plotVafCluster: plotVafCluster

In qingjian1991/MPTevol: Clonal Evolutionary History and Metastatic Routines Analysis for Multiple Primary Tumors

plotVafCluster

Description

Plot variant clustering in each sample by using combination of box, violin and jitter plots.

Usage

plotVafCluster(
  variants,
  cluster.col.name = "cluster",
  vaf.col.names,
  clone.colors = NULL,
  violin = FALSE,
  box = TRUE,
  jitter = TRUE,
  founding.cluster = 1,
  output.file = NULL,
  highlight = NULL,
  highlight.note.col.name = NULL
)

Arguments

variants	data frame of the variants. At least cluster column and VAF or CCF columns are required. Cluster column should contain cluster identities as continuous integer values starting from 1.
cluster.col.name	the column names that containing cluster information (Default = "cluster").
vaf.col.names	the column names of samples containing VAF.
clone.colors	setting clone colors.
violin	whether plotting violin (Default = FALSE).
box	whether plotting box (Default = TRUE).
jitter	whether plotting jitter plot (Default = TRUE).
founding.cluster	the name of founding clones, one of the most important parameters. For most of circumstances, the founding cluster is the cluster with the highest average CCF cluster.
output.file	the output file name (Default = NULL)
highlight	column name to indicate whether highlight the sites (TRUE or FALSE).
highlight.note.col.name	highlight context.

Value

a ggplot object

qingjian1991/MPTevol documentation built on Jan. 30, 2023, 10:16 p.m.