deedee_cat: DeeDee Concordance At the Top Plot

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

Description

deedee_cat creates a Concordance at the Top plot depicting the concordance of genes in the first n elements of the logFC-ranked lists for the given (non-reference) input contrasts against a chosen reference contrast from the input list.

Usage

deedee_cat(data, ref = 1, maxrank = 1000, mode = "up", pthresh = 0.05)

Arguments

data	named list of results from deedee_prepare()
ref	index of the contrast in data to be used as reference contrast (default = 1)
maxrank	highest rank that should be displayed (default = 1000)
mode	sort by highest logFC (up, default), lowest logFC (down) or greatest deviation from zero (both)
pthresh	threshold for p-values to be in-/excluded (default = 0.05)

Value

ggplot object (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_cat(dd_list, ref = 1, maxrank = 1000, mode = "up", pthresh = 0.05)

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