plot_mapper: Plots features on nerve complexes and embeddings

In CamaraLab/TDA-TCGA: An R package for identification of relevant genetic alterations in cancer using topological data analysis

Description

Plots features on nerve complexes and embeddings

Usage

plot_mapper(
  TDAmut_object,
  type = "none",
  features = NULL,
  which_complexes = NULL,
  colorbar_low = "blue",
  colorbar_high = "red",
  seed = 121
)

Arguments

TDAmut_object	object of class TDAmut with expression data, mutation data, nerve complexes, mutational load, and mutational load localization data.
type	type of data for given features. Can take values 'mutation', 'mutational_load', 'expression', or 'none' to plot complexes with no label. By default is 'none'
features	genes of interest in character vector. Only applies if 'mutation' or 'expression' data is selected. By default is NULL
which_complexes	vector of interval and percent combinations specificying which nerve complexes to plot, such as c(int1, percent1, int2, percent2 ...). Can plot all complexes by setting to 'All'. By default is NULL which chooses 3 complexes in the middle of the parameter ranges.
colorbar_low	color of colorbar for lower-range values. By default is 'blue'
colorbar_high	color of colorbar for upper-range values. By default is 'red'
seed	seed value when plotting nerve complex. By default is 121.

Value

Returns plot of nerve complex or embedding with desired features

CamaraLab/TDA-TCGA documentation built on Oct. 30, 2021, 5:14 p.m.