bulk_clones plot "CNV state" legend colors

[igordot]

It seems that the bulk_clones plot is sometimes missing the CNV state colors legend. Is that expected or a bug?

For example, here is the plot from the mouse tutorial with a proper legend:

Compare that to the Interpreting Numbat results vignette where the legend only has two colors:

[teng-gao]

Upgrading from ggplot2 3.4.x -> 3.5.0 caused this .. I raised an issue on their github repo. hopefully they fix it soon.

[igordot]

Thanks for the update! I had some other packages break with ggplot2 3.5.0 as well.

[teunbrand]

Hi, I just stumbled across this by accident.
This is intended, and ggplot2 is not going to remedy this issue.
If you want to include all keys of a layer regardless of whether that value is present in the data, you should use show.legend = TRUE.
By default, only keys are shown for which values exist in the data.

[igordot]

Curiously, I've seen some packages add specific workarounds related to ggplot2 3.5, so it's definitely a widespread issue without a simple elegant fix. For example, hrbrthemes (with over 1k GitHub stars): https://github.com/hrbrmstr/hrbrthemes/blob/6417996c2931b3fa84102b5034a42a920c91fdb9/R/color.r#L20-L23

[teunbrand]

The code you linked to is to silence soft-deprecation warnings, which is unrelated to legend keys. The way to restore old behaviour is to use show.legend argument in layers, which is simple enough.

[trekonom]

As an illustration of the fix proposed by @teunbrand and as a possible workaround one can manually set show.legend=TRUE for the geom_point layer like so:

library(numbat)
#> Loading required package: Matrix
library(dplyr, warn=FALSE)
nb <- readRDS(url("http://pklab.med.harvard.edu/teng/data/nb_TNBC1.rds"))

p <- nb$bulk_clones %>%
  filter(n_cells > 50) %>%
  plot_bulks(
    min_LLR = 10, # filtering CNVs by evidence
    legend = TRUE
  )

for (i in seq_along(p)) {
  p[[i]]$layers[[2]]$show.legend <- TRUE
}

p

^{Created on 2024-09-08 with reprex v2.1.1}

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[teng-gao]

Thanks @teunbrand @trekonom for the solution. Fixed in v1.4.2