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LieberInstitute / spatialLIBD

Code for the spatialLIBD R/Bioconductor package and shiny app
http://LieberInstitute.github.io/spatialLIBD/
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[BUG] `sort_clusters` creates arbitary numeric seqences as legend labels in `vis_grid_clus` plots. #77

Closed boyiguo1 closed 3 months ago

boyiguo1 commented 6 months ago

Thanks for the nice package!

I've been using vis_grid_clus to plot multiple samples together. I noticed the legends representing levels of clustervar are always turning to numbers instead of showing their original labels even when I manually set up with colors. With some debugging, I realize the function sort_clusters might be the culprit for it. 

library(spatialLIBD)
spe <- fetch_data("spatialDLPFC_Visium_example_subset")
spe$spd <- sprintf("SpD_%02d", spe$BayesSpace_harmony_10)
table(spe$spd)
# SpD_01 SpD_02 SpD_03 SpD_04 SpD_05 SpD_06 SpD_07 SpD_08 SpD_09 SpD_10 
#    139    755   1932   2137   1882    688   1805   1511    591    667 
sort_clusters(spe$spd) |> table()
#    1    2    3    4    5    6    7    8    9   10 
# 2137 1932 1882 1805 1511  755  688  667  591  139

As an end results for vis_grid_clus plots, I'm getting plots with no color filled spots and warning messages 1: No shared levels found betweennames(values)of the manual scale and the data's fill values. when running the following line.

k <- unique(spe$spd) |> length()
vis_grid_clus(
  spe,
  "spd",
  return_plots = TRUE,
  colors = set_names(
    Polychrome::palette36.colors(k),
    unique(spe$spd) |> sort()
  )
)

This is because sort_clusters is employed with the default option of sort_clust = TRUE. https://github.com/LieberInstitute/spatialLIBD/blob/77a5303f91edb7b9ffb1ce00b4193dae5d16a8a1/R/vis_grid_clus.R#L69-L72

The problem is metigated by making sort_clust = FALSE as well as providing colors option.

vis_grid_clus(
  spe,
  "spd",
  return_plots = TRUE,
  sort_clust = FALSE,
  colors = set_names(
    Polychrome::palette36.colors(k),
    unique(spe$spd) |> sort()
  )
)

R Session Information

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lcolladotor commented 3 months ago

Hi @boyiguo1,

This has been now resolved in https://github.com/LieberInstitute/spatialLIBD/commit/08c2b2d80a29b1decee578d01f7230b595a9bf5a which also resolved #80.

Best, Leo

Here's the output of your example with version 1.17.6:

suppressPackageStartupMessages(library("spatialLIBD"))
spe <- fetch_data("spatialDLPFC_Visium_example_subset")
#> 2024-07-12 13:23:57.969 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/6f563a40ecf7_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
spe$spd <- sprintf("SpD_%02d", spe$BayesSpace_harmony_10)
vis_grid_clus(
  spe,
  "spd",
  return_plots = TRUE,
  sort_clust = TRUE
)
#> $Br6432_ant

#> 
#> $Br6522_ant

#> 
#> $Br8667_mid


k <- unique(spe$spd) |> length()
vis_grid_clus(
  spe,
  "spd",
  return_plots = TRUE,
  sort_clust = FALSE,
  colors = setNames(
    Polychrome::palette36.colors(k),
    unique(spe$spd) |> sort()
  )
)
#> $Br6432_ant

#> 
#> $Br6522_ant

#> 
#> $Br8667_mid

packageVersion("spatialLIBD")
#> [1] '1.17.6'

Created on 2024-07-12 with reprex v2.1.0