PlotSamplesHighSigExp: Plot hdp signature exposure in each sample. This function...

In steverozen/mSigHdp: Mutational signature discovery using HDP (hierarchical Dirichlet process)

Plot hdp signature exposure in each sample. This function returns the plot of top 5 samples with the highest exposure to a signature. Each spectrum's title is in the form of: Sample Name (Proportion of Signature Assignment). This function is here because it is specific for the signature extraction application.

Description

Plot hdp signature exposure in each sample. This function returns the plot of top 5 samples with the highest exposure to a signature. Each spectrum's title is in the form of: Sample Name (Proportion of Signature Assignment). This function is here because it is specific for the signature extraction application.

Usage

PlotSamplesHighSigExp(
  retval,
  hdpsample,
  input.catalog,
  col_comp = NULL,
  incl_numdata_plot = F,
  ylab_numdata = "Number of data items",
  ylab_exp = "Component exposure",
  leg.title = "Component",
  cex.names = 0.6,
  cex.axis = 0.7,
  mar = c(4, 4, 2, 0.5),
  oma = c(1.5, 1.5, 1, 1)
)

Arguments

retval	An object return from extract_ccc_from_hdp in package hdpx.
hdpsample	A hdpSampleChain-class or hdpSampleMulti-class object including output from extract_components in package hdpx.
input.catalog	Input spectra catalog as a matrix or in ICAMS format.
col_comp	Colors of each component, from 0 to the max number. If NULL, default colors will be used.
incl_numdata_plot	Logical - should an upper barplot indicating the number of data items per DP be included? (Default TRUE).
ylab_numdata	Vertical axis label for numdata plot.
ylab_exp	Vertical axis label for exposure plot.
leg.title	Legend title.
cex.names	Expansion factor for bar labels (dpnames) in exposure plot.
cex.axis	Expansion factor for vertical-axis annotation.
mar	See ?par
oma	See ?par

steverozen/mSigHdp documentation built on Feb. 6, 2023, 1:36 a.m.