Plot a venn diagram for diff ASE (using event names or gene names) between multiple comparison.

Usage

plot_deASE_venn(
  x,
  sample_comparisons,
  regulation = "both",
  fill_color = NULL,
  event_type = NULL,
  ovelap_genes = TRUE,
  ...
)

Arguments

x: an abject of class "parcutils_ase". This is an output of the function run_ase_diff_analysis().
sample_comparisons: a character vector denoting sample comparisons for which ASE to be obtained.
regulation: a character string, default both. Values can be one of the up, down, both, other, all.
fill_color: an argument pass to the function ggvenn::ggvenn.
event_type: a character string denoting event type for which one of the up, down, both, other or all events to be returned based. Choices are: IR, SE, AFE, ALE, A3SS, A5SS and MXE. Default NULL, uses all event types.
ovelap_genes: logical, default TRUE, instead of event_names, overlap gene names.
...: other arguments pass to the function ggvenn::ggvenn

Value

a venn diagram

Examples


se <- SpliceWiz::SpliceWiz_example_NxtSE(novelSplicing = TRUE)
SpliceWiz::colData(se)$treatment <- rep(c("A", "B"), each = 3)
SpliceWiz::colData(se)$replicate <- rep(c("P","Q","R"), 2)
res <- run_ase_diff_analysis(x = se, test_factor = "replicate", test_nom = c("P","Q","R") ,test_denom = c("Q","R","P"),  IRmode ="annotated",  cutoff_lfc = 0.6, cutoff_pval = 1, regul_based_upon = 1)
#> Aug 16 11:35:36 Performing edgeR contrast for included / excluded counts separately
#> Aug 16 11:35:37 Performing edgeR contrast for included / excluded counts together
#> Aug 16 11:35:42 Performing edgeR contrast for included / excluded counts separately
#> Aug 16 11:35:43 Performing edgeR contrast for included / excluded counts together
#> Aug 16 11:35:47 Performing edgeR contrast for included / excluded counts separately
#> Aug 16 11:35:48 Performing edgeR contrast for included / excluded counts together
plot_deASE_venn(x = res, sample_comparisons = c("P_VS_Q","Q_VS_R","R_VS_P"),  event_type = "SE", regulation = "both", ovelap_genes = TRUE)
#> ! Maximum 4 sets can be included in the venn diagram. These sets won't be included: R_VS_P_down and R_VS_P_up

plot_deASE_venn(x = res, sample_comparisons = c("P_VS_Q","Q_VS_R","R_VS_P"),  event_type = "SE", regulation = "up", ovelap_genes = TRUE)

plot_deASE_venn(x = res, sample_comparisons = c("P_VS_Q","Q_VS_R","R_VS_P"),  event_type = "A3SS", regulation = "both", ovelap_genes = TRUE)
#> ! Maximum 4 sets can be included in the venn diagram. These sets won't be included: R_VS_P_down and R_VS_P_up