Issues with Pheatmap
1
0
Entering edit mode
axe880 • 0
@172ed42b
Last seen 2.6 years ago
United Kingdom

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")

enter image description here

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

Thanks in advance

pheatmap • 2.5k views
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1
Entering edit mode
@james-w-macdonald-5106
Last seen 16 minutes ago
United States

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?

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Entering edit mode

Does the ":" between the 2 and the 4 not select for columns 2, 3, and 4? That was my impression but I am new to this. What would the alternative be if not this? Thanks!

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1
Entering edit mode

It does select for 2, 3, and 4. But [2:4,] is rows 2-4. If you want columns, it's [,2:4]. Note which side of the comma the range is on.

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0
Entering edit mode

Ah great I see - I've managed to solve this issue now. Thanks again.

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