Plots upset plot showsing overlapping significant proteins between comparisons
Source:R/plots.R
plot_upset.Rd
Plots upset plot showsing overlapping significant proteins between comparisons
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.
- names
(optional). Specifies the labels for the different subsets. Defaults to the comparison names in colnames(res)
Details
The layout of the resulting upset plot can be easily edited to your liking. Check the vignette of ggupset to see how individual components can be altered.
Examples
se <- prepare_se(report.pg_matrix, expDesign)
#> Imputing along margin 2 (samples/columns).
#> [1] 0.3066195
#> Imputing along margin 1 (features/rows).
#> Warning: 36 rows with more than 50 % entries missing;
#> mean imputation used for these rows
#> Cluster size 5574 broken into 3662 1912
#> Cluster size 3662 broken into 1462 2200
#> Done cluster 1462
#> Cluster size 2200 broken into 1110 1090
#> Done cluster 1110
#> Done cluster 1090
#> Done cluster 2200
#> Done cluster 3662
#> Cluster size 1912 broken into 1379 533
#> Done cluster 1379
#> Done cluster 533
#> Done cluster 1912
res <- get_DEPresults(se, type = 'all')
#> Tested contrasts: neg_ctrl_vs_motif1, neg_ctrl_vs_motif2, motif1_vs_motif2
vd <- plot_upset(res)