Error in hclustfun(distMatrixR, method = method) when I am making a heat map
I am trying to create a heat map with this data in pastebin. However I am getting the error:
Error in hclustfun(distMatrixR, method = method) : NA/NaN/Inf in foreign
function call (arg 10)
In addition:
Warning message: In cor(t(x), use = pa) : the standard deviation is zero which I am failing to trouble shoot. I have attached the code I currently have
library(gplots)
library(heatmap3)
library(RColorBrewer)
library(readxl)
colfunc - colorRampPalette(c(mistyrose, red))
Data - read_excel(TE_polymophism.xlsx)
# N=100
# Data - Data[sample(nrow(Data), N), ]
# Data - Data[order(Data$svtype),]
Data - Data[,2:ncol(Data)]
Data - log2(Data+1)
colnames(Data) - c(AraucanaWhite,Cornell2, ACRB30Weeks, Luoyangwu,RedJungleFowl, Tibetan)
Data_final - as.matrix(Data)
pdf(TE_polymophism.pdf, height = 10, width = 10)
par(oma=c(1,1,1,1))
heatmap3(Data_final,
Colv=T, #To keep the column order (sample order), cluster the genes
scale=none,
hclustfun = ,
labRow= ,
cexCol = 0.9,
key=TRUE,#Show color key
density.info=none,trace=none, na.rm=TRUE)
dev.off()
Category Data Science