#' Plot PSI values of a given alternative splicing event
#'
#' Generate a plot of PSI values for a given exon. The PSI values and
#' corresponding quality scores are typically obtained from the
#' \href{https://www.github.com/vastgroup/vast-tools}{vast-tools}
#' pipeline.
#'
#' @details
#' Plots can be customized via the \code{config} option. Either a data frame or
#' the filepath to the config file can be used. Alternatively, plots can be
#' customized using a limited set of graphical parameters as described above.
#'
#' The order of samples (e.g. columns in \code{x}) as it appears on the
#' resulting plot can be customized using a config file. If a config file is not
#' used and re-ordering is desired, then it must be done manually before calling
#' \code{\link{plot_event}} by altering the columns of \code{x}.
#'
#' If subgroups are defined in \code{config} and \code{subg=TRUE}:
#' \itemize{
#' \item{The mean PSI of the samples within each subgroup are drawn as a single
#' data point.}
#' \item{If \code{subg=TRUE} and \code{errorbar=TRUE}, confidence intervals for
#' the subgroup are derived from a joint beta distribution, fitted to a set of
#' points derived from individual beta distributions corresponding to each
#' sample (see \code{\link{get_beta_ci_subg}}). This is an experimental feature,
#' computationally expensive, and CIs may not be shown for some subgroups,due
#' to failure in fitting the joint distribution, especially for events with low
#' coverage and PSI values near 0 or 1.}
#' \item{Subgroups will be ordered by the minimum \emph{Order} value of their
#' samples, and assigned to the first group to which they are matched.}
#' \item{(Experimental) Instead of computing the average PSI, the individual
#' PSI values can be plotted for each subgroup by setting \code{subg.show}. The
#' default is "mean", which plots the average PSI. The other two options are
#' "all" or "beeswarm". For "all", the individual PSI values and error bars
#' are plotted for each subgroup and sorted in increasing order. For
#' "beeswarm", the optional
#' \href{https://github.com/eclarke/ggbeeswarm}{ggbeeswarm} package is used to
#' create beeswarm scatterplots for each subgroup (error bars are not possible).
#' As this is an optional feature, please manually install the package first
#' before using it: \code{install.packages("ggbeeswarm")}.}
#' }
#'
#' If no subgroups are defined in \code{config}, or \code{subg=FALSE} (default),
#' a subgroup will be defined for each sample, preserving their name and order.
#'
#' If groups and colors are defined in \code{config}, all the samples in a group
#' will be colored with the first color assigned to the group. Else, all
#' samples will be plotted in black.
#'
#' If groups are defined in \code{config} and \code{groupmean=TRUE}, the mean
#' PSI of the samples within each group are drawn as horizontal lines. The
#' colors of the lines are determined by the color set to the first sample of
#' each group by \code{RColorCode} in \code{config}. A corresponding legend key
#' will also be drawn.
#'
#' (See also \code{\link{preprocess_sample_colors}} and \code{vignette('psiplot-usage')}
#' for details on how to use config files).
#'
#' PSI values that have \emph{NA} value are omitted and not plotted.
#'
#' Error bars based on the confidence interval of the PSI estimation can be
#' shown by setting \code{errorbar=TRUE}.
#'
#' @param x A 1-row data frame containing PSI values to be plotted.
#' @param trim_colnames String that must be searched for and trimmed at the end
#' of every sample column in x. If no string must be trimmed, leave as \code{NULL}.
#' @param config Optional configuration settings for \code{plot_event}. Can be
#' a path to the \code{.config} file, or 4/5-column data frame of the \code{.config}
#' file. Use the latter option if you are calling \code{plot_event} multiple times.
#' @param subg Logical indicating whether samples should be subgrouped for plotting.
#' @param subg.show Only applies when \code{subg == TRUE}. Default is \code{mean},
#' in which the average PSI is computed for each subgroup. If \code{all}, then
#' individual point estimates with error bars are shown. If \code{beeswarm}, this is
#' similar to \code{all}, but shown as a beeswarm plot and without error bars.
#' @param qual String indicating the minimun \emph{vast-tools} quality score
#' for the PSI to be accepted. Defaults to \code{'VLOW'}. See the
#' \href{https://github.com/vastgroup/vast-tools/blob/master/README.md}{vast-tools
#' documentation} for details.
#' @param errorbar Logical indicating whether error bars should be drawn.
#' @param groupmean Logical indicating whether grouped means should be drawn.
#' Requires \code{config}.
#' @param col Vector of colors with length matching the number of samples. If
#' specified, this will override the color settings specified in \code{config}.
#' @param title Title of the plot. If \code{NULL} (default), the title generated
#' by \code{\link{make_title}}.
#' @param xlab The x-axis label.
#' @param ylab The y-axis label.
#' @param ylim Range of y-axis.
#' @param cex.main Plot title size (pts).
#' @param cex.yaxis Y-axis font size (pts).
#' @param cex.xaxis X-axis font size (i.e. the sample names) (pts).
#' @param pch Point symbol.
#' @param cex.pch Size of datapoints.
#' @param plot (deprecated) Prints the plot.
#' @param gridlines Logical indicating whether grid lines should be drawn.
#' @param show_group_legend Set to FALSE to avoid showing a legend with the sample
#' groups and their colors.
#' @return ggplot2 object
#' @seealso
#' \code{\link{format_table}} for performing some initial conversion steps of
#' \code{x}.
#'
#' \code{\link{preprocess_sample_colors}} for pre-processing of \code{x}
#' using\code{config}.
#'
#' \code{\link{plot_multievent}} for plotting more than one
#' event in the same plot.
#'
#' @export
#' @import dplyr
#' @import tidyr
#' @import purrr
#' @import ggplot2
#' @examples
#' \dontrun{
#' plot_event(psi[1,])
#
#' # Plot with custom configuration
#' config
#' plot_event(psi[1,], config = config, groupmean=TRUE)
#' plot_event(psi[1,], config = "/path/to/config")
#'
#' # Plot with subgrouped samples
#' config
#' plot_event(psi[1,], config = config, subg = TRUE, errorbar = FALSE)
#'
#' # Plot with subroups and error bars (slow, experimental feature)
#' \dontrun{
#' plot_event(psi[1,], config = config, subg = TRUE, errorbar = TRUE)
#' }
#'
#' # Plot using custom configuration, changing point symbol, and y-axis
#' # scale
#' plot_event(psi[1,], config = config, pch = 9, ylim = c(20, 80))
#' }
plot_event <- function(
x, config = NULL, subg = FALSE,
subg.show = c("mean", "all", "beeswarm"),
trim_colnames = NULL,
qual = c("VLOW","N","LOW","OK","SOK"), errorbar = TRUE,
groupmean = ifelse(is.null(config), FALSE, TRUE), col = NULL,
title = NULL, xlab = "", ylab = "PSI", ylim = c(0,100),
cex.main = 14, cex.yaxis = 12, cex.xaxis = 12,
pch = 20, cex.pch = 3, plot = NULL, gridlines = TRUE,
show_group_legend = TRUE) {
if (!missing(plot)) {
warning("The option 'plot' has been deprecated")
}
if (nrow(x) != 1) {
stop("Too many rows!")
}
qual = match.arg(qual)
subg.show = match.arg(subg.show)
if (subg.show == "beeswarm") {
if (!requireNamespace("ggbeeswarm", quietly = TRUE)) {
stop(paste("Please install the package ggbeeswarm:",
"install.packages(\"ggbeeswarm\")",
"or use the option subg.show = \"all\" instead"))
} else {
errorbar = FALSE
}
}
# Format input
x <- format_table(x,
qual = qual,
trim_colnames=trim_colnames,
short_ids = FALSE)
reordered <- preprocess_sample_colors(x,
config,
expr=F,
col = col,
subg= subg,
multi_col=NULL)
psi <- reordered$data
qual <- reordered$qual
#Subgroups will only be used if the original config had subgroups AND
#if the subg argument was set to TRUE. Otherwise subgroups will be overridden
#with the sample names (1 sample = 1 subgroup)
subg <- all(c(subg==TRUE,
"SubgroupName" %in% colnames(reordered$original_config)))
if (all(is.na(psi))) {
warning("Did not find any points to plot")
}
N <- ifelse(is.null(ncol(psi)), 1, ncol(psi))
if (N < 2) {
stop("Need two or more samples!")
}
# Set plot title
if (is.null(title)) {
title <- make_title(as.character(x$ID))
}
mdata <- suppressMessages(gather(psi,
key = "SampleName",
value = "value"))
mqual <- suppressMessages(gather(qual,
key = "SampleName",
value = "qual"))
# Pool samples according to subgroups using the info in reordered
# (Subgroups equal to samples if subg == F anyway)
sm <- left_join(mdata,mqual,by="SampleName") %>%
left_join(reordered$subgroup,by="SampleName")
if (subg && subg.show == "all") {
smsum <- sm %>%
dplyr::group_by(SampleName, SubgroupName, value) %>%
do(ci = get_beta_ci(.$qual)) %>%
ungroup() %>%
mutate(
lo = map_dbl(ci, 1),
hi = map_dbl(ci, 2)
) %>%
select(SubgroupName, value, lo, hi)
} else if (subg && subg.show == "beeswarm") {
smsum <- select(sm, SubgroupName, value)
} else {
smsum <- sm %>%
dplyr::group_by(SubgroupName)
if(errorbar){
smsum <- smsum %>%
do(m_psi = mean(.$value,na.rm=T),
ci = get_beta_ci_subg(.$value,.$qual)) %>%
ungroup() %>%
mutate(m_psi = map_dbl(m_psi,1),
ci = map(ci,1),
lo = map_dbl(ci,1),
hi = map_dbl(ci,2)) %>%
mutate(m_psi = replace(m_psi,is.na(m_psi),NA)) %>%
select(SubgroupName,
value = m_psi,
lo,hi)
} else {
smsum <- smsum %>%
do(m_psi = mean(.$value,na.rm=T)) %>%
ungroup() %>%
mutate(m_psi = map_dbl(m_psi,1)) %>%
mutate(m_psi = replace(m_psi,is.na(m_psi),NA)) %>%
select(SubgroupName,
value = m_psi)
}
}
smsum <- left_join(reordered$subgroup_order,smsum,by="SubgroupName") %>%
dplyr::arrange(SubgroupOrder)
smsum <- left_join(smsum,reordered$group,by="SubgroupName") %>%
left_join(reordered$group_order,by="GroupName") %>%
arrange(SubgroupOrder) %>%
mutate(SubgroupName=factor(SubgroupName,levels=unique(SubgroupName))) %>%
arrange(GroupOrder) %>%
mutate(GroupName=factor(GroupName,levels=unique(GroupName))) %>%
dplyr::select(Order=SubgroupOrder,
Sample=SubgroupName,
colnames(smsum),
GroupName,
RColorCode)
inherit.aes <- FALSE
if (subg && subg.show == "all") {
gp <- smsum %>%
group_by(Sample) %>%
arrange(Order, value) %>%
mutate(position = rank(value)) %>%
ggplot(aes(x = Sample, y = value, color=GroupName, group=position)) +
geom_point(position=position_dodge(width=.5))
inherit.aes <- TRUE
} else if (subg && subg.show == "beeswarm") {
gp <- smsum %>%
ggplot(aes(x = Sample, y = value, color=GroupName)) +
ggbeeswarm::geom_quasirandom()
} else {
gp <- ggplot(data=smsum) +
geom_point(aes(x=Sample,
y=value,
colour=GroupName),
size = cex.pch,
shape=pch,
show.legend = show_group_legend)
}
gp <- gp +
scale_colour_manual("Sample Group", values=reordered$group_order$RColorCode)
if(errorbar){
gp <- gp + geom_errorbar(inherit.aes = inherit.aes,
aes(x=Sample,
ymin=lo,
ymax=hi,
colour=GroupName),
width=0.1,
position=position_dodge(width=.5),
show.legend = F)
}
# Draw horizontal lines for groups
if (!is.null(config) && groupmean) {
gp <- draw_group_means(gp,
mdata,
reordered)
}
gp <- gp + ylab(ylab) + xlab(xlab) +
ylim(ylim) +
ggtitle(title) +
theme_bw() +
theme(axis.text.x = element_text(angle = 45, hjust = 1, size = cex.xaxis),
axis.text.y = element_text(size = cex.yaxis),
axis.title.y = element_text(size = cex.yaxis),
title = element_text(size = cex.main))
if (!gridlines) {
gp <- gp + theme(panel.grid = element_blank())
}
if (is.null(config)) {
gp <- gp + guides(color=FALSE)
}
return(gp)
}
#' Make plot title
#'
#' Create a plot title using the event ID
#'
#' @param x A character containing the event ID like
#' "\code{S|TSPAN6|chrX:99885756-99885863|108}"
#' @return A character with a human-friendly title with
#' event type, gene symbol, event coordinates, and length
#' @examples
#' \dontrun{
#' f <- format_table(psi)
#' print(make_title(f$ID[1]))
#' }
make_title <- function(x) {
event <- strsplit(as.character(x), split = "\\|")[[1]]
sprintf("%s\n(%s, %s bp, type %s)",
event[2], event[3], event[4], event[1])
}
#' Make plot title (version 2)
#'
#' Create a plot title using the event ID. Returns symbol and event ID.
#'
#' @param gene A vector or character string
#' @param event A vector or character string with same size as \code{gene}
#' @return A character with a human-friendly title with format:
#' \code{GENE (EVENT ID)}
#' @examples
#' \dontrun{
#' print(make_title.2(psi$GENE, psi$EVENT))
#' }
make_title.2 <- function(gene, event) {
sprintf("%s (%s)", gene, event)
}
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