deedee_qq: DeeDee QQ Plot

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

Description

deedee_qq creates a Q-Q-plot comparing the statistical distribution of the logFC of the genes in two input datasets. To compare more than two contrasts against a reference, have a look at deedee_qqmult.

Usage

deedee_qq(
  data,
  select1 = 1,
  select2 = 2,
  color_by = "pval1",
  as_line = FALSE,
  pthresh = 0.05
)

Arguments

data	named list of results from deedee_prepare()
select1	index of first data-list element to be used (default = 1)
select2	index of second data-list element to be used (default = 2)
color_by	indicates which set of values the output should be colored by (possible values = pval1 (default), pval2)
as_line	logical value specifying if the resulting plot should be a line (TRUE) or points (FALSE, default)
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_qq(dd_list, pthresh = 0.05, select = 1, select2 = 2, color_by = "pval1")

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