plotLMCs: plotLMCs
In lutsik/MeDeCom: Decomposition of heterogeneous methylomes

plotLMCs

R Documentation

plotLMCs

Description

A wrapper for various plotting methods for the visualization of LMCs

Usage

plotLMCs(MeDeComSet, type, K = NA, lambda = NA, cg_subset = 1,
  lmc = NA, Tref = NULL, distance = "correlation", center = FALSE,
  n.most.var = NA, D = NULL, sample.characteristic = NULL,
  scatter.matching = FALSE, scatter.smooth = TRUE,
  scatter.cg.feature = NULL, min.similarity = 0)

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
`Tref`	a matrix with reference methylomes
`distance`	distance measure to use
`center`	if `TRUE` the LMC and reference methylome matrices will be row-centered
`n.most.var`	is not `NA` a respective number of CpGs with the highest standard deviation will be plotted
`D`	input data matrix used to derive the LMCs
`min.similarity`	minimal similarity between LMCs and (if available) reference profiles, used to select edges in `"similarity graph"`. Has only an influence if `type`=`"similarity graph"`.

Details

Available plot types include:

boxplot: Boxplot describing the distributions of each of the LMCs and, if available, the reference methylomss.
dendrogram: Dendrogram visualizing a joint hierarchical clustering of LMCs and, if available, the reference methylomes.
heatmap: Heatmap visualizing a distance between LMCs and the reference methylomes.
mds: Joint multidimensional scaling of LMCs and the reference methylomes.
scatterplot: Multi-panel scatterplot of LMCs and reference methylomes.
extremality: Barplot visualizing the value of the regularizer term for each LMC.
distance to center: Barplot visualizing a distance to the data center for each LMC. Input data matrix used to derive the LMCs should be supplied as argument D.