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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plot_contribution.R
\name{plot_contribution}
\alias{plot_contribution}
\title{Plot signature contribution barplot}
\usage{
plot_contribution(
contribution,
signatures = NA,
index = NA,
coord_flip = FALSE,
mode = c("relative", "absolute"),
palette = NA
)
}
\arguments{
\item{contribution}{Signature contribution matrix}
\item{signatures}{Signature matrix.
Necessary when plotting NMF results in "absolute" mode.
It's not necessary in relative mode or when visualizing signature refitting results}
\item{index}{optional sample subset parameter}
\item{coord_flip}{Flip X and Y coordinates, default = FALSE}
\item{mode}{"relative" or "absolute"; to plot the relative contribution or
absolute number of mutations, default = "relative"}
\item{palette}{A color palette like c("#FF0000", "#00FF00", "9999CC") that
will be used as colors in the plot. By default, ggplot2's colors are used
to generate a palette.}
}
\value{
Stacked barplot with contribution of each signature for each sample
}
\description{
Plot contribution of signatures. Can be used on both the results of a NMF
and on the results of signature refitting.
}
\examples{
## Extracting signatures can be computationally intensive, so
## we use pre-computed data generated with the following command:
# nmf_res <- extract_signatures(mut_mat, rank = 2)
nmf_res <- readRDS(system.file("states/nmf_res_data.rds",
package = "MutationalPatterns"
))
## Optionally set column and row names.
colnames(nmf_res$signatures) <- c("Signature A", "Signature B")
rownames(nmf_res$contribution) <- c("Signature A", "Signature B")
## Plot the relative contribution
plot_contribution(nmf_res$contribution)
## Plot the absolute contribution.
## When plotting absolute NMF results, the signatures need to be included.
plot_contribution(nmf_res$contribution,
nmf_res$signature,
mode = "absolute"
)
## Only plot a subset of samples
plot_contribution(nmf_res$contribution,
nmf_res$signature,
mode = "absolute",
index = c(1, 2)
)
## Flip the coordinates
plot_contribution(nmf_res$contribution,
nmf_res$signature,
mode = "absolute",
coord_flip = TRUE
)
## You can also use the results of signature refitting.
## Here we load some data as an example
fit_res <- readRDS(system.file("states/snv_refit.rds",
package = "MutationalPatterns"
))
plot_contribution(fit_res$contribution)
## Or again in absolute mode
plot_contribution(fit_res$contribution,
mode = "absolute"
)
}
\seealso{
\code{\link{extract_signatures}},
\code{\link{mut_matrix}}
}
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