deedee_upset: DeeDee UpSet Plot

In lea-rothoerl/DeeDee: Comparative Evaluation and Visualization of Differential Expression Analyses

Description

deedee_upset creates an UpSet plot depicting the overlaps of differentially expressed genes in the input datasets.

Usage

deedee_upset(data, mode = "both_colored", min_setsize = 10, pthresh = 0.05)

Arguments

data	named list of results from deedee_prepare()
mode	show all overlapping DE genes (both), all overlapping genes colored by DE direction (both_colored, default), only conjointly up-regulated (up) or only conjointly down-regulated (down) genes
min_setsize	the minimum size of intersections to be displayed in the UpSet plot (default = 10)
pthresh	threshold for p-values to be in-/excluded (default = 0.05)

Value

upset element (plottable with show()/print())

Examples

data(DE_results_IFNg_naive, package = "DeeDee")
IFNg_naive <- deedee_prepare(IFNg_naive, "DESeq2")

data(DE_results_IFNg_both, package = "DeeDee")
IFNg_both <- deedee_prepare(IFNg_both, "DESeq2")

data(DE_results_Salm_naive, package = "DeeDee")
Salm_naive <- deedee_prepare(Salm_naive, "DESeq2")

data(DE_results_Salm_both, package = "DeeDee")
Salm_both <- deedee_prepare(Salm_both, "DESeq2")

dd_list <- list(
  IFNg_naive = IFNg_naive, IFNg_both = IFNg_both,
  Salm_naive = Salm_naive, Salm_both = Salm_both
)

deedee_upset(dd_list, pthresh = 0.05, mode = "both_colored", min_setsize = 10)

lea-rothoerl/DeeDee documentation built on Dec. 21, 2021, 9:47 a.m.