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#' Plot the bootstrapped signature contributions
#'
#' Plot the signature contributions retrieved with 'fit_to_signatures_bootstrapped'.
#' The function can plot both the absolute or the relative signature contribution.
#' The graph can be plotted as either a jitter plot or as a barplot.
#'
#' @param contri_boots matrix showing signature contributions across bootstrap iterations.
#' @param mode Either "absolute" for absolute number of mutations, or
#' "relative" for relative contribution, default = "absolute"
#' @param plot_type Either "jitter" for a jitter plot, "barplot" for a barplot, or "dotplot" for a dotplot
#'
#' @return A ggplot2 graph
#' @export
#' @importFrom magrittr %>%
#' @import ggplot2
#' @examples
#' ## Get the bootstrapped signature contributions
#' ## See 'count_indel_contexts()' for more info on how to do this.
#' contri_boots <- readRDS(system.file("states/bootstrapped_snv_refit.rds",
#' package = "MutationalPatterns"
#' ))
#'
#' ## Plot bootstrapped contribution
#' plot_bootstrapped_contribution(contri_boots)
#'
#' ## Plot bootstrapped contribution with relative contributions
#' plot_bootstrapped_contribution(contri_boots, mode = "relative")
#'
#' ## Plot bootstrapped contribution with a barplot
#' plot_bootstrapped_contribution(contri_boots, plot_type = "barplot")
#'
#' ## Plot bootstrapped contribution with a dotplot
#' plot_bootstrapped_contribution(contri_boots, plot_type = "dotplot", mode = "absolute")
plot_bootstrapped_contribution <- function(contri_boots,
mode = c("absolute", "relative"),
plot_type = c("jitter", "barplot", "dotplot")) {
# Match arguments
mode <- match.arg(mode)
plot_type <- match.arg(plot_type)
# These variables use non standard evaluation.
# To avoid R CMD check complaints we initialize them to NULL.
sig <- contri <- lower <- upper <- percentage <- NULL
# Change variables based on relative or absolute mode.
if (mode == "relative") {
contri_boots <- contri_boots / rowSums(contri_boots)
ylab_text <- "Relative mutation contribution"
jitter_height <- 0.02
} else {
ylab_text <- "Nr. contributed mutations"
jitter_height <- 0.2
}
# Convert contri_boots into a long format.
contri_tb <- contri_boots %>%
as.data.frame() %>%
tibble::rownames_to_column("exp") %>%
tidyr::gather(key = "sig", value = "contri", -exp) %>%
dplyr::mutate(
sample = gsub("_[^_]+$", "", exp),
sample = factor(sample, levels = unique(sample)),
sig = factor(sig, levels = unique(sig))
)
# Determine number of signatures
nr_sigs <- length(unique(contri_tb$sig))
if (plot_type == "jitter") {
# Create basis for jitter figure
fig <- ggplot(contri_tb, aes(x = sig, y = contri, color = sig)) +
geom_jitter(stat = "identity", height = jitter_height, size = 0.3) +
scale_color_discrete(guide = "none") +
facet_grid(sample ~ .) +
labs(y = ylab_text)
} else if (plot_type == "barplot") {
# Calculate values for barplot
contri_tb2 <- contri_tb %>%
dplyr::group_by(sample, sig) %>%
dplyr::summarise(
mean = mean(contri),
lower = quantile(contri, 0.025),
upper = quantile(contri, 0.975)
) %>%
dplyr::ungroup()
# Create basis for barplot figure
fig <- ggplot(contri_tb2, aes(x = sig, y = mean, fill = sig)) +
geom_bar(stat = "identity") +
geom_errorbar(aes(ymin = lower, ymax = upper), width = 0.2) +
scale_fill_discrete(guide = "none") +
facet_grid(sample ~ .) +
labs(y = ylab_text)
} else if (plot_type == "dotplot") {
contri_tb3 <- contri_tb %>%
dplyr::group_by(sample, sig) %>%
dplyr::summarise(
mean = mean(contri[contri != 0]),
percentage = sum(contri != 0)/dplyr::n()
) %>%
dplyr::ungroup() %>%
dplyr::filter(!is.na(mean)) %>%
dplyr::mutate(sample = factor(sample, levels = rev(levels(sample))))
max_dot_size <- dplyr::case_when(
nr_sigs >= 40 ~ 5,
nr_sigs >= 30 ~ 7,
nr_sigs >= 20 ~ 8,
nr_sigs >= 10 ~ 10,
TRUE ~ 15
)
fig <- ggplot(contri_tb3, aes(x = sig, y = sample)) +
geom_point(aes(color = percentage, size = mean)) +
scale_color_distiller(palette = "RdYlBu", limits = c(0, 1)) +
scale_size_continuous(range = c(1,max_dot_size)) +
labs(size = "mean contribution",
colour = "percentage contribution",
y = "Sample")
}
## Add extra labels to figure for all types
fig <- fig +
labs(x = "Signature") +
theme_classic() +
theme(
axis.text.x = element_text(angle = 90, size = 10, hjust = 1, vjust = 0.5),
text = element_text(size = 12),
strip.text.y = element_text(size = 8)
)
if (plot_type == 'dotplot') {
fig <- fig +
theme(panel.grid.major = element_line(colour = "gray92"))
}
return(fig)
}
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