C-Ran:ICDom:C-Ran:C~Dom:IC-Ran:C |
| A25 |
Dom:IC-Ran:ICTime:PastDom:ChangedRan:ChangedDom:Birth-Nec:No~Ran:Death-Nec:No |
Time:DiffRan:Changed-Nec:NoDom:Changed-Nec:NoDom:C-Ran:ICDom:C-Ran:C~Dom:IC-Ran:C |
| A26 |
Dom:IC-Ran:ICTime:PastIdentity:Same-Nec:No~Dom:Birth-Nec:No |
Time:DiffDom:Changed-Nec:NoDom:C-Ran:ICDom:C-Ran:CDom:IC-Ran:C |
| A27 |
Dom:IC-Ran:ICTime:PastIdentity:Same~Dom:Changed |
Time:DiffDom:C-Ran:ICDom:C-Ran:C~Dom:IC-Ran:C |
| A28 |
Dom:IC-Ran:ICTime:PastImmediateIdentity:Same~Dom:Changed |
Time:DiffTime:PastDom:C-Ran:ICDom:C-Ran:CDom:IC-Ran:C |
| A29 |
Dom:IC-Ran:IC~Time:Same |
Dom:C-Ran:ICDom:C-Ran:CDom:IC-Ran:C |
| A30 |
Dom:IC-Ran:ICTime:SameRig:Yes |
Dom:C-Ran:ICDom:C-Ran:CDom:IC-Ran:C |
| A31 |
Dom:IC-Ran:ICTime:SameRig:Yes-Nec:No |
Dom:C-Ran:ICDom:C-Ran:CDom:IC-Ran:C |
| A32 |
Dom:IC-Ran:ICTime:SameRig:Yes-Nec:No~TI:AHFAT |
Dom:C-Ran:ICDom:C-Ran:CDom:IC-Ran:C |
| A33 |
Dom:IC-Ran:ICTime:SameRig:Yes~TI:AHFAT |
Dom:C-Ran:ICDom:C-Ran:CDom:IC-Ran:C |
| A34 |
Dom:IC-Ran:OTime:SameRig:Yes-Nec:No |
Dom:C-Ran:O |
| A35 |
Dom:IC-Ran:P~Time:Future |
Time:DiffDom:C-Ran:PDom:C-Ran:O~Dom:IC-Ran:O |
| A36 |
Dom:IC-Ran:P~Time:Same |
Dom:C-Ran:PDom:C-Ran:ODom:IC-Ran:O |
| A37 |
Dom:IC-Ran:PTime:SameRig:Yes |
Dom:C-Ran:PDom:C-Ran:ODom:IC-Ran:O |
| A38 |
Dom:IC-Ran:SDCTime:SameRig:Yes-Nec:No |
Dom:C-Ran:C~Dom:IC-Ran:C |
| A39 |
Dom:IC-Ran:SDCTime:SameRig:Yes-Nec:No~TI:AHFAT |
Dom:C-Ran:C~Dom:IC-Ran:C |
| A40 |
Dom:O-Ran:ICTime:SameRig:Yes |
Dom:O-Ran:C |
| A41 |
Dom:O-Ran:O~Time:Before |
Time:All |
| A42 |
Dom:O-Ran:O~Time:Before/During |
Time:All |
| A43 |
Dom:O-Ran:O~Time:BeforeInverse |
Time:All |
| A44 |
Dom:O-Ran:O~Time:During |
Time:All |
| A45 |
Dom:O-Ran:O~Time:During/Overlaps |
Time:All |
| A46 |
Dom:O-Ran:O~Time:During/OverlapsInverse |
Time:All |
| A47 |
Dom:O-Ran:O~Time:Finishes |
Time:All |
| A48 |
Dom:O-Ran:O~Time:FinishesInverse |
Time:All |
| A49 |
Dom:O-Ran:O~Time:IsEqualTo |
Time:All |
| A50 |
Dom:O-Ran:O~Time:Meets |
Time:All |
| A51 |
Dom:O-Ran:O~Time:MeetsInverse |
Time:All |
| A52 |
Dom:O-Ran:O~Time:Starts |
Time:All |
| A53 |
Dom:O-Ran:O~Time:StartsInverse |
Time:All |
| A54 |
Dom:P-Ran:CTime:SameRan:Birth |
Dom:O-Ran:C~Ran:Changed |
| A55 |
Dom:P-Ran:CTime:SameRan:Changed |
Dom:O-Ran:C |
| A56 |
Dom:P-Ran:CTime:SameRig:Yes |
Dom:O-Ran:C |
| A57 |
Dom:P-Ran:CTime:SameRig:Yes-Nec:No |
Dom:O-Ran:C |
| A58 |
Dom:P-Ran:P~Time:Before/During |
Dom:O-Ran:O~Time:All |
| A59 |
Dom:P-Ran:SDCTime:SameRig:Yes-Nec:No |
Dom:O-Ran:C~Dom:P-Ran:C |
| A60 |
Dom:SDC-Ran:C~Time:Same |
Dom:C-Ran:C |
| A61 |
Dom:SDC-Ran:GDCTime:SameRig:Yes-Nec:No |
Dom:SDC-Ran:C~Dom:C-Ran:C |
| A62 |
Dom:SDC-Ran:ICTime:SameRig:Yes-Nec:No |
Dom:SDC-Ran:C~Dom:C-Ran:C |
| A63 |
Dom:SDC-Ran:ICTime:SameRig:Yes-Nec:No~TI:AHFAT |
Dom:SDC-Ran:C~Dom:C-Ran:C |
| A64 |
Dom:SDC-Ran:PTime:SameRig:Yes-Nec:No |
Dom:C-Ran:P~Dom:C-Ran:O |
| A65 |
Dom:SDC-Ran:SDCTime:SameRig:Yes-Nec:No |
Dom:SDC-Ran:C~Dom:C-Ran:C |
| A66 |
Dom:X-Ran:IC~Time:Same |
|
| A67 |
Dom:X-Ran:XTime:SameRig:Yes-Nec:No |
|
| A68 |
Dom:X-Ran:XTime:SameRig:Yes-Nec:No~TI:AHFAT |
|
l<-annotations
l$TEMP_ANN<-gsub("~"," ",l$TEMP_ANN)
l$TEMP_INF_ANN<-gsub("~"," ",l$TEMP_INF_ANN)
print(xtable(l,digits=c(0,0,0,0)),include.rownames=FALSE,file="annotations.tex")
asis_output("## Requirements Importance Overview")
Requirements Importance Overview
kable(ct_need_suff,row.names = FALSE)
| R1 |
1 |
0.010204 |
34 |
0.346939 |
A1, A2, A9, A10, A11, A20, A23, A29, A30, A31, A32, A35, A38, A40, A43, A47, A54, A55, A57, A58, A60, A63, A68 |
| R10 |
1 |
0.010204 |
39 |
0.397959 |
A2, A4, A5, A6, A7, A8, A9, A11, A18, A20, A21, A22, A24, A25, A26, A27, A28, A29, A30, A31, A32, A33, A34, A35, A36, A37, A38, A41, A42, A43, A47, A48, A49, A51, A52, A53, A58, A66, A68 |
| R11 |
1 |
0.010204 |
31 |
0.316327 |
A2, A38, A41, A43, A50, A51, A58, A60, A63, A68 |
| R12 |
1 |
0.010204 |
22 |
0.224490 |
A2, A12, A13, A23, A32, A38, A68 |
| R13 |
2 |
0.020408 |
33 |
0.336735 |
A2, A11, A14, A23, A32, A38, A39, A52, A57, A59, A61, A62, A63, A64, A68 |
| R14 |
3 |
0.030612 |
25 |
0.255102 |
A2, A11, A38, A39, A57, A59, A61, A63, A68 |
| R15 |
2 |
0.020408 |
31 |
0.316327 |
A2, A5, A7, A21, A26, A31, A32, A33, A36, A51, A68 |
| R16 |
3 |
0.030612 |
4 |
0.040816 |
A2, A32, A51, A63 |
| R17 |
2 |
0.020408 |
29 |
0.295918 |
A2, A41, A43, A50, A51, A58, A60, A63, A68 |
| R18 |
1 |
0.010204 |
49 |
0.500000 |
A2, A11, A14, A23, A31, A32, A38, A39, A40, A43, A51, A52, A57, A59, A61, A62, A63, A64, A68 |
| R19 |
1 |
0.010204 |
40 |
0.408163 |
A2, A4, A5, A6, A7, A8, A18, A20, A21, A22, A24, A25, A26, A27, A28, A29, A31, A32, A38, A40, A41, A43, A47, A48, A51, A52, A53, A57, A59, A61, A64, A68 |
| R2 |
12 |
0.122449 |
2 |
0.020408 |
A2, A63 |
| R20 |
1 |
0.010204 |
21 |
0.214286 |
A6, A22, A35, A40, A42, A60, A63, A65, A68 |
| R21 |
1 |
0.010204 |
22 |
0.224490 |
A9, A38, A41, A54, A55, A57, A68 |
| R22 |
1 |
0.010204 |
24 |
0.244898 |
A9, A14, A38, A39, A40, A54, A55, A59, A61, A63, A64, A68 |
| R23 |
1 |
0.010204 |
31 |
0.316327 |
A9, A23, A32, A38, A39, A54, A55, A57, A59, A61, A63, A64, A68 |
| R24 |
1 |
0.010204 |
31 |
0.316327 |
A10, A26, A29, A31, A32, A35, A38, A39, A40, A57, A59, A62, A64, A68 |
| R25 |
1 |
0.010204 |
21 |
0.214286 |
A11, A38, A39, A41, A43, A44, A59, A68 |
| R26 |
1 |
0.010204 |
25 |
0.255102 |
A11, A20, A32, A35, A38, A40, A42, A54, A59, A63, A64, A68 |
| R27 |
1 |
0.010204 |
38 |
0.387755 |
A11, A14, A18, A19, A23, A26, A32, A35, A38, A39, A51, A57, A59, A61, A62, A63, A64, A68 |
| R28 |
1 |
0.010204 |
24 |
0.244898 |
A11, A26, A32, A41, A43, A57, A68 |
| R29 |
1 |
0.010204 |
24 |
0.244898 |
A11, A17, A19, A20, A26, A32, A33, A35, A39, A68 |
| R3 |
3 |
0.030612 |
27 |
0.275510 |
A2, A26, A30, A31, A32, A33, A68 |
| R30 |
2 |
0.020408 |
22 |
0.224490 |
A11, A39, A43, A57, A59, A61, A62, A63, A64, A68 |
| R31 |
3 |
0.030612 |
22 |
0.224490 |
A11, A31, A32, A38, A57, A68 |
| R32 |
1 |
0.010204 |
25 |
0.255102 |
A11, A38, A39, A42, A43, A57, A59, A61, A63, A64, A68 |
| R33 |
1 |
0.010204 |
28 |
0.285714 |
A11, A31, A38, A40, A41, A43, A52, A57, A59, A60, A61, A62, A63, A67, A68 |
| R34 |
1 |
0.010204 |
1 |
0.010204 |
A11, A23, A41, A57 |
| R35 |
1 |
0.010204 |
34 |
0.346939 |
A14, A23, A32, A38, A39, A41, A43, A57, A59, A61, A62, A63, A64, A68 |
| R36 |
1 |
0.010204 |
18 |
0.183673 |
A15, A66, A68 |
| R37 |
1 |
0.010204 |
23 |
0.234694 |
A19, A26, A43, A45, A46, A68 |
| R38 |
1 |
0.010204 |
24 |
0.244898 |
A20, A22, A26, A32, A35, A54, A68 |
| R39 |
2 |
0.020408 |
23 |
0.234694 |
A23, A32, A38, A43, A57, A58, A68 |
| R4 |
1 |
0.010204 |
24 |
0.244898 |
A2, A4, A5, A6, A8, A21, A26, A32, A45, A46, A68 |
| R40 |
3 |
0.030612 |
21 |
0.214286 |
A23, A32, A41, A43, A68 |
| R41 |
2 |
0.020408 |
31 |
0.316327 |
A23, A32, A38, A39, A41, A57, A59, A61, A62, A63, A64, A68 |
| R42 |
14 |
0.142857 |
1 |
0.010204 |
A23, A32 |
| R43 |
2 |
0.020408 |
22 |
0.224490 |
A23, A26, A68 |
| R44 |
7 |
0.071429 |
23 |
0.234694 |
A23, A32, A38, A59, A61, A63, A64, A68 |
| R45 |
8 |
0.081633 |
22 |
0.224490 |
A23, A38, A39, A57, A59, A63, A68 |
| R46 |
19 |
0.193878 |
21 |
0.214286 |
A26, A68 |
| R47 |
2 |
0.020408 |
26 |
0.265306 |
A26, A29, A31, A32, A35, A66, A68 |
| R48 |
8 |
0.081633 |
25 |
0.255102 |
A26, A31, A32, A68 |
| R49 |
14 |
0.142857 |
19 |
0.193878 |
A31, A68 |
| R5 |
19 |
0.193878 |
1 |
0.010204 |
A2 |
| R50 |
11 |
0.112245 |
19 |
0.193878 |
A32, A39, A68 |
| R51 |
31 |
0.316327 |
18 |
0.183673 |
A32, A68 |
| R52 |
4 |
0.040816 |
2 |
0.020408 |
A32, A38, A41, A59 |
| R53 |
6 |
0.061224 |
19 |
0.193878 |
A32, A58, A68 |
| R54 |
6 |
0.061224 |
1 |
0.010204 |
A38, A41, A57 |
| R55 |
2 |
0.020408 |
21 |
0.214286 |
A38, A42, A58, A60, A63, A68 |
| R56 |
10 |
0.102041 |
1 |
0.010204 |
A38, A57, A63, A64 |
| R57 |
20 |
0.204082 |
1 |
0.010204 |
A38, A59 |
| R58 |
30 |
0.306122 |
18 |
0.183673 |
A38, A68 |
| R59 |
1 |
0.010204 |
20 |
0.204082 |
A38, A39, A60, A68 |
| R6 |
1 |
0.010204 |
32 |
0.326531 |
A2, A9, A23, A32, A38, A40, A41, A42, A43, A44, A45, A54, A58, A60, A63, A68 |
| R60 |
1 |
0.010204 |
23 |
0.234694 |
A38, A40, A43, A60, A63, A65, A68 |
| R61 |
11 |
0.112245 |
18 |
0.183673 |
A39, A57, A61, A68 |
| R62 |
10 |
0.102041 |
19 |
0.193878 |
A40, A63, A68 |
| R63 |
6 |
0.061224 |
1 |
0.010204 |
A40, A59, A64 |
| R64 |
2 |
0.020408 |
18 |
0.183673 |
A40, A42, A44, A45, A58, A68 |
| R65 |
8 |
0.081633 |
24 |
0.244898 |
A43, A51, A68 |
| R66 |
21 |
0.214286 |
1 |
0.010204 |
A43 |
| R67 |
13 |
0.132653 |
21 |
0.214286 |
A51, A68 |
| R68 |
15 |
0.153061 |
1 |
0.010204 |
A51 |
| R69 |
9 |
0.091837 |
1 |
0.010204 |
A54 |
| R7 |
2 |
0.020408 |
36 |
0.367347 |
A2, A14, A32, A38, A39, A43, A51, A52, A57, A59, A61, A62, A63, A64, A68 |
| R70 |
4 |
0.040816 |
19 |
0.193878 |
A54, A55, A57, A68 |
| R71 |
1 |
0.010204 |
19 |
0.193878 |
A56, A57, A59, A68 |
| R72 |
17 |
0.173469 |
1 |
0.010204 |
A57, A59 |
| R73 |
10 |
0.102041 |
18 |
0.183673 |
A60, A68 |
| R74 |
26 |
0.265306 |
18 |
0.183673 |
A63, A68 |
| R75 |
84 |
0.857143 |
17 |
0.173469 |
A68 |
| R8 |
3 |
0.030612 |
29 |
0.295918 |
A2, A11, A23, A32, A38, A39, A57, A59, A63, A64, A68 |
| R9 |
1 |
0.010204 |
32 |
0.326531 |
A2, A3, A16, A17, A26, A30, A31, A32, A33, A35, A36, A40, A58, A63, A68 |
asis_output("## Requirments Coverage (Sufficiency)")
Requirments Coverage (Sufficiency)
# Percentage of ontologies that can are fully covered by the requirement set
ct_rep<-ct_o_repr[c("LID","value","pc")]
ct_rep$pc<-ct_rep$pc*100
#print(xtable(ct_rep[order(-ct_rep$pc),],digits=c(0,0,2,2)),include.rownames=FALSE)
kable(ct_rep[order(-ct_rep$pc),],row.names = FALSE)
| R18 |
49 |
50.0000 |
| R19 |
40 |
40.8163 |
| R10 |
39 |
39.7959 |
| R27 |
38 |
38.7755 |
| R7 |
36 |
36.7347 |
| R1 |
34 |
34.6939 |
| R35 |
34 |
34.6939 |
| R13 |
33 |
33.6735 |
| R6 |
32 |
32.6531 |
| R9 |
32 |
32.6531 |
| R11 |
31 |
31.6327 |
| R15 |
31 |
31.6327 |
| R23 |
31 |
31.6327 |
| R24 |
31 |
31.6327 |
| R41 |
31 |
31.6327 |
| R8 |
29 |
29.5918 |
| R17 |
29 |
29.5918 |
| R33 |
28 |
28.5714 |
| R3 |
27 |
27.5510 |
| R47 |
26 |
26.5306 |
| R14 |
25 |
25.5102 |
| R26 |
25 |
25.5102 |
| R32 |
25 |
25.5102 |
| R48 |
25 |
25.5102 |
| R4 |
24 |
24.4898 |
| R22 |
24 |
24.4898 |
| R28 |
24 |
24.4898 |
| R29 |
24 |
24.4898 |
| R38 |
24 |
24.4898 |
| R65 |
24 |
24.4898 |
| R37 |
23 |
23.4694 |
| R39 |
23 |
23.4694 |
| R44 |
23 |
23.4694 |
| R60 |
23 |
23.4694 |
| R12 |
22 |
22.4490 |
| R21 |
22 |
22.4490 |
| R30 |
22 |
22.4490 |
| R31 |
22 |
22.4490 |
| R43 |
22 |
22.4490 |
| R45 |
22 |
22.4490 |
| R20 |
21 |
21.4286 |
| R25 |
21 |
21.4286 |
| R40 |
21 |
21.4286 |
| R46 |
21 |
21.4286 |
| R55 |
21 |
21.4286 |
| R67 |
21 |
21.4286 |
| R59 |
20 |
20.4082 |
| R49 |
19 |
19.3878 |
| R50 |
19 |
19.3878 |
| R53 |
19 |
19.3878 |
| R62 |
19 |
19.3878 |
| R70 |
19 |
19.3878 |
| R71 |
19 |
19.3878 |
| R36 |
18 |
18.3673 |
| R51 |
18 |
18.3673 |
| R58 |
18 |
18.3673 |
| R61 |
18 |
18.3673 |
| R64 |
18 |
18.3673 |
| R73 |
18 |
18.3673 |
| R74 |
18 |
18.3673 |
| R75 |
17 |
17.3469 |
| R16 |
4 |
4.0816 |
| R2 |
2 |
2.0408 |
| R52 |
2 |
2.0408 |
| R5 |
1 |
1.0204 |
| R34 |
1 |
1.0204 |
| R42 |
1 |
1.0204 |
| R54 |
1 |
1.0204 |
| R56 |
1 |
1.0204 |
| R57 |
1 |
1.0204 |
| R63 |
1 |
1.0204 |
| R66 |
1 |
1.0204 |
| R68 |
1 |
1.0204 |
| R69 |
1 |
1.0204 |
| R72 |
1 |
1.0204 |
print(xtable(ct_rep[order(-ct_rep$pc),],digits=c(0,0,2,2)),include.rownames=FALSE,file="language_sufficient.tex")
asis_output("## Requirments Necessity")
Requirments Necessity
# Percentage of ontologies that need the requirements to be handled
ct_need<-ct_o_need[c("LID","value","pc")]
ct_need$pc<-ct_need$pc*100
#print(xtable(ct_need[order(-ct_need$pc),],digits=c(0,0,2,2)),include.rownames=FALSE)kable(ct_need_suff,row.names = FALSE)
kable(ct_need[order(-ct_need$pc),],row.names = FALSE)
| R75 |
84 |
85.7143 |
| R51 |
31 |
31.6327 |
| R58 |
30 |
30.6122 |
| R74 |
26 |
26.5306 |
| R66 |
21 |
21.4286 |
| R57 |
20 |
20.4082 |
| R5 |
19 |
19.3878 |
| R46 |
19 |
19.3878 |
| R72 |
17 |
17.3469 |
| R68 |
15 |
15.3061 |
| R42 |
14 |
14.2857 |
| R49 |
14 |
14.2857 |
| R67 |
13 |
13.2653 |
| R2 |
12 |
12.2449 |
| R50 |
11 |
11.2245 |
| R61 |
11 |
11.2245 |
| R56 |
10 |
10.2041 |
| R62 |
10 |
10.2041 |
| R73 |
10 |
10.2041 |
| R69 |
9 |
9.1837 |
| R45 |
8 |
8.1633 |
| R48 |
8 |
8.1633 |
| R65 |
8 |
8.1633 |
| R44 |
7 |
7.1429 |
| R53 |
6 |
6.1224 |
| R54 |
6 |
6.1224 |
| R63 |
6 |
6.1224 |
| R52 |
4 |
4.0816 |
| R70 |
4 |
4.0816 |
| R3 |
3 |
3.0612 |
| R8 |
3 |
3.0612 |
| R14 |
3 |
3.0612 |
| R16 |
3 |
3.0612 |
| R31 |
3 |
3.0612 |
| R40 |
3 |
3.0612 |
| R7 |
2 |
2.0408 |
| R13 |
2 |
2.0408 |
| R15 |
2 |
2.0408 |
| R17 |
2 |
2.0408 |
| R30 |
2 |
2.0408 |
| R39 |
2 |
2.0408 |
| R41 |
2 |
2.0408 |
| R43 |
2 |
2.0408 |
| R47 |
2 |
2.0408 |
| R55 |
2 |
2.0408 |
| R64 |
2 |
2.0408 |
| R1 |
1 |
1.0204 |
| R4 |
1 |
1.0204 |
| R6 |
1 |
1.0204 |
| R9 |
1 |
1.0204 |
| R10 |
1 |
1.0204 |
| R11 |
1 |
1.0204 |
| R12 |
1 |
1.0204 |
| R18 |
1 |
1.0204 |
| R19 |
1 |
1.0204 |
| R20 |
1 |
1.0204 |
| R21 |
1 |
1.0204 |
| R22 |
1 |
1.0204 |
| R23 |
1 |
1.0204 |
| R24 |
1 |
1.0204 |
| R25 |
1 |
1.0204 |
| R26 |
1 |
1.0204 |
| R27 |
1 |
1.0204 |
| R28 |
1 |
1.0204 |
| R29 |
1 |
1.0204 |
| R32 |
1 |
1.0204 |
| R33 |
1 |
1.0204 |
| R34 |
1 |
1.0204 |
| R35 |
1 |
1.0204 |
| R36 |
1 |
1.0204 |
| R37 |
1 |
1.0204 |
| R38 |
1 |
1.0204 |
| R59 |
1 |
1.0204 |
| R60 |
1 |
1.0204 |
| R71 |
1 |
1.0204 |
print(xtable(ct_need[order(-ct_need$pc),],digits=c(0,0,2,2)),include.rownames=FALSE,file="language_necessary.tex")
asis_output("## Requirements Analysis: Final table")
Requirements Analysis: Final table
# Percentage of ontologies that need the requirements to be handled
kable(loverview[c("LID","CTN","PCN","CTR","PCR","IMPANN","Importance")],row.names = FALSE)
| R75 |
84 |
0.857143 |
17 |
0.173469 |
1.0000000 |
0.7777776 |
| R58 |
30 |
0.306122 |
18 |
0.183673 |
0.6376539 |
0.4406549 |
| R51 |
31 |
0.316327 |
18 |
0.183673 |
0.6133651 |
0.4361448 |
| R74 |
26 |
0.265306 |
18 |
0.183673 |
0.6219503 |
0.4190780 |
| R46 |
19 |
0.193878 |
21 |
0.214286 |
0.5721404 |
0.3943142 |
| R18 |
1 |
0.010204 |
49 |
0.500000 |
0.1767250 |
0.3776608 |
| R67 |
13 |
0.132653 |
21 |
0.214286 |
0.5806662 |
0.3732106 |
| R49 |
14 |
0.142857 |
19 |
0.193878 |
0.5445712 |
0.3506669 |
| R65 |
8 |
0.081633 |
24 |
0.244898 |
0.4345140 |
0.3226577 |
| R73 |
10 |
0.102041 |
18 |
0.183673 |
0.5293660 |
0.3223200 |
| R50 |
11 |
0.112245 |
19 |
0.193878 |
0.4599776 |
0.3089227 |
| R48 |
8 |
0.081633 |
25 |
0.255102 |
0.3650384 |
0.3052131 |
| R27 |
1 |
0.010204 |
38 |
0.387755 |
0.1729561 |
0.2999488 |
| R62 |
10 |
0.102041 |
19 |
0.193878 |
0.4433587 |
0.2990727 |
| R7 |
2 |
0.020408 |
36 |
0.367347 |
0.1973562 |
0.2986416 |
| R19 |
1 |
0.010204 |
40 |
0.408163 |
0.0984971 |
0.2876992 |
| R35 |
1 |
0.010204 |
34 |
0.346939 |
0.2037797 |
0.2829917 |
| R43 |
2 |
0.020408 |
22 |
0.224490 |
0.4222340 |
0.2803615 |
| R53 |
6 |
0.061224 |
19 |
0.193878 |
0.4287680 |
0.2778862 |
| R13 |
2 |
0.020408 |
33 |
0.336735 |
0.1919276 |
0.2759028 |
| R41 |
2 |
0.020408 |
31 |
0.316327 |
0.2233202 |
0.2730342 |
| R10 |
1 |
0.010204 |
39 |
0.397959 |
0.0747246 |
0.2724096 |
| R8 |
3 |
0.030612 |
29 |
0.295918 |
0.2435023 |
0.2702456 |
| R11 |
1 |
0.010204 |
31 |
0.316327 |
0.2159710 |
0.2664382 |
| R61 |
11 |
0.112245 |
18 |
0.183673 |
0.3547614 |
0.2650421 |
| R45 |
8 |
0.081633 |
22 |
0.224490 |
0.3024944 |
0.2624242 |
| R23 |
1 |
0.010204 |
31 |
0.316327 |
0.2038564 |
0.2621855 |
| R1 |
1 |
0.010204 |
34 |
0.346939 |
0.1289429 |
0.2567207 |
| R44 |
7 |
0.071429 |
23 |
0.234694 |
0.2767942 |
0.2563307 |
| R6 |
1 |
0.010204 |
32 |
0.326531 |
0.1625558 |
0.2546315 |
| R24 |
1 |
0.010204 |
31 |
0.316327 |
0.1819481 |
0.2544947 |
| R17 |
2 |
0.020408 |
29 |
0.295918 |
0.2093780 |
0.2542504 |
| R15 |
2 |
0.020408 |
31 |
0.316327 |
0.1674244 |
0.2534123 |
| R3 |
3 |
0.030612 |
27 |
0.275510 |
0.2329203 |
0.2526420 |
| R14 |
3 |
0.030612 |
25 |
0.255102 |
0.2566133 |
0.2470706 |
| R9 |
1 |
0.010204 |
32 |
0.326531 |
0.1399348 |
0.2466906 |
| R31 |
3 |
0.030612 |
22 |
0.224490 |
0.3111552 |
0.2453840 |
| R59 |
1 |
0.010204 |
20 |
0.204082 |
0.3718106 |
0.2447559 |
| R40 |
3 |
0.030612 |
21 |
0.214286 |
0.3156379 |
0.2400132 |
| R39 |
2 |
0.020408 |
23 |
0.234694 |
0.2860430 |
0.2394969 |
| R47 |
2 |
0.020408 |
26 |
0.265306 |
0.2237881 |
0.2384758 |
| R28 |
1 |
0.010204 |
24 |
0.244898 |
0.2679714 |
0.2360813 |
| R33 |
1 |
0.010204 |
28 |
0.285714 |
0.1716203 |
0.2300353 |
| R70 |
4 |
0.040816 |
19 |
0.193878 |
0.3128993 |
0.2291791 |
| R32 |
1 |
0.010204 |
25 |
0.255102 |
0.2252532 |
0.2280297 |
| R60 |
1 |
0.010204 |
23 |
0.234694 |
0.2621041 |
0.2270772 |
| R55 |
2 |
0.020408 |
21 |
0.214286 |
0.2798224 |
0.2234244 |
| R71 |
1 |
0.010204 |
19 |
0.193878 |
0.3306765 |
0.2233716 |
| R36 |
1 |
0.010204 |
18 |
0.183673 |
0.3411600 |
0.2201067 |
| R38 |
1 |
0.010204 |
24 |
0.244898 |
0.2184980 |
0.2187139 |
| R26 |
1 |
0.010204 |
25 |
0.255102 |
0.1974768 |
0.2182790 |
| R12 |
1 |
0.010204 |
22 |
0.224490 |
0.2499478 |
0.2158654 |
| R37 |
1 |
0.010204 |
23 |
0.234694 |
0.2261509 |
0.2144561 |
| R21 |
1 |
0.010204 |
22 |
0.224490 |
0.2349590 |
0.2106037 |
| R30 |
2 |
0.020408 |
22 |
0.224490 |
0.2210456 |
0.2097355 |
| R22 |
1 |
0.010204 |
24 |
0.244898 |
0.1868302 |
0.2075971 |
| R25 |
1 |
0.010204 |
21 |
0.214286 |
0.2399807 |
0.2054222 |
| R29 |
1 |
0.010204 |
24 |
0.244898 |
0.1757402 |
0.2037041 |
| R4 |
1 |
0.010204 |
24 |
0.244898 |
0.1517237 |
0.1952732 |
| R20 |
1 |
0.010204 |
21 |
0.214286 |
0.1736728 |
0.1821452 |
| R64 |
2 |
0.020408 |
18 |
0.183673 |
0.2063879 |
0.1768118 |
| R57 |
20 |
0.204082 |
1 |
0.010204 |
0.2109392 |
0.1326436 |
| R66 |
21 |
0.214286 |
1 |
0.010204 |
0.1422095 |
0.1125325 |
| R72 |
17 |
0.173469 |
1 |
0.010204 |
0.1613144 |
0.1031746 |
| R5 |
19 |
0.193878 |
1 |
0.010204 |
0.1250034 |
0.0984603 |
| R2 |
12 |
0.122449 |
2 |
0.020408 |
0.1844520 |
0.0981611 |
| R42 |
14 |
0.142857 |
1 |
0.010204 |
0.1745757 |
0.0957818 |
| R68 |
15 |
0.153061 |
1 |
0.010204 |
0.1613325 |
0.0951489 |
| R56 |
10 |
0.102041 |
1 |
0.010204 |
0.2012263 |
0.0890732 |
| R16 |
3 |
0.030612 |
4 |
0.040816 |
0.1892417 |
0.0775866 |
| R52 |
4 |
0.040816 |
2 |
0.020408 |
0.1838592 |
0.0658244 |
| R54 |
6 |
0.061224 |
1 |
0.010204 |
0.1793982 |
0.0653461 |
| R63 |
6 |
0.061224 |
1 |
0.010204 |
0.1141281 |
0.0424334 |
| R69 |
9 |
0.091837 |
1 |
0.010204 |
0.0504517 |
0.0321286 |
| R34 |
1 |
0.010204 |
1 |
0.010204 |
0.1212500 |
0.0248533 |
print(xtable(loverview[c("LID","CTN","PCN","CTR","PCR","IMPANN","Importance")],digits=c(2)),include.rownames=FALSE,file="languages_overview_revised.tex")
print(xtable(head(loverview[c("LID","CTN","PCN","CTR","PCR","IMPANN","Importance")],20),digits=c(2)),include.rownames=FALSE,file="languages_top10.tex")
#write.csv(loverview,file="languages_overview_revised.csv")
Prepare Examples for Developmental ontologies
Prepare Pareto Frontier Plot Plot.ly and partial order
sky1 <- psel(loverview[c("LID","PCN","PCR","IMPANN")], high(PCN) * high(PCR) * high(IMPANN))
sky1$pareto<-"Pareto"
tt<-merge(loverview,sky1[c("LID","pareto")],by="LID",all.x = TRUE)
tt$PCN<-round(tt$PCN*100,2)
tt$PCR<-round(tt$PCR*100,2)
tt$pareto<-as.factor(ifelse(is.na(tt$pareto),"Other","Pareto"))
## Prepare just for developmental ontologies:
pref <- tt[tt$PCN>0&tt$LID %in% LIDSOFDEVELOP,c("LID","PCN","PCR","IMPANN")]
pref<-rbind(pref,data.frame(LID="R0",PCN=max(pref$PCN)+0.01,PCR=max(pref$PCR)+0.01,IMPANN=max(pref$IMPANN)+0.01))
row.names(pref)<-pref$LID
paret <- high(PCN) * high(PCR) * high(IMPANN)
btg <- get_btg(pref, paret)
labels <- paste0(pref$LID)
g<-btg$graph
## requirements on pareto line:
kable(tt[tt$pareto=="Pareto",c("LID","Importance")],row.names = FALSE)
| R7 |
0.2986416 |
| R8 |
0.2702456 |
| R18 |
0.3776608 |
| R35 |
0.2829917 |
| R41 |
0.2730342 |
| R46 |
0.3943142 |
| R48 |
0.3052131 |
| R51 |
0.4361448 |
| R58 |
0.4406549 |
| R65 |
0.3226577 |
| R67 |
0.3732106 |
| R75 |
0.7777776 |
Analysis: Preferential plot (Developmental ontologies)
fine = 1000 # this will adjust the resolving power.
palettex = colorRampPalette(c('red','green'))
graphCol = palettex(fine)[as.numeric(cut(pref$PCR,breaks = fine))]
V(g)$color<-graphCol
pdf('developmental_preference_chart.pdf')
plot.igraph(g, layout = layout_as_tree(g, circular = FALSE),
edge.arrow.size=0.5,
vertex.label.cex=1,
vertex.label.font=2,
vertex.label.family="serif",
vertex.size=pref$PCN/3,
edge.width=3,
vertex.color=V(g)$color,
vertex.label=gsub(" ","\n",pref$LID),
vertex.label.degree = pi/2
)
dev.off()
## quartz_off_screen
## 2
#At first we use Graphviz. If the Rgraphviz package (from Bioconductor) is available, the dot layouter is used to plot the graph resulting in the left figure.
#plot_btg(df, pref, labels)
#If Rgraphviz is not available or we explicitly do not use it via
#plot_btg(df, pref, labels, use_dot = FALSE)