run_comparison_helper: Runs main analysis for all parameter combos specified in...

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

Runs main analysis for all parameter combos specified in colAnns and creates plots.

Description

Runs main analysis for all parameter combos specified in colAnns and creates plots.

Usage

run_comparison_helper(
  ds,
  rowAnns = 1,
  colAnns = NA,
  out_dir = ".",
  feat_sets = NULL,
  var_colors = NULL,
  gradient_palette = NULL,
  corr_method = "pearson",
  pval.test = "t.test",
  pval.label = "p.signif",
  boxplot_log10_y = F,
  paired_analysis_column = NA,
  make.QC.param = F,
  make.QC.feature = F,
  make.feat.plots = F,
  make.het.plot = F,
  make.indiv.boxplot = F,
  make.overview.boxplot = F,
  make.heatmap = F,
  make.corrplot = F,
  make.overview.corrscatt = F,
  make.indiv.corrscatt = F,
  make.barplot = F,
  make.FC.pval.plot = F,
  save_table = 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.
feat_sets	A list of 2 data frames for feature sets and parameters.
var_colors	A named vector with colors as values and annotations/groups as names.
gradient_palette	RColorBrewer palette name for gradients (e.g. heatmap, correlation plots). See RColorBrewer::display.brewer.all() for all options.
corr_method	Method for correlation (one of "pearson","spearman","kendall").
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).
boxplot_log10_y	Log10 the values on y axis for boxplots and patient paired slopegraphs? Logical (T/F). Default is FALSE.
paired_analysis_column	column name in ds$rowAnn to create paired analysis plots for, e.g. PatientID if ds is data for all cores
make.QC.param, make.QC.feature, make.feat.plots, make.het.plot, make.indiv.boxplot, make.overview.boxplot, make.heatmap, make.corrplot, make.overview.corrscatt, make.indiv.corrscatt, make.barplot, make.FC.pval.plot	Logicals (TRUE/FALSE) indicating whether to make these plots. Note: make.indiv.corrscatt = T takes a long time.
save_table	Print MainComparison + ID data to csv file.

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