romicsVolcano: romicsVolcano()

In PNNL-Comp-Mass-Spec/RomicsProcessor: omics-oriented package for reproducible and sharable data processing pipelines

romicsVolcano()

Description

generate one or multiple volcano plots from t.test or wilcox.test run using the functions romicsTtest() or romicsWilcoxTest() respectively

Usage

romicsVolcano(
  romics_object,
  p_type = "p",
  p = 0.05,
  min_fold_change = 0.6,
  colors = c("#2cbcb2", "#242021", "#d44e28"),
  stat_type = "t.test",
  plot = "all",
  plot_type = "ggplot"
)

Arguments

p_type	'p' or 'padj' to indicate the type of tpvalue to consider for the volcano plots.
p	numeric value to indicate the maximum pvalue to use for the coloring of the volcano plot
colors	numeric vector of lenght 3 used to color the features lower, not significantly changing and higher in the considered comparisons.
stat_type	't.test' or 'wilcox.test' to indicate what statistics to use for the volcano plots generation.
plot	either 'all' if all paired comparisons have to be displayed OR a vector of numeric values comprised between 1 and the maximum number of possible plots generated.
plot_type	'plotly' or 'ggplot' to indicate the type of plot to be returned.

Details

generate one or multiple volcano plots from t.test or wilcox.test run using the functions romicsTtest() or romicsWilcoxTest() respectively

Value

This function will print different plot requested

Author(s)

Geremy Clair

PNNL-Comp-Mass-Spec/RomicsProcessor documentation built on March 18, 2023, 5:14 a.m.