Plots a Venn diagram showing overlapping significant proteins

Plots a Venn diagram showing overlapping significant proteins

Usage

plot_venn_diagram(
  res,
  ...,
  comparisons = "all",
  colors = c("#b3e2cd", "#fdcdac", "#cbd5e8", "#f4cae4", "#e6f5c9"),
  names = NULL
)

Arguments

res

A data frame with results from get_DEPresults()

...

Additional results data frames (optional)

comparisons

A character vector specifying which comparisons to include. The default 'all' considers all comparisons present in res.

colors

The colors used for the Venn diagram.

names

(optional). Specifies the labels for the different subsets. Defaults to the comparison names in colnames(res)

Value

A Venn diagram plot

Examples

se <- prepare_se(report.pg_matrix, expDesign)

#> Imputing along margin 1 (features/rows).
#> Warning: 36 rows with more than 50 % entries missing;
#>  mean imputation used for these rows
#> Cluster size 5548 broken into 2203 3345 
#> Cluster size 2203 broken into 1569 634 
#> Cluster size 1569 broken into 1504 65 
#> Cluster size 1504 broken into 645 859 
#> Done cluster 645 
#> Done cluster 859 
#> Done cluster 1504 
#> Done cluster 65 
#> Done cluster 1569 
#> Done cluster 634 
#> Done cluster 2203 
#> Cluster size 3345 broken into 2136 1209 
#> Cluster size 2136 broken into 1087 1049 
#> Done cluster 1087 
#> Done cluster 1049 
#> Done cluster 2136 
#> Done cluster 1209 
#> Done cluster 3345 
res <- get_DEPresults(se, type = 'all')
#> Tested contrasts: neg_ctrl_vs_motif1, neg_ctrl_vs_motif2, motif1_vs_motif2
plot_venn_diagram(res) # Default option
#> INFO [2025-07-10 12:58:40] [[1]]
#> INFO [2025-07-10 12:58:40] venn_list
#> INFO [2025-07-10 12:58:40] 
#> INFO [2025-07-10 12:58:40] $filename
#> INFO [2025-07-10 12:58:40] NULL
#> INFO [2025-07-10 12:58:40] 
#> INFO [2025-07-10 12:58:40] $disable.logging
#> INFO [2025-07-10 12:58:40] T
#> INFO [2025-07-10 12:58:40] 
#> INFO [2025-07-10 12:58:40] $fill
#> INFO [2025-07-10 12:58:40] colors
#> INFO [2025-07-10 12:58:40] 
#> INFO [2025-07-10 12:58:40] $fontfamily
#> INFO [2025-07-10 12:58:40] [1] "sans"
#> INFO [2025-07-10 12:58:40] 
#> INFO [2025-07-10 12:58:40] $fontface
#> INFO [2025-07-10 12:58:40] [1] "bold"
#> INFO [2025-07-10 12:58:40] 
#> INFO [2025-07-10 12:58:40] $cat.fontfamily
#> INFO [2025-07-10 12:58:40] [1] "sans"
#> INFO [2025-07-10 12:58:40] 
#> INFO [2025-07-10 12:58:40] $lty
#> INFO [2025-07-10 12:58:40] [1] 0
#> INFO [2025-07-10 12:58:40] 

plot_venn_diagram(res, colors = c('green', 'blue', 'red')) # Uses non-default
#> INFO [2025-07-10 12:58:40] [[1]]
#> INFO [2025-07-10 12:58:40] venn_list
#> INFO [2025-07-10 12:58:40] 
#> INFO [2025-07-10 12:58:40] $filename
#> INFO [2025-07-10 12:58:40] NULL
#> INFO [2025-07-10 12:58:40] 
#> INFO [2025-07-10 12:58:40] $disable.logging
#> INFO [2025-07-10 12:58:40] T
#> INFO [2025-07-10 12:58:40] 
#> INFO [2025-07-10 12:58:40] $fill
#> INFO [2025-07-10 12:58:40] colors
#> INFO [2025-07-10 12:58:40] 
#> INFO [2025-07-10 12:58:40] $fontfamily
#> INFO [2025-07-10 12:58:40] [1] "sans"
#> INFO [2025-07-10 12:58:40] 
#> INFO [2025-07-10 12:58:40] $fontface
#> INFO [2025-07-10 12:58:40] [1] "bold"
#> INFO [2025-07-10 12:58:40] 
#> INFO [2025-07-10 12:58:40] $cat.fontfamily
#> INFO [2025-07-10 12:58:40] [1] "sans"
#> INFO [2025-07-10 12:58:40] 
#> INFO [2025-07-10 12:58:40] $lty
#> INFO [2025-07-10 12:58:40] [1] 0
#> INFO [2025-07-10 12:58:40] 

# colors
plot_venn_diagram(res, comparisons = c('neg_ctrl_vs_motif1',
                                       'neg_ctrl_vs_motif2')) # Only
#> INFO [2025-07-10 12:58:40] [[1]]
#> INFO [2025-07-10 12:58:40] venn_list
#> INFO [2025-07-10 12:58:40] 
#> INFO [2025-07-10 12:58:40] $filename
#> INFO [2025-07-10 12:58:40] NULL
#> INFO [2025-07-10 12:58:40] 
#> INFO [2025-07-10 12:58:40] $disable.logging
#> INFO [2025-07-10 12:58:40] T
#> INFO [2025-07-10 12:58:40] 
#> INFO [2025-07-10 12:58:40] $fill
#> INFO [2025-07-10 12:58:40] colors
#> INFO [2025-07-10 12:58:40] 
#> INFO [2025-07-10 12:58:40] $fontfamily
#> INFO [2025-07-10 12:58:40] [1] "sans"
#> INFO [2025-07-10 12:58:40] 
#> INFO [2025-07-10 12:58:40] $fontface
#> INFO [2025-07-10 12:58:40] [1] "bold"
#> INFO [2025-07-10 12:58:40] 
#> INFO [2025-07-10 12:58:40] $cat.fontfamily
#> INFO [2025-07-10 12:58:40] [1] "sans"
#> INFO [2025-07-10 12:58:40] 
#> INFO [2025-07-10 12:58:40] $lty
#> INFO [2025-07-10 12:58:40] [1] 0
#> INFO [2025-07-10 12:58:40] 

                                       # includes two comparisons