user — Mar 2, 2014, 5:53 PM
library(lattice)
library(RColorBrewer)
library(gplots)
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Attaching package: 'gplots'
The following object is masked from 'package:stats':
lowess
library(hexbin)
Loading required package: grid
kDat <- read.table("GSE4051_MINI.txt")
str(kDat)
'data.frame': 39 obs. of 6 variables:
$ sample : int 20 21 22 23 16 17 6 24 25 26 ...
$ devStage : Factor w/ 5 levels "4_weeks","E16",..: 2 2 2 2 2 2 2 4 4 4 ...
$ gType : Factor w/ 2 levels "NrlKO","wt": 2 2 2 2 1 1 1 2 2 2 ...
$ crabHammer: num 10.22 10.02 9.64 9.65 8.58 ...
$ eggBomb : num 7.46 6.89 6.72 6.53 6.47 ...
$ poisonFang: num 7.37 7.18 7.35 7.04 7.49 ...
table(kDat$devStage)
4_weeks E16 P10 P2 P6
8 7 8 8 8
table(kDat$gType)
NrlKO wt
19 20
with(kDat,table(devStage,gType))
gType
devStage NrlKO wt
4_weeks 4 4
E16 3 4
P10 4 4
P2 4 4
P6 4 4
prDat <- read.table("GSE4051_data.tsv")
str(prDat, max.level = 0)
'data.frame': 29949 obs. of 39 variables:
prDes <- read.csv("GSE4051_design.csv")
str(prDes)
'data.frame': 39 obs. of 4 variables:
$ sidChar : Factor w/ 39 levels "Sample_1","Sample_10",..: 13 14 15 16 8 9 36 17 18 19 ...
$ sidNum : int 20 21 22 23 16 17 6 24 25 26 ...
$ devStage: Factor w/ 5 levels "4_weeks","E16",..: 2 2 2 2 2 2 2 4 4 4 ...
$ gType : Factor w/ 2 levels "NrlKO","wt": 2 2 2 2 1 1 1 2 2 2 ...
set.seed(540)
(yo <- sample(1:nrow(prDat), size = 20,replace=TRUE))
[1] 1594 25174 23017 10682 29407 11582 20718 12029 28712 25026 593
[12] 2076 4511 1114 27915 25997 9169 1353 7246 10231
hDat <- prDat[yo, ]
str(hDat)
'data.frame': 20 obs. of 39 variables:
$ Sample_20: num 7.38 6.26 7.19 6.15 8.88 ...
$ Sample_21: num 7.21 5.82 7.11 5.86 8.32 ...
$ Sample_22: num 7.3 6.07 7.1 5.94 8.95 ...
$ Sample_23: num 7 6.17 7.01 5.97 8.83 ...
$ Sample_16: num 6.95 6.79 7.91 6.81 10.19 ...
$ Sample_17: num 6.93 6.21 7.15 5.93 8.75 ...
$ Sample_6 : num 7 5.78 6.99 5.83 8.46 ...
$ Sample_24: num 7.07 6.4 7.47 6.11 9.45 ...
$ Sample_25: num 7.18 6.35 7.41 6.34 9.26 ...
$ Sample_26: num 6.94 6.5 7.56 6.35 9.34 ...
$ Sample_27: num 7.15 6.47 7.57 6.36 9.66 ...
$ Sample_14: num 6.9 6.27 7.36 6.31 9.6 ...
$ Sample_3 : num 7.04 6.58 7.5 6.32 9.57 ...
$ Sample_5 : num 6.95 6.57 7.53 6.58 9.77 ...
$ Sample_8 : num 6.96 6.7 7.54 6.67 9.89 ...
$ Sample_28: num 7.12 6.57 7.47 6.33 9.62 ...
$ Sample_29: num 7.12 6.01 7.19 6.13 8.74 ...
$ Sample_30: num 6.99 6.39 7.22 6.26 9.3 ...
$ Sample_31: num 7.01 6.45 7.45 6.38 9.54 ...
$ Sample_1 : num 6.83 6.41 7.43 6.35 9.4 ...
$ Sample_10: num 6.74 6.3 7.41 6.16 9.31 ...
$ Sample_4 : num 6.79 6.45 7.37 6.32 9.39 ...
$ Sample_7 : num 6.95 6.57 7.52 6.87 9.73 ...
$ Sample_32: num 6.88 6.11 7.32 5.98 8.5 ...
$ Sample_33: num 6.74 6.56 7.71 6.6 9.83 ...
$ Sample_34: num 6.71 6.88 7.8 6.78 10.02 ...
$ Sample_35: num 7.01 6.4 7.46 6.34 9.33 ...
$ Sample_13: num 6.69 6.36 7.63 6.34 9.15 ...
$ Sample_15: num 6.96 6.36 7.49 6.38 9.43 ...
$ Sample_18: num 6.66 6.08 7.44 6.3 8.8 ...
$ Sample_19: num 7.11 6.39 7.37 6.51 9.64 ...
$ Sample_36: num 6.72 6.1 7.12 5.82 8.42 ...
$ Sample_37: num 6.79 6.44 7.48 6.15 9.41 ...
$ Sample_38: num 6.63 6.45 7.48 6.26 8.69 ...
$ Sample_39: num 6.72 6.22 7.3 6.13 9.13 ...
$ Sample_11: num 6.55 6.27 7.43 6.1 9.11 ...
$ Sample_12: num 6.83 6.38 7.55 6.45 9.35 ...
$ Sample_2 : num 6.73 6.29 7.53 6.22 8.91 ...
$ Sample_9 : num 7.1 5.98 7.33 6.05 8.72 ...
hDat <- as.matrix(t(hDat))
rownames(hDat) <- with(prDes,
paste(devStage, gType, sidChar, sep="_"))
str(hDat)
num [1:39, 1:20] 7.38 7.21 7.3 7 6.95 ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:39] "E16_wt_Sample_20" "E16_wt_Sample_21" "E16_wt_Sample_22" "E16_wt_Sample_23" ...
..$ : chr [1:20] "1417558_at" "1453150_at" "1450170_x_at" "1430578_at" ...
heatmap(hDat, Rowv = NA, Colv = NA, scale="none", margins = c(5, 8))
heatmap(hDat, Rowv = NA, Colv = NA, col = cm.colors(256),
scale="none", margins = c(5, 8))
jGraysFun <- colorRampPalette(brewer.pal(n = 9, "Greys"))
heatmap(hDat, Rowv = NA, Colv = NA, scale="none", margins = c(5, 8),
col = jGraysFun(256))
heatmap.2(hDat, col = jGraysFun, trace = "none")
heatmap.2(cor(t(hDat)), col = jGraysFun, trace = "none")
set.seed(540)
(yo <- sample(1:ncol(prDat), size = 2))
[1] 3 32
pairDat <- subset(prDat, select = yo)
str(pairDat)
'data.frame': 29949 obs. of 2 variables:
$ Sample_22: num 7.17 9.85 9.91 8.4 8.52 ...
$ Sample_36: num 7.25 9.66 9.51 8.49 8.42 ...
pairs(pairDat)
splom(pairDat, panel = panel.smoothScatter, raster = TRUE)
hexplom(pairDat)
