May I ask for the code used to generate Figure S3?

[levinhein]

May I ask for the code used to generate Figure S3? Thank you!

[miaozhun]

Sure.

library(gplots)
library(RColorBrewer)

sampleNum_1 <- sum(group == 1)
sampleNum_2 <- sum(group == 2)

results.DEs <- results.sig[results.sig$Type == "DEs", ]
results.DEa <- results.sig[results.sig$Type == "DEa", ]
results.DEg <- results.sig[results.sig$Type == "DEg", ]

counts_norm.DEs <- counts_norm[row.names(results.DEs)[1:500],]
counts_norm.DEa <- counts_norm[row.names(results.DEa)[1:500],]
counts_norm.DEg <- counts_norm[row.names(results.DEg)[1:500],]

counts_norm.three <- rbind(counts_norm.DEs, counts_norm.DEa, counts_norm.DEg)
counts_norm.three_log <- log(counts_norm.three + 1)
mainText <- "Top 500 of each of the 3 types DE genes"
heatmap.2(counts_norm.three_log, col = c("blue", rev(heat.colors(255))), lhei = c(1,5.7), RowSideColors = c(rep("green", nrow(counts_norm.DEs)), rep("yellow", nrow(counts_norm.DEa)), rep("purple", nrow(counts_norm.DEg))), ColSideColors = c(rep("red", sampleNum_1), rep("darkblue", sampleNum_2)), dendrogram = "row", Colv = F, scale = "none", labRow = NA, labCol = NA, trace="none", main = mainText)
legend(0.32, 1.04, legend = c("E3", "E4", "DEs", "DEa", "DEg"), horiz = T, col = c("red", "darkblue", "green", "yellow", "purple"), pch = 15, pt.cex=2, xpd=TRUE)