plot_dim_red: Plot dimensionality reduction

In CompEpigen/scMethrix: Fast and efficient summarization of single cell whole genome bisulfate data

Description

Plot dimensionality reduction

Usage

plot_dim_red(
  scm,
  dim_red,
  color_anno = NULL,
  shape_anno = NULL,
  axis_labels = NULL,
  show_dp_labels = FALSE,
  verbose = TRUE
)

Arguments

scm	scMethrix; the single cell methylation experiment
dim_red	string; name of adimensionality reduction from an scMethrix object. Should be a matrix of two columns representing the X and Y coordinates of the dim. red., with each row being a seperate sample
color_anno	string; Column name of colData(m). Default NULL. Will be used as a factor to color different groups. Required methrix object
shape_anno	string; Column name of colData(m). Default NULL. Will be used as a factor to shape different groups. Required methrix object
axis_labels	list of strings; A list of 'X' and 'Y' strings for labels, or NULL if no labels are desired
show_dp_labels	boolean; Flag to show the labels for dots. Default FALSE
verbose	boolean; Flag for outputting function status messages. Default = TRUE

Value

ggplot2 object

CompEpigen/scMethrix documentation built on Nov. 6, 2021, 3:09 p.m.