我只是想出了怎么做,所以我发布了我自己问题的答案,希望它对其他人有用:
require(gplots) # for heatmap.2()
mydata <- read.csv(file="otu_tab_L4.txt", header=T, row.names=1, sep="\t")
#transposes it and makes a matrix
mydata_t <- t(as.matrix(mydata))
#makes Spearman's correlation
cor.matrix <- cor(mydata_t, method = "spearman")
#remove upper part of the matrix, since it gives the same informations
cor.matrix[upper.tri(cor.matrix )] <- NA
#checks matrix dimensions
dim(cor.matrix)
#Finally, I plotted a triangular heatmap of my matrix
##the standard function will put the y labels on the right!! I wanted them on the left! So ##changed the heatmap.2 function code in this way:
####open the code:
fix(heatmap.2)
###modify it in this way:
##when it says: " axis(4, iy, labels = labRow, las = 2, line = -0.5, tick = 0,
cex.axis = cexRow) "
##I put 2 in place of 4!!
heatmap<- heatmap.2(cor.matrix,scale="none",Rowv=NA,Colv=NA,col=rainbow,margins(5,5),cexRow=0.5,cexCol=1.0,key=TRUE,keysize=1.5,trace="none")