Prepare data for plot_DEP_barplot function.

Usage

prepare_barplot_data(res, comparisons = "all", names = NULL)

Arguments

res: A data frame with results from get_DEPresults()
comparisons: A character vector specifying which comparisons to include. The default 'all' considers all comparisons present in res. The bars are plotted in the order of specified comparisons.
names: (optional). Specifies the labels for the different bars. Defaults to the comparison names in colnames(res)

Value

A data frame with the number of significant proteins per condition.

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
data <- prepare_barplot_data(res) # All conditions
data <- prepare_barplot_data(res, comparisons = c('neg_ctrl_vs_motif1',
                                                  'neg_ctrl_vs_motif2')) #
# Only two comparisons included.