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rmatrixheatmaplarge-data

Heatmap for a large matrix and get the clear labels

How to draw a heatmap from a matrix of 305 columns and 865 rows in R.

The code I have written for the matrix is 

nba <- read.csv("mydata.csv", sep=",")

row.names(nba) <- nba[,1]
nba <- nba[,2:865]

nba_matrix <- data.matrix(nba)
nba_heatmap <- heatmap(nba_matrix, Rowv=NA, Colv=NA, col = brewer.pal(9, "Blues"), scale="column", margins=c(5,10))

Now the code gives me the heatmap as shown bellow, but the labels are not clear. Please help me to get a clear heatmap.

enter image description here

Solution

  • since you stated that you need all the labels, the only way I see is reducing the font size. You can do this by setting the cexCol and cexRow parameters in your call to heatmap(); for example like this:

    heatmap(as.matrix(iris[,1:3]),cexRow = 0.1, cexCol = 0.1,)