run_hourglass: Run Hourglass.

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

Run Hourglass.

Description

Run Hourglass according to user specifications. See documentation for format of input parameters.

Usage

run_Hourglass(
  comparisons,
  var_colors,
  feat_sets,
  main_folder = ".",
  datasets = NULL,
  keep_column_colAnn = "Keep.In.Analysis"
)

Arguments

comparisons	A data frame containing comparisons to run compatible with run_hourglass function (i.e. column names are options, rows are each comparison to run). See ?get_comparisons for more info.
var_colors	List of colors, where elements are hex codes and element names are rowAnn variables. e.g. list("Tumour"="#2f4f4Fff", "Stroma"="#d2691eff") See ?get_colors for more info.
feat_sets	A list of 2 data frames for plotting specific rows and columns. See ?get_feat_sets for more info.
main_folder	The output directory for Hourglass analysis, default is working directory.
datasets	Optional. List of 2 elements 1) sample, 2) patient, which are the dataset objects for BySample and ByPatient analysis respectively.
keep_column_colAnn	Optional. Column name in colAnn of which columns to keep in vals, important for QC plots

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