tidyHeatmap Add argument to force direction of an annotation

Add argument to force direction of an annotation

Open antass opened this issue 1 year ago • 3 comments

I'm trying to add a sample annotation to a gene expression heatmap. Since the data is in a tidy format, it is unclear if the annotation column I want to use applies to genes (rows) or samples (columns). I get a tile added on both row and column sides of heat map for the same variable. (Surprisingly this only happens for 1 of 3 variables I'm using to annotate my samples).

Is there a way to specify which annotations/variables go with rows and which with columns?

Thanks for an awesome package!!

my_mat <- structure(list(gene = c("23d4c9accd", "9811052cd0", "bf1591f9c8", 
"8fea8007d7", "4e71370e99", "503e85a48f", "12211f2cab", "23d4c9accd", 
"9811052cd0", "bf1591f9c8", "8fea8007d7", "4e71370e99", "503e85a48f", 
"12211f2cab", "23d4c9accd", "9811052cd0", "bf1591f9c8", "8fea8007d7", 
"4e71370e99", "503e85a48f", "12211f2cab", "23d4c9accd", "9811052cd0", 
"bf1591f9c8", "8fea8007d7", "4e71370e99", "503e85a48f", "12211f2cab", 
"23d4c9accd", "9811052cd0", "bf1591f9c8", "8fea8007d7", "4e71370e99", 
"503e85a48f", "12211f2cab", "23d4c9accd", "9811052cd0", "bf1591f9c8", 
"8fea8007d7", "4e71370e99", "503e85a48f", "12211f2cab", "23d4c9accd", 
"9811052cd0", "bf1591f9c8", "8fea8007d7", "4e71370e99", "503e85a48f", 
"12211f2cab", "23d4c9accd", "9811052cd0", "bf1591f9c8", "8fea8007d7", 
"4e71370e99", "503e85a48f", "12211f2cab", "23d4c9accd", "9811052cd0", 
"bf1591f9c8", "8fea8007d7", "4e71370e99", "503e85a48f", "12211f2cab", 
"23d4c9accd", "9811052cd0", "bf1591f9c8", "8fea8007d7", "4e71370e99", 
"503e85a48f", "12211f2cab", "23d4c9accd", "9811052cd0", "bf1591f9c8", 
"8fea8007d7", "4e71370e99", "503e85a48f", "12211f2cab", "23d4c9accd", 
"9811052cd0", "bf1591f9c8", "8fea8007d7", "4e71370e99", "503e85a48f", 
"12211f2cab", "23d4c9accd", "9811052cd0", "bf1591f9c8", "8fea8007d7", 
"4e71370e99", "503e85a48f", "12211f2cab", "23d4c9accd", "9811052cd0", 
"bf1591f9c8", "8fea8007d7", "4e71370e99", "503e85a48f", "12211f2cab", 
"23d4c9accd", "9811052cd0", "bf1591f9c8", "8fea8007d7", "4e71370e99", 
"503e85a48f", "12211f2cab", "23d4c9accd", "9811052cd0", "bf1591f9c8", 
"8fea8007d7", "4e71370e99", "503e85a48f", "12211f2cab", "23d4c9accd", 
"9811052cd0", "bf1591f9c8", "8fea8007d7", "4e71370e99", "503e85a48f", 
"12211f2cab", "23d4c9accd", "9811052cd0", "bf1591f9c8", "8fea8007d7", 
"4e71370e99", "503e85a48f", "12211f2cab", "23d4c9accd", "9811052cd0", 
"bf1591f9c8", "8fea8007d7", "4e71370e99", "503e85a48f", "12211f2cab", 
"23d4c9accd", "9811052cd0", "bf1591f9c8", "8fea8007d7", "4e71370e99", 
"503e85a48f", "12211f2cab", "23d4c9accd", "9811052cd0", "bf1591f9c8", 
"8fea8007d7", "4e71370e99", "503e85a48f", "12211f2cab", "23d4c9accd", 
"9811052cd0", "bf1591f9c8", "8fea8007d7", "4e71370e99", "503e85a48f", 
"12211f2cab", "23d4c9accd", "9811052cd0", "bf1591f9c8", "8fea8007d7", 
"4e71370e99", "503e85a48f", "12211f2cab", "23d4c9accd", "9811052cd0", 
"bf1591f9c8", "8fea8007d7", "4e71370e99", "503e85a48f", "12211f2cab", 
"23d4c9accd", "9811052cd0", "bf1591f9c8", "8fea8007d7", "4e71370e99", 
"503e85a48f", "12211f2cab", "23d4c9accd", "9811052cd0", "bf1591f9c8", 
"8fea8007d7", "4e71370e99", "503e85a48f", "12211f2cab", "23d4c9accd", 
"9811052cd0", "bf1591f9c8", "8fea8007d7", "4e71370e99", "503e85a48f", 
"12211f2cab", "23d4c9accd", "9811052cd0", "bf1591f9c8", "8fea8007d7", 
"4e71370e99", "503e85a48f", "12211f2cab", "23d4c9accd", "9811052cd0", 
"bf1591f9c8", "8fea8007d7", "4e71370e99", "503e85a48f", "12211f2cab", 
"23d4c9accd", "9811052cd0", "bf1591f9c8", "8fea8007d7", "4e71370e99", 
"503e85a48f", "12211f2cab", "23d4c9accd", "9811052cd0", "bf1591f9c8", 
"8fea8007d7", "4e71370e99", "503e85a48f", "12211f2cab", "23d4c9accd", 
"9811052cd0", "bf1591f9c8", "8fea8007d7", "4e71370e99", "503e85a48f", 
"12211f2cab", "23d4c9accd", "9811052cd0", "bf1591f9c8", "8fea8007d7", 
"4e71370e99", "503e85a48f", "12211f2cab", "23d4c9accd", "9811052cd0", 
"bf1591f9c8", "8fea8007d7", "4e71370e99", "503e85a48f", "12211f2cab", 
"23d4c9accd", "9811052cd0", "bf1591f9c8", "8fea8007d7", "4e71370e99", 
"503e85a48f", "12211f2cab", "23d4c9accd", "9811052cd0", "bf1591f9c8", 
"8fea8007d7", "4e71370e99", "503e85a48f", "12211f2cab", "23d4c9accd", 
"9811052cd0", "bf1591f9c8", "8fea8007d7", "4e71370e99", "503e85a48f", 
"12211f2cab", "23d4c9accd", "9811052cd0", "bf1591f9c8", "8fea8007d7", 
"4e71370e99", "503e85a48f", "12211f2cab", "23d4c9accd", "9811052cd0", 
"bf1591f9c8", "8fea8007d7", "4e71370e99", "503e85a48f", "12211f2cab", 
"23d4c9accd", "9811052cd0", "bf1591f9c8", "8fea8007d7", "4e71370e99", 
"503e85a48f", "12211f2cab"), sample = c("69afaccda6", "69afaccda6", 
"69afaccda6", "69afaccda6", "69afaccda6", "69afaccda6", "69afaccda6", 
"c8140f2cc6", "c8140f2cc6", "c8140f2cc6", "c8140f2cc6", "c8140f2cc6", 
"c8140f2cc6", "c8140f2cc6", "5a7e98232d", "5a7e98232d", "5a7e98232d", 
"5a7e98232d", "5a7e98232d", "5a7e98232d", "5a7e98232d", "c2f7b8ae36", 
"c2f7b8ae36", "c2f7b8ae36", "c2f7b8ae36", "c2f7b8ae36", "c2f7b8ae36", 
"c2f7b8ae36", "d06a461846", "d06a461846", "d06a461846", "d06a461846", 
"d06a461846", "d06a461846", "d06a461846", "b7f606fd99", "b7f606fd99", 
"b7f606fd99", "b7f606fd99", "b7f606fd99", "b7f606fd99", "b7f606fd99", 
"1f4c7ebe5c", "1f4c7ebe5c", "1f4c7ebe5c", "1f4c7ebe5c", "1f4c7ebe5c", 
"1f4c7ebe5c", "1f4c7ebe5c", "32f3962947", "32f3962947", "32f3962947", 
"32f3962947", "32f3962947", "32f3962947", "32f3962947", "b1016e1885", 
"b1016e1885", "b1016e1885", "b1016e1885", "b1016e1885", "b1016e1885", 
"b1016e1885", "4d2b8c3b0e", "4d2b8c3b0e", "4d2b8c3b0e", "4d2b8c3b0e", 
"4d2b8c3b0e", "4d2b8c3b0e", "4d2b8c3b0e", "aeaea63b2b", "aeaea63b2b", 
"aeaea63b2b", "aeaea63b2b", "aeaea63b2b", "aeaea63b2b", "aeaea63b2b", 
"d9f2de4c6e", "d9f2de4c6e", "d9f2de4c6e", "d9f2de4c6e", "d9f2de4c6e", 
"d9f2de4c6e", "d9f2de4c6e", "dd0c24d980", "dd0c24d980", "dd0c24d980", 
"dd0c24d980", "dd0c24d980", "dd0c24d980", "dd0c24d980", "76fcf26d96", 
"76fcf26d96", "76fcf26d96", "76fcf26d96", "76fcf26d96", "76fcf26d96", 
"76fcf26d96", "b0a9df4e2c", "b0a9df4e2c", "b0a9df4e2c", "b0a9df4e2c", 
"b0a9df4e2c", "b0a9df4e2c", "b0a9df4e2c", "f4c96715ba", "f4c96715ba", 
"f4c96715ba", "f4c96715ba", "f4c96715ba", "f4c96715ba", "f4c96715ba", 
"1ea0af4bfd", "1ea0af4bfd", "1ea0af4bfd", "1ea0af4bfd", "1ea0af4bfd", 
"1ea0af4bfd", "1ea0af4bfd", "a6323e1812", "a6323e1812", "a6323e1812", 
"a6323e1812", "a6323e1812", "a6323e1812", "a6323e1812", "3896318001", 
"3896318001", "3896318001", "3896318001", "3896318001", "3896318001", 
"3896318001", "5e1f4358f7", "5e1f4358f7", "5e1f4358f7", "5e1f4358f7", 
"5e1f4358f7", "5e1f4358f7", "5e1f4358f7", "a3e575a3d6", "a3e575a3d6", 
"a3e575a3d6", "a3e575a3d6", "a3e575a3d6", "a3e575a3d6", "a3e575a3d6", 
"862b760dbd", "862b760dbd", "862b760dbd", "862b760dbd", "862b760dbd", 
"862b760dbd", "862b760dbd", "8b4e5a4346", "8b4e5a4346", "8b4e5a4346", 
"8b4e5a4346", "8b4e5a4346", "8b4e5a4346", "8b4e5a4346", "1fdf1272ff", 
"1fdf1272ff", "1fdf1272ff", "1fdf1272ff", "1fdf1272ff", "1fdf1272ff", 
"1fdf1272ff", "8dd86cc3ca", "8dd86cc3ca", "8dd86cc3ca", "8dd86cc3ca", 
"8dd86cc3ca", "8dd86cc3ca", "8dd86cc3ca", "6894ea116f", "6894ea116f", 
"6894ea116f", "6894ea116f", "6894ea116f", "6894ea116f", "6894ea116f", 
"591a098489", "591a098489", "591a098489", "591a098489", "591a098489", 
"591a098489", "591a098489", "aa5c7ad759", "aa5c7ad759", "aa5c7ad759", 
"aa5c7ad759", "aa5c7ad759", "aa5c7ad759", "aa5c7ad759", "f57ef76df7", 
"f57ef76df7", "f57ef76df7", "f57ef76df7", "f57ef76df7", "f57ef76df7", 
"f57ef76df7", "a82dbaf481", "a82dbaf481", "a82dbaf481", "a82dbaf481", 
"a82dbaf481", "a82dbaf481", "a82dbaf481", "805031c46d", "805031c46d", 
"805031c46d", "805031c46d", "805031c46d", "805031c46d", "805031c46d", 
"42f46327f8", "42f46327f8", "42f46327f8", "42f46327f8", "42f46327f8", 
"42f46327f8", "42f46327f8", "7d31735f10", "7d31735f10", "7d31735f10", 
"7d31735f10", "7d31735f10", "7d31735f10", "7d31735f10", "e0aec6c8b1", 
"e0aec6c8b1", "e0aec6c8b1", "e0aec6c8b1", "e0aec6c8b1", "e0aec6c8b1", 
"e0aec6c8b1", "3bfe15e0d9", "3bfe15e0d9", "3bfe15e0d9", "3bfe15e0d9", 
"3bfe15e0d9", "3bfe15e0d9", "3bfe15e0d9", "7fccfe2004", "7fccfe2004", 
"7fccfe2004", "7fccfe2004", "7fccfe2004", "7fccfe2004", "7fccfe2004", 
"2357b8996a", "2357b8996a", "2357b8996a", "2357b8996a", "2357b8996a", 
"2357b8996a", "2357b8996a", "4b7e162a38", "4b7e162a38", "4b7e162a38", 
"4b7e162a38", "4b7e162a38", "4b7e162a38", "4b7e162a38", "cb50ad058c", 
"cb50ad058c", "cb50ad058c", "cb50ad058c", "cb50ad058c", "cb50ad058c", 
"cb50ad058c", "d9693ec59a", "d9693ec59a", "d9693ec59a", "d9693ec59a", 
"d9693ec59a", "d9693ec59a", "d9693ec59a"), treatment = structure(c(2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L), levels = c("Control", "AG120", "AG881"
), class = "factor"), timepoint = structure(c(1L, 1L, 1L, 1L, 
1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L), levels = c("pre", "post"), class = "factor"), 
    response = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 
    3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L), levels = c("PD", "PR", "CR"), class = "factor"), TPM = c(19.380045, 
    0, 3.267072, 3.968264, 6.030809, 13.413329, 0, 38.130024, 
    0.113256, 0.343518, 1.168443, 2.921347, 14.0089, 0.199056, 
    15.35862, 0.269429, 0.06675, 0.08171, 1.459363, 12.183334, 
    0.081186, 6.769901, 0, 0.206705, 0.493409, 1.281004, 7.219058, 
    0, 25.200628, 2.080746, 0.913836, 2.495217, 4.828447, 6.885907, 
    0.048215, 13.504421, 0.298124, 0.077277, 0.086118, 2.235733, 
    11.103624, 0.078631, 18.708677, 0, 1.12623, 1.481046, 3.351257, 
    18.233658, 0.222725, 23.83412, 0.182229, 0.935622, 1.246243, 
    2.596699, 19.366228, 0.17308, 18.548864, 0.199853, 0.102659, 
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    2.187107, 8.071058, 0, 11.604349, 0.972779, 0.135701, 0.497012, 
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    -0.482694624169388, -0.359288198243399, -0.716640100985938, 
    -0.916345125608135, 0.0481865852193022)), row.names = c(NA, 
-280L), class = c("tbl_df", "tbl", "data.frame"))

my_heatmap <- my_mat %>%
      heatmap(gene,
              sample,
              TPM.scaled,
              scale = "row",
              palette_value = circlize::colorRamp2(
        seq(-2, 2, length.out = 11),
        RColorBrewer::brewer.pal(11, "RdBu"))
        ) %>%
      add_tile(c(treatment, timepoint, response))

    my_heatmap

Aug 16 '22 19:08 antass

Hello @antass,

you have only one value of treatment.

> my_mat |> distinct(treatment)
# A tibble: 1 × 1
  treatment
  <fct>    
1 AG120

It is a bit strange to want to plot a unique value as annotation, you can simply write it in the methods and figure caption. Of course, with one value, it is impossible to understand if it is row or column-wise. This is such an odd scenario that I would not like to add complexity to the interface to allow that.

Am I seeying this right?

Aug 22 '22 03:08 stemangiola

Hi @stemangiola, thanks so much for taking a look.

Yes, that's correct. In this example, the treatment variable only has one value. This is a possible outcome of user filtering via a Shiny app. They might want to see multiple treatments on one plot, or just one, etc.. If they happen to choose a single treatment, I could add a conditional line to exclude the variable from annotation..

Just trying to see how I could generalize my code without having to foresee every possibility (which I'm sure you're also trying to do haha ;))

So just to double check I'm not missing anything: there is no way to specify which variables are column annotations and which are row, right?

Thanks again!

Aug 22 '22 15:08 antass

At the moment no, is all automatic. I see now your use case make sense.

Let me ponder on the cost of adding a new argument. Let's leave this issue open.

Aug 22 '22 21:08 stemangiola

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Add argument to force direction of an annotation

tidyHeatmap
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