omaromeir — Feb 7, 2014, 9:35 PM
library(lattice)
kDat <- readRDS("GSE4051_MINI.rds")
str(kDat)
'data.frame': 39 obs. of 7 variables:
$ sidChar : chr "Sample_20" "Sample_21" "Sample_22" "Sample_23" ...
$ sidNum : num 20 21 22 23 16 17 6 24 25 26 ...
$ devStage : Factor w/ 5 levels "E16","P2","P6",..: 1 1 1 1 1 1 1 2 2 2 ...
$ gType : Factor w/ 2 levels "wt","NrlKO": 1 1 1 1 2 2 2 1 1 1 ...
$ 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)
E16 P2 P6 P10 4_weeks
7 8 8 8 8
xyplot(eggBomb + poisonFang ~ crabHammer, kDat, groups=gType, auto.key = TRUE, outer=TRUE, grid=TRUE)
nDat <-with(kDat, data.frame(sidChar, sidNum, devStage, gType, crabHammer, probeset = factor(rep(c("eggBomb", "poisonFang"), each = nrow(kDat))), geneExp = c(eggBomb, poisonFang)))
str(nDat)
'data.frame': 78 obs. of 7 variables:
$ sidChar : Factor w/ 39 levels "Sample_1","Sample_10",..: 13 14 15 16 8 9 36 17 18 19 ...
$ sidNum : num 20 21 22 23 16 17 6 24 25 26 ...
$ devStage : Factor w/ 5 levels "E16","P2","P6",..: 1 1 1 1 1 1 1 2 2 2 ...
$ gType : Factor w/ 2 levels "wt","NrlKO": 1 1 1 1 2 2 2 1 1 1 ...
$ crabHammer: num 10.22 10.02 9.64 9.65 8.58 ...
$ probeset : Factor w/ 2 levels "eggBomb","poisonFang": 1 1 1 1 1 1 1 1 1 1 ...
$ geneExp : num 7.46 6.89 6.72 6.53 6.47 ...
xyplot(geneExp ~ crabHammer | probeset, nDat, grid = TRUE, groups = devStage, auto.key = TRUE)
oDat <- with(kDat, data.frame(sidChar, sidNum, devStage, gType, probeset = factor(rep(c("crabHammer", "eggBomb", "poisonFang"), each = nrow(kDat))), geneExp = c(crabHammer, eggBomb, poisonFang)))
str(oDat)
'data.frame': 117 obs. of 6 variables:
$ sidChar : Factor w/ 39 levels "Sample_1","Sample_10",..: 13 14 15 16 8 9 36 17 18 19 ...
$ sidNum : num 20 21 22 23 16 17 6 24 25 26 ...
$ devStage: Factor w/ 5 levels "E16","P2","P6",..: 1 1 1 1 1 1 1 2 2 2 ...
$ gType : Factor w/ 2 levels "wt","NrlKO": 1 1 1 1 2 2 2 1 1 1 ...
$ probeset: Factor w/ 3 levels "crabHammer","eggBomb",..: 1 1 1 1 1 1 1 1 1 1 ...
$ geneExp : num 10.22 10.02 9.64 9.65 8.58 ...
stripplot(~ geneExp | probeset , oDat, layout = c(nlevels(oDat$probeset), 1), groups = gType, auto.key= TRUE)
stripplot(geneExp ~ devStage | probeset, oDat, groups = gType, auto.key = TRUE, type = c('p','a'))
densityplot(~ geneExp | gType, oDat)
densityplot(~ geneExp, oDat, groups = gType)
jBw <- 0.2
jn <- 400
densityplot(~ geneExp, oDat,
groups = devStage, auto.key = TRUE,
bw = jBw, n = jn,
main = paste("bw =", jBw, ", n =", jn))
bwplot(geneExp ~ devStage, oDat)
bwplot(geneExp ~ devStage | gType, oDat,panel = panel.violin)
# Heat maps
prDat <- read.table("GSE4051_data.tsv")
str(prDat, max.level = 0)
'data.frame': 29949 obs. of 39 variables:
prDes <- readRDS("GSE4051_design.rds")
str(prDes)
'data.frame': 39 obs. of 4 variables:
$ sidChar : chr "Sample_20" "Sample_21" "Sample_22" "Sample_23" ...
$ sidNum : num 20 21 22 23 16 17 6 24 25 26 ...
$ devStage: Factor w/ 5 levels "E16","P2","P6",..: 1 1 1 1 1 1 1 2 2 2 ...
$ gType : Factor w/ 2 levels "wt","NrlKO": 1 1 1 1 2 2 2 1 1 1 ...
set.seed(1)
(yo <- sample(1:nrow(prDat), size = 50))
[1] 7952 11145 17156 27198 6040 26902 28287 19786 18837 1850 6167
[12] 5286 20568 11499 23046 14899 21481 29690 11375 23269 27975 6350
[23] 19503 3758 7997 11555 401 11442 26023 10184 14424 17938 14766
[34] 5571 24751 19997 23759 3229 21647 12302 24554 19353 23416 16540
[45] 15842 23605 698 14271 21897 20713
hDat <- prDat[yo, ]
str(hDat)
'data.frame': 50 obs. of 39 variables:
$ Sample_20: num 8.3 8.25 6.91 6.79 6.4 ...
$ Sample_21: num 8.33 9.14 6.55 6.23 6.69 ...
$ Sample_22: num 8.43 8.19 6.59 6.69 6.14 ...
$ Sample_23: num 8.49 8.66 6.58 6.34 6.34 ...
$ Sample_16: num 8.51 6.66 7.75 7.25 5.5 ...
$ Sample_17: num 8.18 7.95 6.85 6.38 7.51 ...
$ Sample_6 : num 7.96 8.45 7.42 6.19 7.64 ...
$ Sample_24: num 8.34 7.49 7.17 6.84 5.83 ...
$ Sample_25: num 8.14 7.39 7.12 7.02 5.85 ...
$ Sample_26: num 8.45 6.94 7.46 7.43 6.32 ...
$ Sample_27: num 8.25 6.5 7.23 6.91 5.8 ...
$ Sample_14: num 8.46 6.99 7.14 6.78 6.29 ...
$ Sample_3 : num 8.53 7.14 7.23 6.88 6.15 ...
$ Sample_5 : num 8.45 6.71 7.36 6.92 6 ...
$ Sample_8 : num 8.62 6.66 7.9 6.97 5.95 ...
$ Sample_28: num 8.63 6.46 7.45 7.17 6.03 ...
$ Sample_29: num 8.58 7.84 6.72 6.91 6.31 ...
$ Sample_30: num 8.28 7.01 6.81 6.75 5.81 ...
$ Sample_31: num 8.47 6.88 7.18 6.89 5.79 ...
$ Sample_1 : num 8.66 6.81 7.22 6.56 6.03 ...
$ Sample_10: num 8.68 7.41 6.97 6.5 5.99 ...
$ Sample_4 : num 8.74 7.23 6.91 6.78 5.82 ...
$ Sample_7 : num 8.69 6.61 7.43 7.1 5.64 ...
$ Sample_32: num 9.7 7.62 6.96 6.89 6.82 ...
$ Sample_33: num 8.72 6.83 7.36 7.21 5.93 ...
$ Sample_34: num 8.58 6.73 7.63 7.19 5.93 ...
$ Sample_35: num 8.54 6.91 7.14 6.71 5.59 ...
$ Sample_13: num 8.73 6.83 7.14 6.46 6.25 ...
$ Sample_15: num 8.57 6.86 7.12 6.72 5.84 ...
$ Sample_18: num 8.96 6.95 6.96 6.31 6.44 ...
$ Sample_19: num 8.65 6.69 7.03 6.91 6.32 ...
$ Sample_36: num 10.41 7.9 6.57 6.87 6.09 ...
$ Sample_37: num 9.48 6.36 6.99 6.85 6.08 ...
$ Sample_38: num 10.14 7.24 6.95 6.99 6.13 ...
$ Sample_39: num 9.48 6.21 6.97 7.13 6.02 ...
$ Sample_11: num 9.09 6.23 7 6.4 6.22 ...
$ Sample_12: num 9.21 6.47 7.17 6.78 5.76 ...
$ Sample_2 : num 9.05 6.2 7.2 6.54 5.9 ...
$ Sample_9 : num 8.89 7.67 6.86 6.72 6.26 ...
hDat <- as.matrix(t(hDat))
rownames(hDat) <- with(prDes, paste(devStage, gType, sidChar, sep="_"))
str(hDat)
num [1:39, 1:50] 8.3 8.33 8.43 8.49 8.51 ...
- 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 [1:50] "1426822_at" "1431375_s_at" "1440076_at" "1456157_at" ...
heatmap(hDat)
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))
