plotExchangeSpectra_indel: Plot the spectra of nucleotide exchanges of INDELs

In YAPSA: Yet Another Package for Signature Analysis

Description

Plots the spectra of nucelotides in their triplet contexts. If several columns are present in the input data frame, the spectra are ploted for every column seperatly. The function is only suitable for a INDEL spectra and for SNV representation the funtion plotExchangeSpectra should be used.

Usage

plotExchangeSpectra_indel(
  in_catalogue_df,
  in_colour_vector = NULL,
  in_show_indel = FALSE,
  in_show_axis_title = FALSE,
  in_scales = "free_x",
  in_refLine = NULL,
  in_refAlpha = 0.5,
  in_background = NULL
)

Arguments

in_catalogue_df	Numerical data frame encoding the exchange spectra to be displayed, either a mutational catalogue V or a signatures matrix W
in_colour_vector	Specifies the colours of the INDELs if non-null
in_show_indel	Whether or not to show the INDEL names on the x-axis
in_show_axis_title	Whether or not to show the name of the y-axis
in_scales	Argument passed on to facet_grid
in_refLine	If non-null, value on the y-axis at which a horizontal line is to be drawn
in_refAlpha	Transparency of the horizontal line if it is to be drawn
in_background	Option to provide a background theme, e.g. theme_grey

Value

The generated barplot - a ggplot2 plot

Examples

data(sigs_pcawg)
plotExchangeSpectra_indel(PCAWG_SP_ID_sigs_df[,c(6,8)])

YAPSA documentation built on Nov. 8, 2020, 4:59 p.m.