Heatmap.2 draw a X if column name start by number

Question

[joseluis.gonzalez]

Hi all,

I'm having problems when heatmap.2 plot the column names if the first character is a number. Heatmap.2 add a X just before the number, and I don't know how to solve it.

The data matrix:

,1A,1B,1C,2A,2B,2C
Actinobacteria,22.30,3.44,4.48,8.23,14.90,12.82
Bacteroidetes,0.48,5.53,0.15,4.01,5.92,1.89
Balneolaeota,1.61,2.37,2.21,0.11,0.11,0.07
Candidatus Dadabacteria,0.10,0.12,29.39,0.00,0.00,0.00
Chloroflexi,0.09,0.20,0.50,4.65,11.29,8.00
Cyanobacteria,20.41,3.56,0.38,40.89,2.31,23.07
Firmicutes,47.58,64.02,48.88,15.40,14.32,7.20
Gemmatimonadetes,0.00,0.01,0.22,0.42,0.86,1.01
Proteobacteria,14.14,16.31,11.59,22.59,43.47,40.51
Planctomycetes,1.04,1.21,0.64,1.57,3.89,3.81
Rhodothermaeota,10.94,2.81,0.81,0.17,0.69,0.77
Candidatus Patescibacteria,0.33,0.24,0.07,1.58,1.33,0.37

The R script:

Phylum_data <- read.csv("phylum.txt")
phylum_rnames <- Phylum_data[,1]
phyl_dat <- data.matrix(Phylum_data[,2:ncol(Phylum_data)])
rownames(phyl_dat) <- phylum_rnames


heatmap.2(phyl_dat,
          dendrogram = "column", Colv = T, Rowv = NA,
          scale = "none", col= colorRampPalette(brewer.pal(9, "Blues"))(100),
          key = TRUE, density.info = "none", key.title = NA, key.xlab = "Abundance (%)",
          trace = "none",
          margins =c(8,17),
          cellnote = round(phyl_dat, 1),
          labRow=as.expression(lapply(rownames(nerja_datos_filo), function(a) bquote(italic(.(a))))), 
          notecol = "red",
          main = "Diversity at Phylum level",
          cexRow = 1.5,
          lhei = c(1,8), lwid = c(1,3)
)

When the heatmap is plotted, the colnames appear as "X1A" "X1B"... How could I proceed to remove the X??

Answer 1

[joseluis.gonzalez]

I answer myself. The problem was in read.csv("phylum.txt"), I should have added check.names=FALSE.

Thanks!