plot1D: Original plotting function: Creates the 1D density plot in...

In Wedge-Oxford/dpclust: DPClust - An R package for subclonal reconstruction of tumours using sequencing data

Original plotting function: Creates the 1D density plot in either allele fraction, mutation copy number or fraction of tumour cells space.

Description

Original plotting function: Creates the 1D density plot in either allele fraction, mutation copy number or fraction of tumour cells space.

Usage

plot1D(density, polygon.data, pngFile = NA, density.from = 0,
  x.max = NA, y.max = NA, y = NULL, N = NULL,
  mutationCopyNumber = NULL, no.chrs.bearing.mut = NULL,
  samplename = "", CALR = numeric(0), cluster.locations = NULL,
  mutation.assignments = NULL, mutationTypes = NULL)

Arguments

density	Is a two column data frame. First column x-axis density line, second column y-axis density line.
polygon.data	Contains the coordinates of the 95% confidence interval around the density line.
pngFile	Where to save the figure (Default: NA)
density.from	Startpoint from where density is drawn (Default: 0)
x.max	Maximum values on x axis in the plot (Default: NA, determine from data)
y.max	Maximum values on y axis in the plot (Default: NA, determine from data)
y	MutCount data, only used when mutationCopyNumber is not supplied (Default: NULL)
N	Total count (mutCount+WTCount), only used when mutationCopyNumber is not supplied (Default: NULL)
mutationCopyNumber	Mutation copy number data, when not supplied y and N are required (Default: NULL)
no.chrs.bearing.mut	Copynumber (multiplicity) adjustment per mutation, when not supplied the plot will either contain mutation copy number or allele frequencies (Default: NULL)
samplename	Name of the sample under analysis (Default: empty string)
cluster.locations	Locations in the space to be plotted where clusters reside (Default: NULL)
mutation.assignments	Mutation assignments (Default: NULL)
mutationTypes	Type of each mutation, different mutation types can be plot with different colours (Default: NULL)
CARL	Legacy annotation parameter, no longer used (Default: empty numeric)

Author(s)

dw9, sd11

Wedge-Oxford/dpclust documentation built on July 6, 2024, 2:02 p.m.