[BUG] vis_grid_clus cannot handle logical variables #80

lahuuki · 2024-06-11T15:22:00Z

I noticed some strange behavior in vis_grid_clus() when trying to plot logical variables such as in_tissue, the same variables plot as expected in vis_clus(). Converting the lgl to factor does not fix this.

Example in `spatialDLPFC_Visium_example_subset`

library("spatialLIBD")

spe <- fetch_data("spatialDLPFC_Visium_example_subset")

## works on integer data
type(spe$BayesSpace_harmony_02)
# [1] "integer"

vis_grid_clus(
    spe = spe,
    clustervar = "BayesSpace_harmony_02",
    pdf = here::here(plot_dir, "spe_DLPFC_grid-BayesSpace_harmony_02.pdf"),
    sort_clust = FALSE,
    point_size = 2
)

Doesn't work with logical data

## convert to logical
spe$BayesSpace_harmony_02_lgl <- spe$BayesSpace_harmony_02 ==1
table(spe$BayesSpace_harmony_02)

## vis_clus works fine
png(here::here(plot_dir, "spe_DLPFC_BayesSpace_harmony_02_lgl.png"))
vis_clus(
    sampleid = "Br6432_ant",
    spe = spe,
    clustervar = "BayesSpace_harmony_02_lgl",
    point_size = 2
)
dev.off()

##vis grib clus returns all blank points + unuseful warning
vis_grid_clus(
    spe = spe,
    clustervar = "BayesSpace_harmony_02_lgl",
    pdf = here::here(plot_dir, "spe_DLPFC_grid-BayesSpace_harmony_02_lgl.pdf"),
    sort_clust = FALSE,
    point_size = 2
)
# Warning messages:
# 1: No shared levels found between `names(values)` of the manual scale and the data's fill values. 
# 2: No shared levels found between `names(values)` of the manual scale and the data's fill values.

## sort_clust = TRUE throws error
vis_grid_clus(
    spe = spe,
    clustervar = "BayesSpace_harmony_02_lgl",
    pdf = here::here(plot_dir, "spe_DLPFC_grid-BayesSpace_harmony_02_lgl.pdf"),
    sort_clust = TRUE,
    point_size = 2
)

# Error in `[[<-`(`*tmp*`, clustervar, value = c(`TRUE` = 1L, `NA` = NA,  : 
#                                                    1239 elements in value to replace 12107 elements

options(width = 120)
## insert session info here
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.3 (2024-02-29)
 os       macOS Sonoma 14.5
 system   x86_64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/New_York
 date     2024-06-11
 rstudio  2024.04.1+748 Chocolate Cosmos (desktop)
 pandoc   NA

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 [1] /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library

Note. spatialLIBD is a recent github version

Additional Context

I found this bug plotting data from the LFF_spatial_ERC project: more examples of this issue

Is the package installed via bioconda? No

The text was updated successfully, but these errors were encountered:

lcolladotor · 2024-07-12T15:00:51Z

Thanks for the report @lahuuki!

Here's how things behave now in spatialLIBD version 1.17.6. See 08c2b2d for more details on the internal changes to sort_clusters() and get_colors().

Best,
Leo

suppressPackageStartupMessages(library("spatialLIBD"))
spe <- fetch_data("spatialDLPFC_Visium_example_subset")
#> 2024-07-12 10:58:34.14279 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/6f563a40ecf7_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1

spe$BayesSpace_harmony_02_lgl <- spe$BayesSpace_harmony_02 ==1
set.seed(20240712)
spe$BayesSpace_harmony_02_lgl[sample(seq_len(ncol(spe)), 2000)] <- NA

vis_grid_clus(
    spe = spe,
    clustervar = "BayesSpace_harmony_02_lgl",
    return_plots = TRUE,
    sort_clust = FALSE,
    point_size = 2
)
#> $Br6432_ant

#> 
#> $Br6522_ant

#> 
#> $Br8667_mid

vis_grid_clus(
    spe = spe,
    clustervar = "BayesSpace_harmony_02_lgl",
    return_plots = TRUE,
    sort_clust = TRUE,
    point_size = 2
)
#> $Br6432_ant

#> 
#> $Br6522_ant

#> 
#> $Br8667_mid

vis_clus(
    sampleid = "Br6432_ant",
    spe = spe,
    clustervar = "BayesSpace_harmony_02_lgl",
    point_size = 2
)

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

^{Created on 2024-07-12 with reprex v2.1.0}

Co-authored-by: Louise Huuki <lahuuki@gmail.com>

lcolladotor closed this as completed in 08c2b2d Jul 12, 2024

lcolladotor added a commit that referenced this issue Jul 12, 2024

v1.17.6 -- related to #80

4c7274f

lcolladotor mentioned this issue Jul 12, 2024

[BUG] sort_clusters creates arbitary numeric seqences as legend labels in vis_grid_clus plots. #77

Closed

lcolladotor added a commit that referenced this issue Jul 12, 2024

Edited add_qc_metrics() to match recent changes related to #80

9280e5c

Co-authored-by: Louise Huuki <lahuuki@gmail.com>

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[BUG] vis_grid_clus cannot handle logical variables #80

[BUG] vis_grid_clus cannot handle logical variables #80

lahuuki commented Jun 11, 2024

lcolladotor commented Jul 12, 2024

[BUG] vis_grid_clus cannot handle logical variables #80

[BUG] vis_grid_clus cannot handle logical variables #80

Comments

lahuuki commented Jun 11, 2024

Example in spatialDLPFC_Visium_example_subset

Doesn't work with logical data

Additional Context

Is the package installed via bioconda? No

lcolladotor commented Jul 12, 2024

Example in `spatialDLPFC_Visium_example_subset`