deedee_qqmult: DeeDee QQ Plot with Multiple Contrasts

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

Description

deedee_qqmult creates a plot containing Q-Q-lines comparing the statistical distribution of the logFC of the genes in each input datasets to a contrast chosen from the input data. For a Q-Q plot comparing two contrasts in a p-value-colored manner, have a look at deedee_qq.

Usage

deedee_qqmult(data, ref = 1, 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)
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_qqmult(dd_list, pthresh = 0.05, ref = 1)

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