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#' Plot signature contribution barplot
#'
#' Plot contribution of signatures. Can be used on both the results of a NMF
#' and on the results of signature refitting.
#'
#' @param contribution Signature contribution matrix
#' @param signatures Signature matrix.
#' Necessary when plotting NMF results in "absolute" mode.
#' It's not necessary in relative mode or when visualizing signature refitting results
#' @param index optional sample subset parameter
#' @param coord_flip Flip X and Y coordinates, default = FALSE
#' @param mode "relative" or "absolute"; to plot the relative contribution or
#' absolute number of mutations, default = "relative"
#' @param 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.
#'
#' @return Stacked barplot with contribution of each signature for each sample
#'
#' @import ggplot2
#' @importFrom magrittr %>%
#'
#' @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}}
#'
#' @export
plot_contribution <- function(contribution,
signatures = NA,
index = NA,
coord_flip = FALSE,
mode = c("relative", "absolute"),
palette = NA) {
# Match argument
mode <- match.arg(mode)
# optional subsetting if index parameter is provided
if (!.is_na(index)) {
contribution <- contribution[, index, drop = FALSE]
}
# These variables use non standard evaluation.
# To avoid R CMD check complaints we initialize them to NULL.
Sample <- Contribution <- Signature <- NULL
# When working on NMF results, the contribution needs to be multiplied by the signature colSums.
if (mode == "absolute" & !.is_na(signatures)) {
# calculate signature contribution in absolute number of signatures
total_signatures <- colSums(signatures)
abs_contribution <- contribution * total_signatures
}
# Make data long. Also create factors for ordering.
tb <- contribution %>%
as.data.frame() %>%
tibble::rownames_to_column("Signature") %>%
tidyr::pivot_longer(-Signature, names_to = "Sample", values_to = "Contribution") %>%
dplyr::mutate(
Sample = factor(Sample, levels = unique(Sample)),
Signature = factor(Signature, levels = unique(Signature))
)
# Different plotting between absolute and relative
if (mode == "absolute") {
bar_geom <- geom_bar(stat = "identity", colour = "black")
y_lab <- "Absolute contribution \n (no. mutations)"
} else if (mode == "relative") {
bar_geom <- geom_bar(position = "fill", stat = "identity", colour = "black")
y_lab <- "Relative contribution"
}
# Determine what signatures are present for the legend.
present_sigs <- tb %>%
dplyr::filter(Contribution != 0) %>%
dplyr::pull(Signature) %>%
unique()
#Create plot
plot <- ggplot(tb, aes(x = Sample, y = Contribution, fill = Signature)) +
bar_geom +
labs(x = "", y = y_lab) +
scale_fill_discrete(breaks = present_sigs) +
theme_bw() +
theme(
panel.grid.minor.x = element_blank(),
panel.grid.major.x = element_blank(),
panel.grid.minor.y = element_blank(),
panel.grid.major.y = element_blank()
)
# Allow custom color palettes.
if (!.is_na(palette)) {
plot <- plot + scale_fill_manual(name = "Signature", values = palette)
}
# Handle coord_flip.
if (coord_flip) {
plot <- plot + coord_flip() + xlim(rev(levels(factor(tb$Sample))))
} else {
plot <- plot + xlim(levels(factor(tb$Sample)))
}
return(plot)
}
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