Files given: .txt file ready for heat from

Setup

#new correlatin plot

rm(list=ls())

library(RColorBrewer)

library("gplots")

Using gplots to make the heatmaps

1. Import data

• import the.txt file - it was already heatmap ready

I couldn't figure out how to make 2 sidebars appear on the same plot. So my alternative solution was to make 2 of the same heatmap with different side bars, and then just manually cut and assemble the sidebars in powerpoint

• heatmap.2() was used to make the heatmaps.

  • use RowSideColors = c( rep("colorname", number of rows), rep()) to specify the side row's colors

    • Example below will code for blue 3 in the first 6 rows, and then make red in the next six spaces...etcs :

    • RowSideColors = c( # grouping row-variables into different colors

    • rep("blue3", 6), #dark blue

    • rep("#ef062d", 6), #red

    • rep("blue", 5), #blue

    • rep("#e131b5", 3), #pink

    • rep("blue", 1), #blue

    • rep("#e131b5", 3)),

• par(oma=c(2,0,0,20),xpd=TRUE). parameters of the outside margins we adjusted, and xpd = TRUE, allows us to draw outside plot area

#color side bar 1

png(paste0("1Peng_reordered_phenolowtri_rguptri_matrix.png"),width = 15*300, height = 12*300, res = 300, pointsize = 10)

par(oma=c(2,0,0,20),xpd=TRUE)# xpd allows Draw outside plot area

heatmap.2(dfMatrix,dendrogram ='none', trace = "none",density.info = "none", Colv = NA, Rowv = NA,

labCol = FALSE,cexRow =3, offsetRow=11,breaks=seq(-1, 1, length.out=200.1),

key.title="",key.xlab="", key.par=list(mar=c(4,0,1,2), cex=1.0, cex.lab=2.0, cex.axis=2.0),

col= col1(200),

RowSideColors = c( # grouping row-variables into different colors

rep("paleturquoise4", 12), # area darker turquoise

rep("paleturquoise2", 12)), #thickness

lmat=rbind(c(3,0,0,4,5), c(0,0,2,1,0)), #specifying the bar to be on the right

lhei=c(0.5,4),

lwid=c(0.1,0.1,4,0.25,1))

dev.off()

Color sidebar 2 (the same as 1 except the side bars are colored differently)

Manually position the images together in powerpoint, and then export.

• Can export using export function or using print function and save as PostScripts and then convert to tiff