Nothing
R/plot_wrapper.R
In synergyfinder: Calculate and Visualize Synergy Scores for Drug Combinations
Defines functions
PlotSynergy
PlotDoseResponse
Documented in
PlotDoseResponse
PlotSynergy
# Copyright Shuyu Zheng and Jing Tang - All Rights Reserved
# Unauthorized copying of this file, via any medium is strictly prohibited
# Proprietary and confidential
# Written by Shuyu Zheng <shuyu.zheng@helsinki.fi>, March 2021
#
# SynergyFinder
#
# Functions on this page:
#
# PlotDoseResponse: Visualize the Drug Combination Dose-response Data
#' Visualize the Drug Combination Dose-response Data
#'
#' A function to visualize the drug combination dose-response data
#'
#' @param data A list object generated by function \code{\link{ReshapeData}}.
#' @param block_ids A vector of characters/integers or NULL. It contains the
#' block IDs for the blocks to visualize. By default, it is NULL so that the
#' visualization of all the drug combinations in input \code{data}.
#' @param drugs A vector of characters or integers with length of 2. It contains
#' the index for two drugs to plot. For example, \code{c(1, 2)} indicates to
#' plot "drug1" and "drug2" in the input \code{data}.
#' @param adjusted A logical value. If it is \code{FALSE}, original response
#' matrix will be plotted. If it is \code{TRUE}, adjusted response matrix will
#' be plotted.
#' @param statistic A character or NULL. It indicates the statistics printed
#' in the plot while there are replicates in input data. Available values are:
#' \itemize{
#' \item \strong{sem} Standard error of mean;
#' \item \strong{ci} 95% confidence interval.
#' }
#' If it is \code{NULL}, no statistics will be printed.
#' @param summary_statistic A vector of characters or NULL. It indicates the
#' summary statistics printed in heatmap for all the \code{plot_value} in
#' whole combination matrix. Available values are:
#' \itemize{
#' \item \strong{mean} Median value for all the responses or synergy
#' scores in the matrix;
#' \item \strong{median} Median value for all the responses or synergy
#' scores in the matrix;
#' \item \strong{quantile_90} 90% quantile. User could change the number to
#' print different sample quantile. For example quantile_50 equal to median.
#' }
#' If it is \code{NULL}, no statistics will be printed.
#' @param high_value_color An R color value. It indicates the color for the
#' high values.
#' @param low_value_color An R color value. It indicates the color for low
#' values.
#' @param point_color An R color value. It indicates the color for points in
#' dose response curve plots.
#' @param curve_color An R color value. It indicates the color for curves in
#' dose response curve plots.
#' @param text_size_scale A numeric value. It is used to control the size
#' of text in the plot. All the text size will multiply by this scale factor.
#' @param heatmap_text_label_size_scale A numeric value. It is used to control
#' the size of text labels in the heatmap plot. It only works while
#' \code{plot_type = "heatmap"}.
#' @param heatmap_text_label_color NULL or an R color value. It is used to
#' control the color of text labels in the heatmap plot. If it is \code{NULL},
#' text label will not be shown.It only works while
#' \code{plot_type = "heatmap"}.
#' @param heatmap_plot_title A character value to indicate the plot title for
#' the heatmap.
#' @param curve_plot_title A character value to indicate the plot title for
#' the dose-response curve.
#' @param Emin A numeric or \code{NA}. the minimal effect of the drug used in
#' the 4-parameter log-logistic function to fit the dose-response curve. If
#' it is not NA, it is fixed the value assigned by the user. Default setting
#' is \code{NA}.
#' @param Emax A numeric or \code{NA}. the maximal effect of the drug used in
#' the 4-parameter log-logistic function to fit the dose-response curve. If
#' it is not NA, it is fixed the value assigned by the user. Default setting
#' is \code{NA}.
#' @param save_file A parameter to specify if the visualization results are
#' saved as pdf files in current working directory or not. If it is FALSE,
#' the results are returned as a list of the plots. It is FALSE by default.
#' @param file_type A character. It indicates the format of files you want to
#' save as. Default is "pdf". Available values are "jpeg", "bmp", "png",
#' "tiff", "pdf", "svg".
#' @param file_name A character vector. It indicates the file names, if
#' user chose to save the plot to local directory.If it is not defined by
#' user, a default name will be assigned.
#' @param width a numeric value. It indicates the width of saved file.
#' @param height a numeric value. It indicates the height of saved file.
#'
#' @return A list of plot objects recorded by \link[grDevices]{recordPlot}. The
#' plot will be saved into a local file if \code{save_file = TRUE}. If
#' \code{save_file = FALSE}, the plot will be printed in default graphic
#' device.
#'
#' @author
#' \itemize{
#' \item Shuyu Zheng \email{shuyu.zheng@helsinki.fi}
#' \item Jing Tang \email{jing.tang@helsinki.fi}
#' }
#'
#' @import ggplot2
#' @export
#'
#' @examples
#' \dontrun{
#' data("mathews_screening_data")
#' data <- ReshapeData(mathews_screening_data)
#' plots <- PlotDoseResponse(data)
#' }
PlotDoseResponse <- function(data,
block_ids = c(1),
drugs = c(1, 2),
adjusted = TRUE,
statistic = NULL,
summary_statistic = "mean",
high_value_color = "#A90217",
low_value_color = "#2166AC",
point_color = "#C24B40",
curve_color = "black",
text_size_scale = 1,
heatmap_text_label_size_scale = 1,
heatmap_text_label_color = "#000000",
curve_plot_title = NULL,
heatmap_plot_title = NULL,
Emin = NA,
Emax = NA,
save_file = FALSE,
file_type = "pdf",
file_name = NULL,
width = 12,
height = 6) {
# 1. Check the input data
if (!is.list(data)) {
stop("Input data is not in list format!")
}
if (!all(c("drug_pairs", "response") %in% names(data))) {
stop("Input data should contain at least tow elements: 'drug_pairs' and
'response'. Please prepare your data with 'ReshapeData' function.")
}
# 2. Select the dose response table for plotting.
if (adjusted) {
plot_value = "response"
} else {
plot_value = "response_origin"
}
# 3. Select block
if (!is.null(block_ids)) {
no_block_id <- setdiff(block_ids, data$drug_pairs$block_id)
if (length(no_block_id) > 0) {
stop(
"Selected block_ids ",
paste(unique(no_block_id), sep = ", "),
" are not found in the input data. Please check the input data."
)
}
} else {
block_ids <- data$drug_pairs$block_id
}
plots <- vector(mode = "list", length = length(block_ids))
names(plots) <- block_ids
i <- 1
for (b in block_ids) {
# ggplot object for heatmap
dose_response_plot <- Plot2DrugHeatmap(
data,
plot_block = b,
drugs = drugs,
plot_value = plot_value,
statistic = statistic,
title_text_size_scale = text_size_scale,
summary_statistic = summary_statistic,
high_value_color = high_value_color,
low_value_color = low_value_color,
plot_title = heatmap_plot_title,
text_label_size_scale = heatmap_text_label_size_scale,
text_label_color = heatmap_text_label_color
)
# plot dose response curve
graphics::plot.new()
graphics::layout(matrix(c(1, 3, 2, 3), 2, 2, byrow = TRUE))
for (i in drugs){
PlotDoseResponseCurve(
data,
plot_block = b,
drug_index = i,
plot_setting = list(
mgp = c(2, 0.5, 0),
font.main = 2,
cex.main = 1 / 12 * 13.5,
cex.sub = 1
),
plot_subtitle = "",
grid = grid,
point_color = point_color,
curve_color = curve_color,
Emin = Emin,
Emax = Emax,
plot_new = FALSE,
text_size_scale = text_size_scale,
plot_title = curve_plot_title
)
}
# vps <- baseViewports()
# pushViewport()
print(dose_response_plot, vp = grid::viewport(
height = grid::unit(1, "npc"),
width = grid::unit(0.5, "npc"),
just = c("left", "top"),
y = 1, x = 0.5
))
# popViewport()
merge_plot <- grDevices::recordPlot()
plots[[b]] <- merge_plot
if (save_file) {
if (is.null(file_name)) {
if (adjusted) {
file <- paste(
data$drug_pairs[which(data$drug_pairs$block_id == b),
paste0("drug", drugs)],
"adjusted_dose_response_block",
b,
sep = "_"
)
} else {
file <- paste(
data$drug_pairs[which(data$drug_pairs$block_id == b),
paste0("drug", drugs)],
"original_dose_response_block",
b,
sep = "_"
)
}
} else {
file <- file_name[i]
i <- i + 1
}
if (!file_type %in% c("jpeg", "bmp", "png", "tiff", "pdf", "svg")) {
warning(
"Can not save plot in ", file_type, " format. Avaliable formats are ",
"'svg', 'jpeg', 'bmp', 'png', 'tiff', and 'pdf'.")
} else if (file_type == "pdf") {
grDevices::pdf(paste(file, file_type, sep = "."),
width = width, height = height
)
} else if (file_type == "svg") {
grDevices::svg(paste(file, file_type, sep = "."),
width = width, height = height
)
} else {
do.call(file_type, args = list(
filename = paste(file, file_type, sep = "."),
width = width, height = height,
units = "in", res = 600
))
}
#
# grDevices::jpeg(file_name, width = 800, height = 600)
grDevices::replayPlot(merge_plot)
grDevices::dev.off()
}
}
return(plots)
}
#' Plot Interaction Landscape for Synergy Scores
#'
#' A function to visualize the synergy scores for drug combinations as 2D or 3D
#' interaction landscape over the dose-response matrix.
#'
#' @param data A list object generated by function
#' \code{\link{CalculateSynergy}}
#' @param type A character value. It specifies the type of the plot. Available
#' values are:
#' \itemize{
#' \item \strong{2D} Visualize 2D interactive landscape with contour plot.
#' \item \strong{heatmap} Heatmap for synergy scores.
#' \item \strong{3D} Visualize 3D surface for interactive landscape.
#' }
#' @param method A character value. It indicates which synergy score to be
#' visualized. Available values are "ZIP", "HSA", "Bliss", or "Loewe".
#' @param block_ids A parameter to specify which drug combination if there are
#' many drug combinations in the data. By default, it is NULL so that the
#' synergy score visualization of all the drug combinations in the data is
#' returned.
#' @param drugs A vector of characters or integers with length of 2. It contains
#' the index for two drugs to plot. For example, \code{c(1, 2)} indicates to
#' plot "drug1" and "drug2" in the input \code{data}.
#' @param col_range A vector of two integers. They specify the starting and
#' ending concentration of the drug on x-axis. Use e.g., c(1, 3) to specify
#' that only from 1st to 3rd concentrations of the drug on x-axis are used. By
#' default, it is NULl so all the concentrations are used.
#' @param row_range A vector of two integers. They specify the starting and
#' ending concentration of the drug on y-axis. Use e.g., c(1, 3) to specify
#' that only from 1st to 3rd concentrations of the drug on y-axis are used. By
#' default, it is NULl so all the concentrations are used.
#' @param statistic A character or NULL. It indicates the statistics printed
#' in the plot while there are replicates in input data. Available values are:
#' \itemize{
#' \item \strong{sem} Standard error of mean;
#' \item \strong{ci} 95\% confidence interval.
#' }
#' If it is \code{NULL}, no statistics will be printed. \strong{Note}: It only
#' works in Heatmap plot.
#' @param summary_statistic A vector of characters or NULL. It indicates the
#' summary statistics for all the \code{plot_value} in whole combination
#' matrix. Available values are:
#' \itemize{
#' \item \strong{mean} Median value for all the responses or synergy
#' scores in the matrix;
#' \item \strong{median} Median value for all the responses or synergy
#' scores in the matrix;
#' \item \strong{quantile_90} 90\% quantile. User could change the number to
#' print different sample quantile. For example quantile_50 equal to median.
#' }
#' If it is \code{NULL}, no statistics will be printed.
#' @param plot_title A character value. It specifies the plot title. If it is
#' \code{NULL}, the function will automatically generate a title.
#' @param interpolate_len An integer. It specifies how many values need to be
#' interpolated between two concentrations. It is used to control the
#' smoothness of the synergy surface in the contour plot and surface plot.
#' \strong{Note}: It only works in 2D and 3D plots.
#' @param high_value_color An R color value. It indicates the color for the
#' high values.
#' @param low_value_color An R color value. It indicates the color for low
#' values.
#' @param text_size_scale A numeric value. It is used to control the size
#' of text in the plot. All the text size will multiply by this scale factor.
#' @param heatmap_text_label_size_scale A numeric value. It is used to control
#' the size of text labels in the heatmap plot. It only works while
#' \code{plot_type = "heatmap"}.
#' @param heatmap_text_label_color NULL or an R color value. It is used to
#' control the color of text labels in the heatmap plot. If it is \code{NULL},
#' text label will not be shown. It only works while
#' \code{plot_type = "heatmap"}.
#' @param surface_grid A logical value. It indicates whether to add grids on the
#' surface. It only works while \code{plot_type = "3D"}.
#' @param dynamic A logic value. It indicates whether to generate interactive
#' plot wit package "plotly" or static plot with package "ggplot2"/"lattice".
#' @param display A logic value. It specifies whether to automatically display
#' plots while calling the function.
#' @param save_file A logic value. It specifies if the interaction landscapes
#' is saved by calling \link[ggplot2]{ggsave} function ("2D" or "heatmap"
#' plots) or plot saving function defined by \code{device} ("3D" plots). By
#' default, it is FALSE. \strong{Note}: It doesn't work while
#' \code{dynamic = TRUE}, because installation of "Orca" is required for
#' exporting plotly plots. Please check
#' https://plotly.com/r/static-image-export/ for more details.
#' @param file_name A character vector. It indicates the file names. If it is
#' not defined by user, a default name will be assigned. \strong{Note}: It
#' only works while \code{save_file = TRUE}.
#' @param file_path A character vector. It indicates the path to save file.
#' If it is not defined by user, a default name will be assigned.
#' \strong{Note}: It only works while \code{save_file = TRUE}.
#' @param width A numeric value. It indicates the width of the output plot.
#' \strong{Note}: It only works while \code{save_file = TRUE}.
#' @param height A numeric value. It indicates the height of the output plot.
#' \strong{Note}: It only works while \code{save_file = TRUE}.
#' @param units A character value. It indicates the units for \code{width} and
#' \code{height} for saved plots. It is used to set the \code{units}
#' parameter in function \link[ggplot2]{ggsave} or the function selected by
#' \code{device} (It will not work on "pdf" and "svg" devices. There units
#' are always in inch.). \strong{Note}: It only works while
#' \code{save_file = TRUE}.
#' @param device A character value. It indicates the device to use for saving
#' plots. If \code{type = "3D"}, the corresponding device function in package
#' "grDevices" will be called to save the plots. If
#' \code{type = "2D"/"heatmap"}, it will be used to set the parameter
#' \code{device} in function \link[ggplot2]{ggsave}.
#' \strong{Note}: It only works while \code{save_file = TRUE}.
#'
#' @return A list of ggplot objects.
#'
#' @author
#' \itemize{
#' \item Liye He \email{liye.he@helsinki.fi},
#' \item Shuyu Zheng \email{shuyu.zheng@helsinki.fi}
#' }
#'
#' @export
#'
#' @examples
#' data("mathews_screening_data")
#' data <- ReshapeData(mathews_screening_data)
#' data <- CalculateSynergy(data)
#' plots <- PlotSynergy(data, "2D", block_ids = NULL)
PlotSynergy <- function(data,
type = "2D",
method = "ZIP",
block_ids = c(1),
drugs = c(1, 2),
row_range = NULL,
col_range = NULL,
statistic = NULL,
summary_statistic = "mean",
plot_title = NULL,
interpolate_len = 3,
high_value_color = "#A90217",
low_value_color = "#2166AC",
text_size_scale = 1,
heatmap_text_label_size_scale = 1,
heatmap_text_label_color = "#000000",
surface_grid = TRUE,
dynamic = FALSE,
display = TRUE,
save_file = FALSE,
file_name = NULL,
file_path = NULL,
height = 6,
width = 6,
units = "in",
device = "pdf") {
# Check input data
if (!is.list(data)) {
stop("Input data is not a list format!")
}
if(is.null(block_ids)) {
block_ids <- unique(data$drug_pairs$block_id)
}
# Container for plots
plots <- vector(mode = "list", length = length(block_ids))
names(plots) <- block_ids
i <- 1
for (block in block_ids) {
drug_pair <- data$drug_pairs[data$drug_pairs$block_id == block, ]
if (type == "2D") {
fig <- Plot2DrugContour(
data = data,
plot_block = block,
drugs = drugs,
dynamic = dynamic,
plot_value = paste0(method, "_synergy"),
summary_statistic = summary_statistic,
plot_title = plot_title,
interpolate_len = interpolate_len,
high_value_color = high_value_color,
low_value_color = low_value_color,
row_range = row_range,
col_range = col_range,
text_size_scale = text_size_scale)
if (display) {
fig
}
} else if (type == "heatmap") {
fig <- Plot2DrugHeatmap(
data = data,
plot_block = block,
drugs = drugs,
statistic = statistic,
dynamic = dynamic,
plot_value = paste0(method, "_synergy"),
summary_statistic = summary_statistic,
plot_title = plot_title,
high_value_color = high_value_color,
low_value_color = low_value_color,
row_range = row_range,
col_range = col_range,
title_text_size_scale = text_size_scale,
text_label_size_scale = heatmap_text_label_size_scale,
text_label_color = heatmap_text_label_color)
if (display) {
fig
}
} else if (type == "3D") {
fig <- Plot2DrugSurface(
data = data,
plot_block = block,
drugs = drugs,
interpolate_len = interpolate_len,
dynamic = dynamic,
plot_value = paste0(method, "_synergy"),
summary_statistic = summary_statistic,
plot_title = plot_title,
high_value_color = high_value_color,
low_value_color = low_value_color,
row_range = row_range,
col_range = col_range,
grid = surface_grid,
text_size_scale = text_size_scale)
if (display) {
if (dynamic) {
fig
} else {
print(fig)
}
}
} else {
stop("The type of plot '", type, "' is not available. Available values
for parameter 'type' are: 2D, 3D, or heatmap.")
}
plots[[block]] <- fig
# Save plots
if(save_file) {
if (dynamic) {
warning("Saving dynamic surface plot from plotly requires installation",
" of Orca. This function can not save such plot as static ",
"images, but return the plotly object.",
"Please check https://plotly.com/r/static-image-export/ to see",
"how to export plotly plot objects to local directory.")
} else {
if (is.null(file_name)) {
file <-paste(
c(drug_pair[, paste0("drug", drugs)],
"synergy",
block,
method,
type),
collapse = "_"
)
} else {
file <- file_name[i]
i <- i + 1
}
# Set width and height according to plot types
if (type == "3D") {
if (!device %in% c("jpeg", "bmp", "png", "tiff", "pdf", "svg")){
warning("Can not save plot in ", device, " format. Avaliable formats
are 'svg', 'jpeg', 'bmp', 'png', 'tiff',and 'pdf'.")
} else if (device == "pdf") {
grDevices::pdf(paste(file, device, sep = "."),
width = width, height = height)
} else if (device == "svg") {
grDevices::svg(
paste(file, device, sep = "."),
width = width,
height = height)
} else {
do.call(
device,
args = list(
filename = paste(file, device, sep="."),
width = width,
height = height,
units = units,
res = 600)
)
}
grDevices::replayPlot(fig)
grDevices::dev.off()
} else {
ggplot2::ggsave(
filename = paste(file, device, sep="."),
plot = plots[[block]],
path = file_path,
width = width,
height = height,
device = device,
units = units
)
}
}
}
}
return(plots)
}
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Defines functions PlotSynergy PlotDoseResponse
Documented in PlotDoseResponse PlotSynergy
# Copyright Shuyu Zheng and Jing Tang - All Rights Reserved
# Unauthorized copying of this file, via any medium is strictly prohibited
# Proprietary and confidential
# Written by Shuyu Zheng <shuyu.zheng@helsinki.fi>, March 2021
#
# SynergyFinder
#
# Functions on this page:
#
# PlotDoseResponse: Visualize the Drug Combination Dose-response Data
#' Visualize the Drug Combination Dose-response Data
#'
#' A function to visualize the drug combination dose-response data
#'
#' @param data A list object generated by function \code{\link{ReshapeData}}.
#' @param block_ids A vector of characters/integers or NULL. It contains the
#' block IDs for the blocks to visualize. By default, it is NULL so that the
#' visualization of all the drug combinations in input \code{data}.
#' @param drugs A vector of characters or integers with length of 2. It contains
#' the index for two drugs to plot. For example, \code{c(1, 2)} indicates to
#' plot "drug1" and "drug2" in the input \code{data}.
#' @param adjusted A logical value. If it is \code{FALSE}, original response
#' matrix will be plotted. If it is \code{TRUE}, adjusted response matrix will
#' be plotted.
#' @param statistic A character or NULL. It indicates the statistics printed
#' in the plot while there are replicates in input data. Available values are:
#' \itemize{
#' \item \strong{sem} Standard error of mean;
#' \item \strong{ci} 95% confidence interval.
#' }
#' If it is \code{NULL}, no statistics will be printed.
#' @param summary_statistic A vector of characters or NULL. It indicates the
#' summary statistics printed in heatmap for all the \code{plot_value} in
#' whole combination matrix. Available values are:
#' \itemize{
#' \item \strong{mean} Median value for all the responses or synergy
#' scores in the matrix;
#' \item \strong{median} Median value for all the responses or synergy
#' scores in the matrix;
#' \item \strong{quantile_90} 90% quantile. User could change the number to
#' print different sample quantile. For example quantile_50 equal to median.
#' }
#' If it is \code{NULL}, no statistics will be printed.
#' @param high_value_color An R color value. It indicates the color for the
#' high values.
#' @param low_value_color An R color value. It indicates the color for low
#' values.
#' @param point_color An R color value. It indicates the color for points in
#' dose response curve plots.
#' @param curve_color An R color value. It indicates the color for curves in
#' dose response curve plots.
#' @param text_size_scale A numeric value. It is used to control the size
#' of text in the plot. All the text size will multiply by this scale factor.
#' @param heatmap_text_label_size_scale A numeric value. It is used to control
#' the size of text labels in the heatmap plot. It only works while
#' \code{plot_type = "heatmap"}.
#' @param heatmap_text_label_color NULL or an R color value. It is used to
#' control the color of text labels in the heatmap plot. If it is \code{NULL},
#' text label will not be shown.It only works while
#' \code{plot_type = "heatmap"}.
#' @param heatmap_plot_title A character value to indicate the plot title for
#' the heatmap.
#' @param curve_plot_title A character value to indicate the plot title for
#' the dose-response curve.
#' @param Emin A numeric or \code{NA}. the minimal effect of the drug used in
#' the 4-parameter log-logistic function to fit the dose-response curve. If
#' it is not NA, it is fixed the value assigned by the user. Default setting
#' is \code{NA}.
#' @param Emax A numeric or \code{NA}. the maximal effect of the drug used in
#' the 4-parameter log-logistic function to fit the dose-response curve. If
#' it is not NA, it is fixed the value assigned by the user. Default setting
#' is \code{NA}.
#' @param save_file A parameter to specify if the visualization results are
#' saved as pdf files in current working directory or not. If it is FALSE,
#' the results are returned as a list of the plots. It is FALSE by default.
#' @param file_type A character. It indicates the format of files you want to
#' save as. Default is "pdf". Available values are "jpeg", "bmp", "png",
#' "tiff", "pdf", "svg".
#' @param file_name A character vector. It indicates the file names, if
#' user chose to save the plot to local directory.If it is not defined by
#' user, a default name will be assigned.
#' @param width a numeric value. It indicates the width of saved file.
#' @param height a numeric value. It indicates the height of saved file.
#'
#' @return A list of plot objects recorded by \link[grDevices]{recordPlot}. The
#' plot will be saved into a local file if \code{save_file = TRUE}. If
#' \code{save_file = FALSE}, the plot will be printed in default graphic
#' device.
#'
#' @author
#' \itemize{
#' \item Shuyu Zheng \email{shuyu.zheng@helsinki.fi}
#' \item Jing Tang \email{jing.tang@helsinki.fi}
#' }
#'
#' @import ggplot2
#' @export
#'
#' @examples
#' \dontrun{
#' data("mathews_screening_data")
#' data <- ReshapeData(mathews_screening_data)
#' plots <- PlotDoseResponse(data)
#' }
PlotDoseResponse <- function(data,
block_ids = c(1),
drugs = c(1, 2),
adjusted = TRUE,
statistic = NULL,
summary_statistic = "mean",
high_value_color = "#A90217",
low_value_color = "#2166AC",
point_color = "#C24B40",
curve_color = "black",
text_size_scale = 1,
heatmap_text_label_size_scale = 1,
heatmap_text_label_color = "#000000",
curve_plot_title = NULL,
heatmap_plot_title = NULL,
Emin = NA,
Emax = NA,
save_file = FALSE,
file_type = "pdf",
file_name = NULL,
width = 12,
height = 6) {
# 1. Check the input data
if (!is.list(data)) {
stop("Input data is not in list format!")
}
if (!all(c("drug_pairs", "response") %in% names(data))) {
stop("Input data should contain at least tow elements: 'drug_pairs' and
'response'. Please prepare your data with 'ReshapeData' function.")
}
# 2. Select the dose response table for plotting.
if (adjusted) {
plot_value = "response"
} else {
plot_value = "response_origin"
}
# 3. Select block
if (!is.null(block_ids)) {
no_block_id <- setdiff(block_ids, data$drug_pairs$block_id)
if (length(no_block_id) > 0) {
stop(
"Selected block_ids ",
paste(unique(no_block_id), sep = ", "),
" are not found in the input data. Please check the input data."
)
}
} else {
block_ids <- data$drug_pairs$block_id
}
plots <- vector(mode = "list", length = length(block_ids))
names(plots) <- block_ids
i <- 1
for (b in block_ids) {
# ggplot object for heatmap
dose_response_plot <- Plot2DrugHeatmap(
data,
plot_block = b,
drugs = drugs,
plot_value = plot_value,
statistic = statistic,
title_text_size_scale = text_size_scale,
summary_statistic = summary_statistic,
high_value_color = high_value_color,
low_value_color = low_value_color,
plot_title = heatmap_plot_title,
text_label_size_scale = heatmap_text_label_size_scale,
text_label_color = heatmap_text_label_color
)
# plot dose response curve
graphics::plot.new()
graphics::layout(matrix(c(1, 3, 2, 3), 2, 2, byrow = TRUE))
for (i in drugs){
PlotDoseResponseCurve(
data,
plot_block = b,
drug_index = i,
plot_setting = list(
mgp = c(2, 0.5, 0),
font.main = 2,
cex.main = 1 / 12 * 13.5,
cex.sub = 1
),
plot_subtitle = "",
grid = grid,
point_color = point_color,
curve_color = curve_color,
Emin = Emin,
Emax = Emax,
plot_new = FALSE,
text_size_scale = text_size_scale,
plot_title = curve_plot_title
)
}
# vps <- baseViewports()
# pushViewport()
print(dose_response_plot, vp = grid::viewport(
height = grid::unit(1, "npc"),
width = grid::unit(0.5, "npc"),
just = c("left", "top"),
y = 1, x = 0.5
))
# popViewport()
merge_plot <- grDevices::recordPlot()
plots[[b]] <- merge_plot
if (save_file) {
if (is.null(file_name)) {
if (adjusted) {
file <- paste(
data$drug_pairs[which(data$drug_pairs$block_id == b),
paste0("drug", drugs)],
"adjusted_dose_response_block",
b,
sep = "_"
)
} else {
file <- paste(
data$drug_pairs[which(data$drug_pairs$block_id == b),
paste0("drug", drugs)],
"original_dose_response_block",
b,
sep = "_"
)
}
} else {
file <- file_name[i]
i <- i + 1
}
if (!file_type %in% c("jpeg", "bmp", "png", "tiff", "pdf", "svg")) {
warning(
"Can not save plot in ", file_type, " format. Avaliable formats are ",
"'svg', 'jpeg', 'bmp', 'png', 'tiff', and 'pdf'.")
} else if (file_type == "pdf") {
grDevices::pdf(paste(file, file_type, sep = "."),
width = width, height = height
)
} else if (file_type == "svg") {
grDevices::svg(paste(file, file_type, sep = "."),
width = width, height = height
)
} else {
do.call(file_type, args = list(
filename = paste(file, file_type, sep = "."),
width = width, height = height,
units = "in", res = 600
))
}
#
# grDevices::jpeg(file_name, width = 800, height = 600)
grDevices::replayPlot(merge_plot)
grDevices::dev.off()
}
}
return(plots)
}
#' Plot Interaction Landscape for Synergy Scores
#'
#' A function to visualize the synergy scores for drug combinations as 2D or 3D
#' interaction landscape over the dose-response matrix.
#'
#' @param data A list object generated by function
#' \code{\link{CalculateSynergy}}
#' @param type A character value. It specifies the type of the plot. Available
#' values are:
#' \itemize{
#' \item \strong{2D} Visualize 2D interactive landscape with contour plot.
#' \item \strong{heatmap} Heatmap for synergy scores.
#' \item \strong{3D} Visualize 3D surface for interactive landscape.
#' }
#' @param method A character value. It indicates which synergy score to be
#' visualized. Available values are "ZIP", "HSA", "Bliss", or "Loewe".
#' @param block_ids A parameter to specify which drug combination if there are
#' many drug combinations in the data. By default, it is NULL so that the
#' synergy score visualization of all the drug combinations in the data is
#' returned.
#' @param drugs A vector of characters or integers with length of 2. It contains
#' the index for two drugs to plot. For example, \code{c(1, 2)} indicates to
#' plot "drug1" and "drug2" in the input \code{data}.
#' @param col_range A vector of two integers. They specify the starting and
#' ending concentration of the drug on x-axis. Use e.g., c(1, 3) to specify
#' that only from 1st to 3rd concentrations of the drug on x-axis are used. By
#' default, it is NULl so all the concentrations are used.
#' @param row_range A vector of two integers. They specify the starting and
#' ending concentration of the drug on y-axis. Use e.g., c(1, 3) to specify
#' that only from 1st to 3rd concentrations of the drug on y-axis are used. By
#' default, it is NULl so all the concentrations are used.
#' @param statistic A character or NULL. It indicates the statistics printed
#' in the plot while there are replicates in input data. Available values are:
#' \itemize{
#' \item \strong{sem} Standard error of mean;
#' \item \strong{ci} 95\% confidence interval.
#' }
#' If it is \code{NULL}, no statistics will be printed. \strong{Note}: It only
#' works in Heatmap plot.
#' @param summary_statistic A vector of characters or NULL. It indicates the
#' summary statistics for all the \code{plot_value} in whole combination
#' matrix. Available values are:
#' \itemize{
#' \item \strong{mean} Median value for all the responses or synergy
#' scores in the matrix;
#' \item \strong{median} Median value for all the responses or synergy
#' scores in the matrix;
#' \item \strong{quantile_90} 90\% quantile. User could change the number to
#' print different sample quantile. For example quantile_50 equal to median.
#' }
#' If it is \code{NULL}, no statistics will be printed.
#' @param plot_title A character value. It specifies the plot title. If it is
#' \code{NULL}, the function will automatically generate a title.
#' @param interpolate_len An integer. It specifies how many values need to be
#' interpolated between two concentrations. It is used to control the
#' smoothness of the synergy surface in the contour plot and surface plot.
#' \strong{Note}: It only works in 2D and 3D plots.
#' @param high_value_color An R color value. It indicates the color for the
#' high values.
#' @param low_value_color An R color value. It indicates the color for low
#' values.
#' @param text_size_scale A numeric value. It is used to control the size
#' of text in the plot. All the text size will multiply by this scale factor.
#' @param heatmap_text_label_size_scale A numeric value. It is used to control
#' the size of text labels in the heatmap plot. It only works while
#' \code{plot_type = "heatmap"}.
#' @param heatmap_text_label_color NULL or an R color value. It is used to
#' control the color of text labels in the heatmap plot. If it is \code{NULL},
#' text label will not be shown. It only works while
#' \code{plot_type = "heatmap"}.
#' @param surface_grid A logical value. It indicates whether to add grids on the
#' surface. It only works while \code{plot_type = "3D"}.
#' @param dynamic A logic value. It indicates whether to generate interactive
#' plot wit package "plotly" or static plot with package "ggplot2"/"lattice".
#' @param display A logic value. It specifies whether to automatically display
#' plots while calling the function.
#' @param save_file A logic value. It specifies if the interaction landscapes
#' is saved by calling \link[ggplot2]{ggsave} function ("2D" or "heatmap"
#' plots) or plot saving function defined by \code{device} ("3D" plots). By
#' default, it is FALSE. \strong{Note}: It doesn't work while
#' \code{dynamic = TRUE}, because installation of "Orca" is required for
#' exporting plotly plots. Please check
#' https://plotly.com/r/static-image-export/ for more details.
#' @param file_name A character vector. It indicates the file names. If it is
#' not defined by user, a default name will be assigned. \strong{Note}: It
#' only works while \code{save_file = TRUE}.
#' @param file_path A character vector. It indicates the path to save file.
#' If it is not defined by user, a default name will be assigned.
#' \strong{Note}: It only works while \code{save_file = TRUE}.
#' @param width A numeric value. It indicates the width of the output plot.
#' \strong{Note}: It only works while \code{save_file = TRUE}.
#' @param height A numeric value. It indicates the height of the output plot.
#' \strong{Note}: It only works while \code{save_file = TRUE}.
#' @param units A character value. It indicates the units for \code{width} and
#' \code{height} for saved plots. It is used to set the \code{units}
#' parameter in function \link[ggplot2]{ggsave} or the function selected by
#' \code{device} (It will not work on "pdf" and "svg" devices. There units
#' are always in inch.). \strong{Note}: It only works while
#' \code{save_file = TRUE}.
#' @param device A character value. It indicates the device to use for saving
#' plots. If \code{type = "3D"}, the corresponding device function in package
#' "grDevices" will be called to save the plots. If
#' \code{type = "2D"/"heatmap"}, it will be used to set the parameter
#' \code{device} in function \link[ggplot2]{ggsave}.
#' \strong{Note}: It only works while \code{save_file = TRUE}.
#'
#' @return A list of ggplot objects.
#'
#' @author
#' \itemize{
#' \item Liye He \email{liye.he@helsinki.fi},
#' \item Shuyu Zheng \email{shuyu.zheng@helsinki.fi}
#' }
#'
#' @export
#'
#' @examples
#' data("mathews_screening_data")
#' data <- ReshapeData(mathews_screening_data)
#' data <- CalculateSynergy(data)
#' plots <- PlotSynergy(data, "2D", block_ids = NULL)
PlotSynergy <- function(data,
type = "2D",
method = "ZIP",
block_ids = c(1),
drugs = c(1, 2),
row_range = NULL,
col_range = NULL,
statistic = NULL,
summary_statistic = "mean",
plot_title = NULL,
interpolate_len = 3,
high_value_color = "#A90217",
low_value_color = "#2166AC",
text_size_scale = 1,
heatmap_text_label_size_scale = 1,
heatmap_text_label_color = "#000000",
surface_grid = TRUE,
dynamic = FALSE,
display = TRUE,
save_file = FALSE,
file_name = NULL,
file_path = NULL,
height = 6,
width = 6,
units = "in",
device = "pdf") {
# Check input data
if (!is.list(data)) {
stop("Input data is not a list format!")
}
if(is.null(block_ids)) {
block_ids <- unique(data$drug_pairs$block_id)
}
# Container for plots
plots <- vector(mode = "list", length = length(block_ids))
names(plots) <- block_ids
i <- 1
for (block in block_ids) {
drug_pair <- data$drug_pairs[data$drug_pairs$block_id == block, ]
if (type == "2D") {
fig <- Plot2DrugContour(
data = data,
plot_block = block,
drugs = drugs,
dynamic = dynamic,
plot_value = paste0(method, "_synergy"),
summary_statistic = summary_statistic,
plot_title = plot_title,
interpolate_len = interpolate_len,
high_value_color = high_value_color,
low_value_color = low_value_color,
row_range = row_range,
col_range = col_range,
text_size_scale = text_size_scale)
if (display) {
fig
}
} else if (type == "heatmap") {
fig <- Plot2DrugHeatmap(
data = data,
plot_block = block,
drugs = drugs,
statistic = statistic,
dynamic = dynamic,
plot_value = paste0(method, "_synergy"),
summary_statistic = summary_statistic,
plot_title = plot_title,
high_value_color = high_value_color,
low_value_color = low_value_color,
row_range = row_range,
col_range = col_range,
title_text_size_scale = text_size_scale,
text_label_size_scale = heatmap_text_label_size_scale,
text_label_color = heatmap_text_label_color)
if (display) {
fig
}
} else if (type == "3D") {
fig <- Plot2DrugSurface(
data = data,
plot_block = block,
drugs = drugs,
interpolate_len = interpolate_len,
dynamic = dynamic,
plot_value = paste0(method, "_synergy"),
summary_statistic = summary_statistic,
plot_title = plot_title,
high_value_color = high_value_color,
low_value_color = low_value_color,
row_range = row_range,
col_range = col_range,
grid = surface_grid,
text_size_scale = text_size_scale)
if (display) {
if (dynamic) {
fig
} else {
print(fig)
}
}
} else {
stop("The type of plot '", type, "' is not available. Available values
for parameter 'type' are: 2D, 3D, or heatmap.")
}
plots[[block]] <- fig
# Save plots
if(save_file) {
if (dynamic) {
warning("Saving dynamic surface plot from plotly requires installation",
" of Orca. This function can not save such plot as static ",
"images, but return the plotly object.",
"Please check https://plotly.com/r/static-image-export/ to see",
"how to export plotly plot objects to local directory.")
} else {
if (is.null(file_name)) {
file <-paste(
c(drug_pair[, paste0("drug", drugs)],
"synergy",
block,
method,
type),
collapse = "_"
)
} else {
file <- file_name[i]
i <- i + 1
}
# Set width and height according to plot types
if (type == "3D") {
if (!device %in% c("jpeg", "bmp", "png", "tiff", "pdf", "svg")){
warning("Can not save plot in ", device, " format. Avaliable formats
are 'svg', 'jpeg', 'bmp', 'png', 'tiff',and 'pdf'.")
} else if (device == "pdf") {
grDevices::pdf(paste(file, device, sep = "."),
width = width, height = height)
} else if (device == "svg") {
grDevices::svg(
paste(file, device, sep = "."),
width = width,
height = height)
} else {
do.call(
device,
args = list(
filename = paste(file, device, sep="."),
width = width,
height = height,
units = units,
res = 600)
)
}
grDevices::replayPlot(fig)
grDevices::dev.off()
} else {
ggplot2::ggsave(
filename = paste(file, device, sep="."),
plot = plots[[block]],
path = file_path,
width = width,
height = height,
device = device,
units = units
)
}
}
}
}
return(plots)
}
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