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morinlab / GAMBLR.viz

Collection of functions to make plots for Genomic Analysis of Mature B-cell Lymphomas in R
https://morinlab.github.io/GAMBLR.viz/
MIT License
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`fancy_propcov_plot` returns warning message #14

Closed vladimirsouza closed 7 months ago

vladimirsouza commented 8 months ago

The warning message:

The `fun.y` argument of `stat_summary()` is deprecated as of ggplot2 3.3.0.
ℹ Please use the `fun` argument instead.

The issue can be reproduced by running the examples:

#load packages
library(dplyr)

#get sample IDs for available genome samples
genome_collated = collate_results(seq_type_filter = "genome") %>% 
  pull(sample_id)

#subset the collated samples on BL samples
my_samples = get_gambl_metadata() %>% 
  dplyr::filter(sample_id %in% genome_collated) %>% 
  dplyr::filter(pathology == "BL") %>% pull(sample_id)

fancy_propcov_plot(these_sample_ids = my_samples)
vladimirsouza commented 8 months ago

I just changed the argument fun.y of stat_summary to fun and the issue was solved and the plot is apparently the same.