R stat heatmap problem

Question

[sparrowquality]

I am using R for cluster analysis visualized by heatmap. Previously it worked perfectly, but reinstalling the software (and the whole system) started to bring errors. Here is the script:

library("gplots")
library("amap")
setwd("C:/Users/Zed/Documents/R/")
data_matrix=read.csv(file=("f:/CE_FASC.csv"), row.names=1)
marker_names=rownames(data_matrix)
sample_ids=colnames(data_matrix)
#mydist=function(c) {dist(c,method="euclidian")}
mydist=distfun = function(matrix) as.dist(Dist(matrix, method = "spearman"))
#myclust=function(c) {hclust(c,method="average")}
myclust=function(c) {hclust(c,method="complete")}
pdf(file="result1.pdf")
main_title="heatmap of clustered markers"
par(cex.main=1)
heatmap.2(as.matrix(data_matrix), hclustfun=myclust, distfun=mydist, na.rm = TRUE, scale="none", dendrogram="column", margins=c(6,6), 
Rowv=TRUE, Colv=TRUE, symbreaks=FALSE, key=TRUE, symkey=FALSE, 
density.info="none", trace="none", main=main_title, labCol=sample_ids, labRow=marker_names, cexRow=1, col=rev(heat.colors(75)))
dev.off()*

Than the error:

Error in heatmap.2(as.matrix(data_matrix), hclustfun = myclust, distfun = mydist, : `x' must be a numeric matrix

The source file (csv) is ok.

[Nicolas Rosewick]

Could you post a subset of your data_matrix : data_matrix[1:10,] . And also could you do is(data_matrix)

[sparrowquality]

"D1,D2,D3,D4
CD34,0,0,0,0
CD44,64,93,84,33
CD47,90,93,90,84
CD54,51,78,42,47
CD73,91,92,89,86
CD90,12,17,0,0
CD105,51,78,69,0
CD106,41,39,73,0
CD112,73,78,83,78
CD146,73,45,54,0
CD166,75,79,84,78
CD325,76,62,89,79"

[Jean-Karim Heriche]

This looks like your csv file, not the output of R data_matrix[1:10,]

[Jean-Karim Heriche]

From the docs:

as.matrix is a generic function. The method for data frames will return a character matrix if there is only atomic columns and any non-(numeric/logical/complex) column...

You may find this blog post enlightening.

[sparrowquality]

Til this time it worked, but if I delete it it is still not doing the cluster analysis and the heatmap..

[Jean-Karim Heriche]

I don't understand. What worked and what did you delete ? Most likely, the integers in your data frame are treated as factor levels and converted to character type. Try the data.matrix() function which tries to coerce a data frame to a numeric matrix.

[H.Hasani]

Your code works as it is with me, I got the mentioned error only when I remove the function as.matrix.

I can only conclude that your csv file is the problem. Did the code work previously with this particular file or other files.

[sparrowquality]

Yes, I realized as well. CSV made by old MS Excell is working...with new versions not. THX your help.

Answer 1

[sparrowquality]

"D1,D2,D3,D4
CD34,0,0,0,0
CD44,64,93,84,33
CD47,90,93,90,84
CD54,51,78,42,47
CD73,91,92,89,86
CD90,12,17,0,0
CD105,51,78,69,0
CD106,41,39,73,0
CD112,73,78,83,78
CD146,73,45,54,0
CD166,75,79,84,78
CD325,76,62,89,79"

[ivivek_ngs]

Classical heat map plot with row.names=1 and header=T and then view the matrix and plot the heatmap and see if you can see them or not. Do you have a row with all 0 then filter row with all 0 since they will creat NA error