PrepPeakModuleHeatmap: Function for prep data to plot peak module heatmap using...

PrepPeakModuleHeatmapR Documentation

Function for prep data to plot peak module heatmap using Complex Heatmap

Description

Function for prep data to plot peak module heatmap using Complex Heatmap

Usage

PrepPeakModuleHeatmap(
  peak_normalised_matrix,
  cell_metadata,
  col_order,
  custom_order_column = NULL,
  custom_order = NULL,
  hclust_SEACells = FALSE,
  hclust_SEACells_within_groups = TRUE,
  peak_modules,
  peak_row_annotation = TRUE,
  scale_data = TRUE,
  log_path = NULL
)

Arguments

peak_normalised_matrix

matrix of peak normalised data, rows are peaks and columns are cells

cell_metadata

data frame of cell metadata, rows are cells and columns are metadata

col_order

vector of column names to order cells by

custom_order_column

column name to order cells by custom ordering

custom_order

vector of cell names to order cells by custom ordering

hclust_SEACells

logical, whether to hclust SEACells

hclust_SEACells_within_groups

logical, whether to hclust SEACells within SEACell groups

peak_modules

list of peak modules, each element is a vector of peak IDs

peak_row_annotation

logical, whether to add peak row annotation

scale_data

logical, whether to scale data

log_path

path to save logs (hclust dendograms), if NULL no logs will be saved

Value

plot_data list containing plot data, column annotation and row annotation


alexthiery/scHelper documentation built on Aug. 26, 2023, 3:42 p.m.