Order Pheatmap by Annotation
I Am Attempting to Make a Figure Using the Package Pheatmap. I Would Like to Group the Data by the Annotation That I Am Using, but It Won't Group Together. My...
I am attempting to make a figure using the package pheatmap. I would like to group the data by the annotation that I am using, but it won't group together.
My data is here:
sub_samp <- structure(c(1, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0,
1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1,
0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0,
1, 1, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1,
1, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 1,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), .Dim = c(20L,
9L), .Dimnames = list(c("GQQG", "RAPM", "RGQI", "GYNY", "SPTGGSYNX",
"SRLPSDX", "SLXVAGTNEK", "RXVQYGTDT", "SLTXASVE", "SRXGTSGRADE",
"QLDY", "XPRHQTYE", "SXPGTGKSA", "PAVS", "SPRXVTE", "SRDXGPNYG",
"TGTXLE", "PEAH", "SLQGGXT", "SPSARDRVGX"), c("pt11_protected",
"pt12_protected", "pt14_protected", "pt15_protected", "pt16_protected",
"pt17_protected", "pt18_protected", "pt19_protected", "pt20_protected"
)))
sub_anno <- structure(list(seq_share = c("shared", "shared", "shared", "shared",
"shared", "shared", "unshared", "unshared", "unshared", "unshared",
"unshared", "unshared", "unshared", "unshared", "unshared", "unshared",
"unshared", "unshared", "unshared", "unshared")), .Names = "seq_share", row.names = c("XPRHQTYE",
"GQQG", "GYNY", "QLDY", "RGQI", "SRLPSDX", "PAVS", "PEAH", "RXVQYGTDT",
"RAPM", "SXPGTGKSA", "SLXVAGTNEK", "SLQGGXT", "SLTXASVE", "SPRXVTE",
"SPSARDRVGX", "SPTGGSYNX", "SRXGTSGRADE", "SRDXGPNYG", "TGTXLE"
), class = "data.frame")
I am using the above data (derived from dput(xyz_data)) and running the following code for the pheatmap
pheatmap::pheatmap(sub_samp, annotation_row = sub_anno)
How can I get the data to group together by the annotation?
1 Answer
To specify a predetermined row order in pheatmap you should first turn off the row clustering and then manually order your matrix.
Using the data you provided this is fairly straight forward.
# 1) reorder the matrix based in the annotation
sub_samp_ordered <- sub_samp[rownames(sub_anno), ]
# 2) plot heatmap with no row clusters
pheatmap::pheatmap(sub_samp_ordered, annotation_row = sub_anno, cluster_rows = F)
Which results in:
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