plot1D_2: ggplot2 based density figure that can show CNA-pseudo-SNVs...

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

ggplot2 based density figure that can show CNA-pseudo-SNVs separately. Currently this figure only can plot the CCF space.

Description

ggplot2 based density figure that can show CNA-pseudo-SNVs separately. Currently this figure only can plot the CCF space.

Usage

plot1D_2(density, polygon.data, mutationCopyNumber, no.chrs.bearing.mut,
  pngFile = NA, density.from = 0, x.max = NA, y.max = NA,
  y = NULL, N = NULL, samplename = "", CALR = numeric(0),
  cluster.locations = NULL, mutation.assignments = NULL,
  mutationTypes = rep("SNV", length(mutationCopyNumber)),
  font_sizes = list(plot.title = 50, axis.text = 25, axis.title = 35,
  legend.text = 25, legend.title = 25, legend.position = "bottom"),
  cbPalette = c("lightgray", "red", "blue"))

Arguments

density	Density as returned by Gibbs.subclone.density.est.1d.
polygon.data	Polygon data as returned by Gibbs.subclone.density.est.1d.
mutationCopyNumber	Mutation copy number matrix to be used to construct the CCF space.
no.chrs.bearing.mut	Multiplicity matrix to be used to construct the CCF space.
pngFile	Filename of the PNG file to be created. If NA is supplied the figure is returned (Default: NA).
density.from	Legacy parameter that is no longer used (Default: 0).
x.max	Max value on the x-axis to be plotted (Default: NA, then determined based on the data).
y.max	Max value on the y-axis to be plotted (Default: NA, then determined based on the data).
y	Legacy parameter that is used in the original figure to be able to plot different spaces. This value should be the number of supporting variant reads. It has no effect here. (Default: NULL).
N	Legacy parameter that is used in the original figure to be able to plot different spaces. This value should be the total number of reads. It has no effect here. (Default: NULL).
samplename	Name of the sample to be put on top of the figure.
CALR	Legacy parameter that is no longer used.
cluster.locations	Locations of where clusters were found. A vectical line is plotted for each cluster.
mutation.assignments	Vector with hard assignment of mutations to clusters - optional, is used for plotting (Default: NULL)
mutationTypes	Vector with mutation types. The background histogram can be coloured by mutation type (Default: SNV)
font_sizes	A list that defines the size of the fonts in the title, axis and legends (Default: Best settings for 1500x1000 plot).
cbPalette	Colours for mutation types: Grey for first mutation type (SNVs), orange for second (CNAs), as defined in LoadData

Author(s)

sd11

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