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Feature request: use named vectors for discrete palettes in tiles #113
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Hello @drejom, it is a good idea. For now, I believe you can control the colour pairing, ordering the levels of the factors Please try and let me know. If that works, you could add this example to the README of tidyHeatmap to share this example with the community. |
I'd love to contribute however I can - this (like your others) is a fantastic package, and so useful! I've tried a few different approaches trying to understand how colours are allocated but was left a bit baffled. Maybe another eg would help: I couldn't work out why when reversing the factor library(RColorBrewer)
library(ALL)
library(tidyverse)
library(tidyHeatmap)
#> tidyHeatmap version 1.10.0
# Use the ALL data from Bioconductor
data(ALL)
# Make a tidy expression table with metadata
exprs(ALL)[sample(12625, 20, FALSE), ] |>
as_tibble(rownames = "affy_id") |>
pivot_longer(-affy_id, names_to = "cod", values_to = "exprs") |>
mutate(cod = sub("^0*", "", cod)) |>
left_join(pData(ALL), by = join_by(cod)) |>
# Reverse the factor levels for `mol.biol`
mutate(mol.biol_rev = factor(mol.biol, levels = rev(levels(mol.biol)))) |>
# Plot a heatmap with some tiles
heatmap(affy_id, cod, exprs) |>
annotation_tile(mol.biol, palette = brewer.pal(6, "Spectral")) |>
annotation_tile(mol.biol_rev, palette = brewer.pal(6, "Spectral"))
display.brewer.pal(6, "Spectral") Created on 2023-04-05 with reprex v2.0.2 Session infosessioninfo::session_info()
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Thanks for the enthusiasm. I see; this means that while I keep factors for I should not convert to a character (if possible) and, in doing so, lose user control. If you have some throughput (it could be a good experience becoming a co-developer), try to see when in the "journey" of the Fixing this would elegantly address your customisation need (and we can, in the future, also consider named character vectors, although that might have bigger implications and edge cases we are not seeing now). [EDIT] I see that the order is maintained in the legend. This means that
|
OK great! I see the annotation_tiles() function in methods.R: Line 361 in 849bf51
Looks like it should be straightforward. I'll have a go and get back to you! |
Great, it is not always straightforward, but once you understand the logic, you will be able to change all sorts of things ;) Looking forward to receiving your pull request! |
Hello @stemangiola , I was trying to use factors for discrete palettes as @drejom tried but I didn't get any robust results regarding the mapping of colors to the vector of interest. you make the palette a list : then in the function Line 374 in 849bf51
when(how_many_discrete>0 ~ tail(., -how_many_discrete) , ~ (.)) you drop some colors from a vector? Is it just one vector of palette_discrete that has all the inserted custom annotations?
|
my_input_heatmap@palette_discrete is a list of palettes every annotation gets a palette, that then is eliminated from the available pool. Any contribution on this issue would be much appreciated! |
It's quite odd. |
If things are as planned, the order should reflect the factor levels, or alphabetical order if the columns in not a factor. |
Not actually. |
When using a custom palette for example with tiles,
annotation_tile()
expects a vector of colours, but it would be good if it could accept a named vector, so that colours can be applied to the levels of a factor in a predictable way.Eg:
Gives unexpected results:
![plot](https://user-images.githubusercontent.com/91294/230040663-4c3fc54b-daac-459c-b000-3b730c269409.png)
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