run_paired_analysis: Makes plots to look at subgroup differences within the same...

In kazeera/hourglass: This Package Provides Visualizations of Annotated Numeric Data

Makes plots to look at subgroup differences within the same patient

Description

Makes plots to look at subgroup differences within the same patient

Usage

run_paired_analysis(
  ds,
  rowAnns,
  colAnns = NA,
  out_dir = ".",
  var_colors = NULL,
  pair_id = 1,
  pval.test = "t.test",
  pval.label = "p.signif",
  log10_y = F
)

Arguments

ds	A dataset object (a list with vals, rowAnn, colAnn, comparison, name).
rowAnns	A character vector of 1-2 column names in ds$rowAnn. c(MainComparison, Subgroup)
colAnns	A character vector of 1-2 column names in ds$colAnn. c(Parameter, Feature/Stain/Gene)
out_dir	The output directory where the plot will be saved, default is current working directory.
var_colors	A named vector with colors as values and annotations/groups as names.
pair_id	Name or index of column in ds$rowAnn that count as patients or groups to pair by, i.e. which ID to average over, e.g. patient ID (if there are multiple rows per patient)
pval.test	Which two-samples testing should be used? String corresponding to "method" parameter in stat_compare_means. Allowed values are "t.test" and "wilcox.test".
pval.label	How to display p-values? String corresponding to "label" parameter in stat_compare_means. Allowed values are "p.signif" (stars) and "p.format" (number).

kazeera/hourglass documentation built on April 5, 2025, 7:18 a.m.