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#' Peptide abundance profile plot
#'
#' `r lifecycle::badge('deprecated')`
#' This function was deprecated due to its name changing to `peptide_profile_plot()`.
#'
#' @return A list of peptide profile plots.
#' @keywords internal
#' @export
plot_peptide_profiles <- function(...) {
# This function has been renamed and is therefore deprecated.
lifecycle::deprecate_warn("0.2.0",
"plot_peptide_profiles()",
"peptide_profile_plot()",
details = "This function has been renamed."
)
peptide_profile_plot(...)
}
#' Peptide abundance profile plot
#'
#' Creates a plot of peptide abundances across samples. This is helpful to investigate effects of
#' peptide and protein abundance changes in different samples and conditions.
#'
#' @param data a data frame that contains at least the input variables.
#' @param sample a character column in the \code{data} data frame that contains sample names.
#' @param peptide a character column in the \code{data} data frame that contains peptide or
#' precursor names.
#' @param intensity_log2 a numeric column in the \code{data} data frame that contains log2
#' transformed intensities.
#' @param grouping a character column in the \code{data} data frame that contains groups by which
#' the data should be split. This can be for example protein IDs.
#' @param targets a character vector that specifies elements of the grouping column which should
#' be plotted. This can also be \code{"all"} if plots for all groups should be created. Depending
#' on the number of elements in your grouping column this can be many plots.
#' @param complete_sample a logical value that indicates if samples that are completely missing for
#' a given protein should be shown on the x-axis of the plot anyway. The default value is `FALSE`.
#' @param protein_abundance_plot a logical value. If the input for this plot comes directly from
#' \code{calculate_protein_abundance} this argument can be set to \code{TRUE}. This displays all
#' peptides in gray, while the protein abundance is displayed in green.
#' @param interactive a logical value that indicates whether the plot should be interactive
#' (default is FALSE). If this is TRUE only one target can be supplied to the function. Interactive
#' plots cannot be exported either.
#' @param export a logical value that indicates if plots should be exported as PDF. The output
#' directory will be the current working directory. The name of the file can be chosen using the
#' \code{export_name} argument.
#' @param export_name a character vector that provides the name of the exported file if
#' \code{export = TRUE}.
#'
#' @return A list of peptide profile plots.
#' @import ggplot2
#' @import progress
#' @importFrom magrittr %>%
#' @importFrom dplyr distinct pull filter
#' @importFrom tidyr drop_na
#' @importFrom rlang !! ensym
#' @importFrom plotly ggplotly
#' @importFrom purrr map2
#' @importFrom utils data
#' @export
#'
#' @examples
#' \donttest{
#' # Create example data
#' data <- data.frame(
#' sample = c(
#' rep("S1", 6),
#' rep("S2", 6),
#' rep("S1", 2),
#' rep("S2", 2)
#' ),
#' protein_id = c(
#' rep("P1", 12),
#' rep("P2", 4)
#' ),
#' precursor = c(
#' rep(c("A1", "A2", "B1", "B2", "C1", "D1"), 2),
#' rep(c("E1", "F1"), 2)
#' ),
#' peptide = c(
#' rep(c("A", "A", "B", "B", "C", "D"), 2),
#' rep(c("E", "F"), 2)
#' ),
#' intensity = c(
#' rnorm(n = 6, mean = 15, sd = 2),
#' rnorm(n = 6, mean = 21, sd = 1),
#' rnorm(n = 2, mean = 15, sd = 1),
#' rnorm(n = 2, mean = 15, sd = 2)
#' )
#' )
#'
#' # Calculate protein abundances and retain precursor
#' # abundances that can be used in a peptide profile plot
#' complete_abundances <- calculate_protein_abundance(
#' data,
#' sample = sample,
#' protein_id = protein_id,
#' precursor = precursor,
#' peptide = peptide,
#' intensity_log2 = intensity,
#' method = "sum",
#' for_plot = TRUE
#' )
#'
#' # Plot protein abundance profile
#' # protein_abundance_plot can be set to
#' # FALSE to to also colour precursors
#' peptide_profile_plot(
#' data = complete_abundances,
#' sample = sample,
#' peptide = precursor,
#' intensity_log2 = intensity,
#' grouping = protein_id,
#' targets = c("P1"),
#' protein_abundance_plot = TRUE
#' )
#' }
peptide_profile_plot <- function(data,
sample,
peptide,
intensity_log2,
grouping,
targets,
complete_sample = FALSE,
protein_abundance_plot = FALSE,
interactive = FALSE,
export = FALSE,
export_name = "peptide_profile_plots") {
. <- NULL
n_samples <- length(unique(dplyr::pull(data, {{ sample }})))
protti_colours <- "placeholder" # assign a placeholder to prevent a missing global variable warning
utils::data("protti_colours", envir = environment()) # then overwrite it with real data
if (missing(targets)) stop("Please provide at least one target to plot!")
input <- data %>%
dplyr::distinct({{ sample }}, {{ peptide }}, {{ intensity_log2 }}, {{ grouping }}) %>%
tidyr::drop_na({{ intensity_log2 }})
if (complete_sample) {
input <- input %>%
tidyr::complete({{ sample }}, {{ grouping }}) %>%
tidyr::fill({{ peptide }}, .direction = "downup")
}
if (!("all" %in% targets)) {
input <- input %>%
dplyr::filter({{ grouping }} %in% targets) %>%
split(dplyr::pull(., !!ensym(grouping)))
}
if ("all" %in% targets) {
groups <- length(unique(dplyr::pull(data, {{ grouping }})))
message("Splitting into ", groups, " groups and returning ", groups, " plots.")
input <- input %>%
split(dplyr::pull(., !!ensym(grouping)))
}
pb <- progress::progress_bar$new(
total = length(input),
format = " Creating plots [:bar] :current/:total (:percent) :eta"
)
plot <- purrr::map2(
.x = input,
.y = names(input),
.f = ~ {
pb$tick()
ggplot2::ggplot(.x, ggplot2::aes({{ sample }}, {{ intensity_log2 }}, group = {{ peptide }}, color = {{ peptide }})) +
ggplot2::geom_point() +
ggplot2::geom_line(size = 1) +
ggplot2::labs(
title = paste("Peptide profiles:", .y),
x = "Sample",
y = "Intensity [log2]",
col = "Peptides"
) +
ggplot2::theme_bw() +
{
if (length(unique(dplyr::pull(.x, {{ peptide }}))) > 25) ggplot2::theme(legend.position = "none")
} +
ggplot2::theme(
plot.title = ggplot2::element_text(size = 20),
axis.title.x = ggplot2::element_text(size = 15),
axis.text.y = ggplot2::element_text(size = 15),
axis.text.x = ggplot2::element_text(size = 12, angle = 75, hjust = 1),
axis.title.y = ggplot2::element_text(size = 15),
legend.title = ggplot2::element_text(size = 15),
legend.text = ggplot2::element_text(size = 15),
strip.text.x = ggplot2::element_text(size = 15),
strip.text = ggplot2::element_text(size = 15),
strip.background = ggplot2::element_blank()
) +
{
# repeated colours to have enough even for proteins with many peptides
if (protein_abundance_plot == FALSE) ggplot2::scale_color_manual(values = rep(protti_colours, 10))
} +
{
if (protein_abundance_plot == TRUE) {
ggplot2::scale_color_manual(values = c(rep("gray", length(unique(dplyr::pull(.x, {{ peptide }}))) - 1), "green"))
}
}
}
)
if (interactive == FALSE) {
if (export == TRUE) {
grDevices::pdf(
file = paste0(export_name, ".pdf"),
width = 10 * ceiling(n_samples / 10), # more samples need wider plot
height = 6
)
suppressWarnings(print(plot))
grDevices::dev.off()
} else {
return(suppressWarnings(suppressMessages(print(plot))))
}
}
if (interactive == TRUE) {
if (length(targets) > 1) {
stop(strwrap("Please only provide one target for interactive plots!",
prefix = "\n", initial = ""
))
}
if (export == TRUE) {
stop(strwrap("Interactive plots cannot be exported! Please decide if you
want an interactive plot or if you want to export your plots.",
prefix = "\n", initial = ""
))
}
plotly::ggplotly(plot[[1]], tooltip = c("x", "y", "group"))
}
}
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