plotProportions: plotProportions

In lutsik/MeDeCom: Decomposition of heterogeneous methylomes

plotProportions

Description

A wrapper for various plotting methods for the visualization of mixing proportions

Usage

plotProportions(
  MeDeComSet,
  type,
  K,
  lambda,
  cg_subset = 1,
  lmc = NA,
  Aref = NULL,
  ref.profile = NA,
  sample.characteristic = NULL,
  heatmap.clusterCols = FALSE,
  heatmap.clusterRows = FALSE,
  ...
)

Arguments

MeDeComSet	an object with MeDeCom results
type	plot type, a character of length 1 (see Details)
K	value of parameter k to use
lambda	value of parameter lambda to use
cg_subset	which CpG subset to use
lmc	which LMC to use for visualization
Aref	a matrix with reference methylomes
...	Extra variables based to proportion.lineplot

Details

Available plot types include:

heatmap

Lineplot of proportions recovered by MeDeCom and reference proportions.

barplot

Stacked barplot of proportions recovered by MeDeCom.

lineplot

Lineplot of proportions recovered by MeDeCom and, if available, reference proportions.

scatterplot

Lineplot of proportions recovered by MeDeCom and reference proportions.

lutsik/MeDeCom documentation built on July 15, 2024, 4:51 a.m.