Hi everyone,

Generating a pheatmap for my analysis. Everything is going to plan except for the colouring of the map itself - only some samples are being coloured whilst the rest are blank.

Here is my script:

sampledist <- dist(t(assay(vsd)), method = "euclidean")
sampledist_matrix <- as.matrix(sampledist)
colors <- colorRampPalette(rev(brewer.pal(9, "YlGnBu")))(255)

Specify colours for experimental design annotations:

variety_clr <- brewer.pal(3, "Set3")[c(1,3)]
names(variety_clr) <- unique(coldata$Variety)
time_clr <- brewer.pal(4, "Set1")
names(time_clr) <- unique(coldata$Time)
annotation_colours <- list(Tissue = c(Leaf = "forestgreen", Root = "red"),
                           Variety = variety_clr, Time = time_clr)

# plot
phm_ed <- pheatmap(sampledist_matrix,
                   clustering_distance_rows=sampledist,
                   clustering_distance_cols=sampledist,
                   clustering_method = "average",
                   treeheight_row = 80,
                   treeheight_col = 80,
                   annotation_col = coldata[2:4,],
                   annotation_row = coldata[2:4,],
                   annotation_colors = annotation_colours,
                   show_rownames = TRUE,
                   show_colnames = FALSE,
                   cellwidth = 15,
                   cellheight = 15,
                   cutree_rows = 2,
                   cutree_cols = 2,
                   col=colors,
                   fontsize = 12,
                   border_color = "black")

If anyone could shed any light as to why this might be I would appreciate the help.

Thanks in advance

These two lines select only three rows:

annotation_col = coldata[2:4,],
                   annotation_row = coldata[2:4,],

Where I would imagine you meant to choose those three columns instead?