Uk5

Here we plot the correlation matrix and the first 3 eigenvectors of Uk2.

library('knitr')

## Warning: package 'knitr' was built under R version 3.2.5

knitr::opts_chunk$set(cache=TRUE)
opts_chunk$set(fig.path = "/Users/sarahurbut/Dropbox/PaperEdits/Paper/Figureswithres/") 
covmat=readRDS("../../Results_Data/covmatwithzero.rds")

covmat=readRDS("../../Data_vhat/covmatwithvhat.rds")

z.stat=read.table("../../Data/maxz.txt")
names=colnames(z.stat)
pis=readRDS("../../Data_vhat/piswithvhat.rds")$pihat
pi.mat=matrix(pis[-length(pis)],ncol=54,nrow=22,byrow = T)

library(gplots)
library(ggplot2)
library('colorRamps')
#install.packages("fields")
library(fields)
k=5
colSums(pi.mat)[k]

## [1] 0.06533516

hclust.2=function (d, method = "average", members = NULL) {hclust(d, method, members)}
  x=cov2cor(covmat[[k]])
x[x<0]=0
  colnames(x)=names
  rownames(x)=names

h=read.table(paste0("../../Data/uk",k,"rowIndices.txt"))[,1]

Lattice

library(lattice)


clrs <- colorRampPalette(rev(c("#D73027","#FC8D59","#FEE090","#FFFFBF",
                               "#E0F3F8","#91BFDB","#4575B4")))(64)
#clrs[63:64] <- "darkviolet"
lat=x[rev(h),rev(h)]
lat[lower.tri(lat)] <- NA
print(levelplot(lat,col.regions = clrs,xlab = "",ylab = "",colorkey = TRUE))

And the SVD Plots:

missing.tissues=c(7,8,19,20,24,25,31,34,37)
color.gtex=read.table("../../Data/GTExColors.txt",sep = '\t', comment.char = '')[-missing.tissues,]
col = as.character(color.gtex[,2])


k=5
h=read.table(paste0("../../Data/uk",k,"rowIndices.txt"))[,1]

g=1
v=svd(covmat[[k]])$v[h,]
rownames(v)=colnames(v)=names[h]
par(mar=c(8,4.1,4.1,2.1))
barplot(v[,g]/v[which.max(abs(v[,g])),g],las=2,main=paste("Eigenvector",g,"of Uk",k),cex.names = 0.5,col=col[h],names=names[h])