create_plots_helper: Create plots helper

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

Create plots helper

Description

Create plots helper

Usage

create_plots_helper(
  ds,
  rowAnns = 1,
  colAnns = NA,
  out_dir = ".",
  labels = "",
  var_colors = NA,
  clust_row = F,
  clust_col = F,
  gradient_palette = "RdBu",
  corr_method = "pearson",
  pval.test = "t.test",
  pval.label = "p.signif",
  boxplot_log10_y = 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
)

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)
var_colors	A named character vector of colors (R or hex), where the names are the groups in row annotations and column annotations
clust_row, clust_col	Logicals indicating whether to cluster rows and columns in heatmap.
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.

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