R/ploteachexp.R
In volkmannp/ntbgraphics: Visualization of NTB Data
Defines functions
ploteachexp
Documented in
ploteachexp
#' @title Plot single NTB experiments
#'
#' @author Paul Volkmann
#'
#' @name ploteachexp
#'
#' @description A function that takes experiments (columns) of an NTB dataset
#' and visualizes the data as customized boxplots. Requires function 'getexpdata' internally.
#' For right formatting of your files, please consider the "ReadMe for ntbgraphics".
#'
#' @param expname name of an experiment respectively column in dataframe of the NTB dataset to be analyzed
#' within quotation marks;
#' no default
#' @param directory specifies file directory of 'Meta Behavior' and 'Animal List' files within quotation
#' marks (mind correct spelling of both files and 'directory'!);
#' no default
#' @param analysis specifies the kind of experiment performed within quotation marks;
#' "2arm_ko","2arm_tg", "2arm_sd", "2arm_treat",
#' "4arm_sd_ko", "4arm_sd_tg", "4arm_treat_ko", "4arm_treat_tg"
#' (tg for transgenic, ko for knockout;
#' 4arm_sd_x assumes a stress paradigm with social defeat (sd) and housing or handling control (hc) as
#' control;
#' 4arm_treat_x assumes a treatment paradigm with treated (treat) and untreated (untreat) animals;
#' 2arm_x assumes wildtype controls (wt) for tg and ko, housing or handling controls (hc) for sd and
#' untreated controls (untreat) for treated animals;
#' ('analysis' defines the kind of experiment performed, respectively the kind of analysis preferred -
#' you can easily perform 2arm analysis for 4arm experiments looking only at the groups of interest,
#' but not the other way around);
#' default: "2arm_ko"
#' @param exclude.animals excluding animals from analysis by RFID;
#' user has to provide a vector containing characters within quotation marks (e.g. by using
#' c("900200000067229", "900200000065167")) with all animals he wants to exclude from the final plotting;
#' if FALSE is provided, no animal will be excluded;
#' default: FALSE
#' @param orderlevelcond defines order of boxplots in plot within quotation marks:
#' "other", "gtblock", "etblock", "2rev";
#' "other" for alphabetical order in case of 4arm; also for default order of 2arm experiments
#' (which displays the 'control' first, then the 'condition');
#' "gtblock" for order wt_x, wt_y, tg_x, tg_y;
#' "etblock" for order x_hc, y_hc, x_sd, y_sd;
#' "2rev" for inverse order of 2arm default only, meaning displaying the 'condition' first, then the
#' 'control';
#' default: "other"
#' @param acceptable.nas defines the maximum number of NAs allowed within the same row;
#' if number of actual NAs within one row is bigger than the number provided, the row will be excluded from
#' table and following plotting;
#' if the number of acceptable NAs should be unlimited, no value has to be provided;
#' default: "unlimited"
#' @param saveplotdir file directory where to save plots within quotation marks;
#' you may set to FALSE if you do not want to save plot to PDF;
#' default: location of Behavior and Animal List files as specified in 'directory'
#'
#' @return boxplot, optionally saved as PDF
#'
#' @export
#'
#' @examples ploteachexp(expname = "Meanspeed",
#' directory = paste0(system.file("extdata", package = "ntbgraphics", mustWork = T),"/"))
#'
#' @examples ploteachexp(expname = "Center",
#' directory = paste0(system.file("extdata", package = "ntbgraphics", mustWork = T),"/"),
#' analysis = "4arm_sd_tg",
#' exclude.animals = c("900200000068816"),
#' orderlevelcond = "etblock",
#' acceptable.nas = 4,
#' saveplotdir = paste0(system.file("../plots", package = "ntbgraphics", mustWork = T),"/"))
ploteachexp <- function(expname,
directory,
analysis = c("2arm_ko","2arm_tg", "2arm_sd", "2arm_treat",
"4arm_sd_ko", "4arm_sd_tg", "4arm_treat_ko", "4arm_treat_tg"),
exclude.animals = FALSE,
orderlevelcond = c("other", "gtblock", "etblock", "2rev"),
acceptable.nas = "unlimited",
saveplotdir = directory) {
# turn warnings off
options(warn=-1)
# check if expname is provided
if (missing(expname)) {
stop("Please provide expname!")
}
# check if saveplotdir exists
if (saveplotdir != FALSE && dir.exists(saveplotdir) == FALSE) {
stop(sprintf("The path for saving the plot as specified in saveplotdir `%s` does not exist!",
saveplotdir))
}
# ensure that in case of no provided argument, first one of list is taken
analysis <- analysis[1]
orderlevelcond <- orderlevelcond[1]
# get data
data.animal.joined <- getexpdata(directory, analysis = analysis, ordercolumns = "ntb", exclude.animals,
orderlevelcond = orderlevelcond, acceptable.nas = acceptable.nas,
return.matrix = F)
# check if expname exists in files provided
col.names.expname <- colnames(data.animal.joined)
if (expname %in% col.names.expname != TRUE) {
stop(sprintf("The expname `%s` does not exist within the provided Meta Behavior!",
expname))
}
# define axis limits
ymin = min(data.animal.joined[[expname]], na.rm = TRUE)*0.25
ymax = max(data.animal.joined[[expname]], na.rm = TRUE)*1.25
# plotting
outplot <- ggplot(data.animal.joined, aes_string(x="Condition", y=expname, fill="Condition"))
# boxplot with transparent filling
outplot <- outplot + geom_boxplot(alpha = 0.4) +
# choose colors (GT first, than other factors)
`if`(analysis == "4arm_sd_tg" && orderlevelcond == "gtblock",
scale_fill_manual(values=c("#b4b4b4", "#3c3c3c", "#00BFFF", "#1e24fc"))) +
`if`(analysis == "4arm_sd_tg" && orderlevelcond == "gtblock",
scale_color_manual(values=c("#b4b4b4", "#3c3c3c", "#00BFFF", "#1e24fc"))) +
`if`(analysis == "4arm_sd_ko" && orderlevelcond == "gtblock",
scale_fill_manual(values=c("#b4b4b4", "#3c3c3c", "#00BFFF", "#1e24fc"))) +
`if`(analysis == "4arm_sd_ko" && orderlevelcond == "gtblock",
scale_color_manual(values=c("#b4b4b4", "#3c3c3c", "#00BFFF", "#1e24fc"))) +
`if`(analysis == "4arm_treat_tg" && orderlevelcond == "gtblock",
scale_fill_manual(values=c("#b4b4b4", "#3c3c3c", "#00BFFF", "#1e24fc"))) +
`if`(analysis == "4arm_treat_tg" && orderlevelcond == "gtblock",
scale_color_manual(values=c("#b4b4b4", "#3c3c3c", "#00BFFF", "#1e24fc"))) +
`if`(analysis == "4arm_treat_ko" && orderlevelcond == "gtblock",
scale_fill_manual(values=c("#b4b4b4", "#3c3c3c", "#00BFFF", "#1e24fc"))) +
`if`(analysis == "4arm_treat_ko" && orderlevelcond == "gtblock",
scale_color_manual(values=c("#b4b4b4", "#3c3c3c", "#00BFFF", "#1e24fc"))) +
# choose colors (Condition first, than other factors)
`if`(analysis == "4arm_sd_tg" && orderlevelcond == "etblock",
scale_fill_manual(values=c("#b4b4b4", "#00BFFF", "#3c3c3c", "#1e24fc"))) +
`if`(analysis == "4arm_sd_tg" && orderlevelcond == "etblock",
scale_color_manual(values=c("#b4b4b4", "#00BFFF", "#3c3c3c", "#1e24fc"))) +
`if`(analysis == "4arm_sd_ko" && orderlevelcond == "etblock",
scale_fill_manual(values=c("#b4b4b4", "#00BFFF", "#3c3c3c", "#1e24fc"))) +
`if`(analysis == "4arm_sd_ko" && orderlevelcond == "etblock",
scale_color_manual(values=c("#b4b4b4", "#00BFFF", "#3c3c3c", "#1e24fc"))) +
`if`(analysis == "4arm_treat_tg" && orderlevelcond == "etblock",
scale_fill_manual(values=c("#b4b4b4", "#00BFFF", "#3c3c3c", "#1e24fc"))) +
`if`(analysis == "4arm_treat_tg" && orderlevelcond == "etblock",
scale_color_manual(values=c("#b4b4b4", "#00BFFF", "#3c3c3c", "#1e24fc"))) +
`if`(analysis == "4arm_treat_ko" && orderlevelcond == "etblock",
scale_fill_manual(values=c("#b4b4b4", "#00BFFF", "#3c3c3c", "#1e24fc"))) +
`if`(analysis == "4arm_treat_ko" && orderlevelcond == "etblock",
scale_color_manual(values=c("#b4b4b4", "#00BFFF", "#3c3c3c", "#1e24fc"))) +
# choose colors (alphabetical)
`if`(analysis == "4arm_sd_tg" && orderlevelcond == "other",
scale_fill_manual(values=c("#00BFFF", "#1e24fc", "#b4b4b4", "#3c3c3c"))) +
`if`(analysis == "4arm_sd_tg" && orderlevelcond == "other",
scale_color_manual(values=c("#00BFFF", "#1e24fc", "#b4b4b4", "#3c3c3c"))) +
`if`(analysis == "4arm_sd_ko" && orderlevelcond == "other",
scale_fill_manual(values=c("#00BFFF", "#1e24fc", "#b4b4b4", "#3c3c3c"))) +
`if`(analysis == "4arm_sd_ko" && orderlevelcond == "other",
scale_color_manual(values=c("#00BFFF", "#1e24fc", "#b4b4b4", "#3c3c3c"))) +
`if`(analysis == "4arm_treat_tg" && orderlevelcond == "other",
scale_fill_manual(values=c("#00BFFF", "#1e24fc", "#b4b4b4", "#3c3c3c"))) +
`if`(analysis == "4arm_treat_tg" && orderlevelcond == "other",
scale_color_manual(values=c("#00BFFF", "#1e24fc", "#b4b4b4", "#3c3c3c"))) +
`if`(analysis == "4arm_treat_ko" && orderlevelcond == "other",
scale_fill_manual(values=c("#00BFFF", "#1e24fc", "#b4b4b4", "#3c3c3c"))) +
`if`(analysis == "4arm_treat_ko" && orderlevelcond == "other",
scale_color_manual(values=c("#00BFFF", "#1e24fc", "#b4b4b4", "#3c3c3c"))) +
# choose colors (alphabetical order first, than other factors)
`if`(analysis == "2arm_tg", scale_fill_manual(values=c("#3c3c3c", "#1e24fc"))) +
`if`(analysis == "2arm_tg", scale_color_manual(values=c("#3c3c3c", "#1e24fc"))) +
`if`(analysis =="2arm_ko", scale_fill_manual(values=c("#3c3c3c", "#1e24fc"))) +
`if`(analysis == "2arm_ko", scale_color_manual(values=c("#3c3c3c", "#1e24fc"))) +
`if`(analysis == "2arm_sd", scale_fill_manual(values=c("#3c3c3c", "#1e24fc"))) +
`if`(analysis == "2arm_sd", scale_color_manual(values=c("#3c3c3c", "#1e24fc"))) +
`if`(analysis =="2arm_treat", scale_fill_manual(values=c("#3c3c3c", "#1e24fc"))) +
`if`(analysis == "2arm_treat", scale_color_manual(values=c("#3c3c3c", "#1e24fc"))) +
# add data points
geom_point(pch = 21, stroke=1.3, position = position_jitterdodge()) +
# title of axes
ylab(paste0(expname, "Score")) +
xlab("Condition") +
# range of y-axis
coord_cartesian(ylim = c(ymin, ymax)) +
# asterisks for significance
`if`(analysis == "4arm_sd_tg" || analysis == "4arm_sd_ko" ||
analysis == "4arm_treat_tg" || analysis == "4arm_treat_ko",
geom_signif(test = "t.test",
comparisons = list(c(1, 2),
c(3, 4),
c(2, 3),
c(2, 4)),
y=c(0.85*ymax, 0.85*ymax, 0.89*ymax, 0.95*ymax),
map_signif_level = c("***"=0.001, "**"=0.01, "*"=0.05),
textsize = 5, tip_length = 0.005)) +
`if`(analysis == "2arm_tg" || analysis == "2arm_ko" ||
analysis == "2arm_sd" || analysis == "2arm_treat",
geom_signif(test = "t.test",
comparisons = list(c(1, 2)),
y=0.89*ymax,
map_signif_level = c("***"=0.001, "**"=0.01, "*"=0.05),
textsize = 5, tip_length = 0.005)) +
# customize title
ggtitle(expname) +
# choose theme for layout (theme_choose)
theme_bw() +
# customize title position and size
theme(plot.title = element_text(hjust = 0.5)) +
theme(plot.title = element_text(size = 35)) +
# all elements blank
theme(panel.grid.major = element_blank(),
panel.border = element_blank(),
panel.grid.minor = element_blank(),
legend.key = element_blank(),
strip.background = element_blank(),
# customize axes
axis.line.y = element_line(colour = "black", size=1),
axis.ticks.x = element_blank(),
axis.text.x = element_text(angle=0, size=21),
axis.text.y = element_text(angle=0, size=18),
text = element_text(size=27),
# customize legend
legend.text = element_text(size=20),
legend.title = element_text(size=27))
# save pdf
`if`(!(saveplotdir =="FALSE"), ggsave(filename = paste0(saveplotdir, "/", "Boxplot_", expname, ".pdf"),
width = 7,
height = 5))
# return plot
return(outplot)
# turn warnings back on
options(warn=0)
}
volkmannp/ntbgraphics documentation built on March 3, 2020, 1:25 p.m.
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Defines functions ploteachexp
Documented in ploteachexp
#' @title Plot single NTB experiments
#'
#' @author Paul Volkmann
#'
#' @name ploteachexp
#'
#' @description A function that takes experiments (columns) of an NTB dataset
#' and visualizes the data as customized boxplots. Requires function 'getexpdata' internally.
#' For right formatting of your files, please consider the "ReadMe for ntbgraphics".
#'
#' @param expname name of an experiment respectively column in dataframe of the NTB dataset to be analyzed
#' within quotation marks;
#' no default
#' @param directory specifies file directory of 'Meta Behavior' and 'Animal List' files within quotation
#' marks (mind correct spelling of both files and 'directory'!);
#' no default
#' @param analysis specifies the kind of experiment performed within quotation marks;
#' "2arm_ko","2arm_tg", "2arm_sd", "2arm_treat",
#' "4arm_sd_ko", "4arm_sd_tg", "4arm_treat_ko", "4arm_treat_tg"
#' (tg for transgenic, ko for knockout;
#' 4arm_sd_x assumes a stress paradigm with social defeat (sd) and housing or handling control (hc) as
#' control;
#' 4arm_treat_x assumes a treatment paradigm with treated (treat) and untreated (untreat) animals;
#' 2arm_x assumes wildtype controls (wt) for tg and ko, housing or handling controls (hc) for sd and
#' untreated controls (untreat) for treated animals;
#' ('analysis' defines the kind of experiment performed, respectively the kind of analysis preferred -
#' you can easily perform 2arm analysis for 4arm experiments looking only at the groups of interest,
#' but not the other way around);
#' default: "2arm_ko"
#' @param exclude.animals excluding animals from analysis by RFID;
#' user has to provide a vector containing characters within quotation marks (e.g. by using
#' c("900200000067229", "900200000065167")) with all animals he wants to exclude from the final plotting;
#' if FALSE is provided, no animal will be excluded;
#' default: FALSE
#' @param orderlevelcond defines order of boxplots in plot within quotation marks:
#' "other", "gtblock", "etblock", "2rev";
#' "other" for alphabetical order in case of 4arm; also for default order of 2arm experiments
#' (which displays the 'control' first, then the 'condition');
#' "gtblock" for order wt_x, wt_y, tg_x, tg_y;
#' "etblock" for order x_hc, y_hc, x_sd, y_sd;
#' "2rev" for inverse order of 2arm default only, meaning displaying the 'condition' first, then the
#' 'control';
#' default: "other"
#' @param acceptable.nas defines the maximum number of NAs allowed within the same row;
#' if number of actual NAs within one row is bigger than the number provided, the row will be excluded from
#' table and following plotting;
#' if the number of acceptable NAs should be unlimited, no value has to be provided;
#' default: "unlimited"
#' @param saveplotdir file directory where to save plots within quotation marks;
#' you may set to FALSE if you do not want to save plot to PDF;
#' default: location of Behavior and Animal List files as specified in 'directory'
#'
#' @return boxplot, optionally saved as PDF
#'
#' @export
#'
#' @examples ploteachexp(expname = "Meanspeed",
#' directory = paste0(system.file("extdata", package = "ntbgraphics", mustWork = T),"/"))
#'
#' @examples ploteachexp(expname = "Center",
#' directory = paste0(system.file("extdata", package = "ntbgraphics", mustWork = T),"/"),
#' analysis = "4arm_sd_tg",
#' exclude.animals = c("900200000068816"),
#' orderlevelcond = "etblock",
#' acceptable.nas = 4,
#' saveplotdir = paste0(system.file("../plots", package = "ntbgraphics", mustWork = T),"/"))
ploteachexp <- function(expname,
directory,
analysis = c("2arm_ko","2arm_tg", "2arm_sd", "2arm_treat",
"4arm_sd_ko", "4arm_sd_tg", "4arm_treat_ko", "4arm_treat_tg"),
exclude.animals = FALSE,
orderlevelcond = c("other", "gtblock", "etblock", "2rev"),
acceptable.nas = "unlimited",
saveplotdir = directory) {
# turn warnings off
options(warn=-1)
# check if expname is provided
if (missing(expname)) {
stop("Please provide expname!")
}
# check if saveplotdir exists
if (saveplotdir != FALSE && dir.exists(saveplotdir) == FALSE) {
stop(sprintf("The path for saving the plot as specified in saveplotdir `%s` does not exist!",
saveplotdir))
}
# ensure that in case of no provided argument, first one of list is taken
analysis <- analysis[1]
orderlevelcond <- orderlevelcond[1]
# get data
data.animal.joined <- getexpdata(directory, analysis = analysis, ordercolumns = "ntb", exclude.animals,
orderlevelcond = orderlevelcond, acceptable.nas = acceptable.nas,
return.matrix = F)
# check if expname exists in files provided
col.names.expname <- colnames(data.animal.joined)
if (expname %in% col.names.expname != TRUE) {
stop(sprintf("The expname `%s` does not exist within the provided Meta Behavior!",
expname))
}
# define axis limits
ymin = min(data.animal.joined[[expname]], na.rm = TRUE)*0.25
ymax = max(data.animal.joined[[expname]], na.rm = TRUE)*1.25
# plotting
outplot <- ggplot(data.animal.joined, aes_string(x="Condition", y=expname, fill="Condition"))
# boxplot with transparent filling
outplot <- outplot + geom_boxplot(alpha = 0.4) +
# choose colors (GT first, than other factors)
`if`(analysis == "4arm_sd_tg" && orderlevelcond == "gtblock",
scale_fill_manual(values=c("#b4b4b4", "#3c3c3c", "#00BFFF", "#1e24fc"))) +
`if`(analysis == "4arm_sd_tg" && orderlevelcond == "gtblock",
scale_color_manual(values=c("#b4b4b4", "#3c3c3c", "#00BFFF", "#1e24fc"))) +
`if`(analysis == "4arm_sd_ko" && orderlevelcond == "gtblock",
scale_fill_manual(values=c("#b4b4b4", "#3c3c3c", "#00BFFF", "#1e24fc"))) +
`if`(analysis == "4arm_sd_ko" && orderlevelcond == "gtblock",
scale_color_manual(values=c("#b4b4b4", "#3c3c3c", "#00BFFF", "#1e24fc"))) +
`if`(analysis == "4arm_treat_tg" && orderlevelcond == "gtblock",
scale_fill_manual(values=c("#b4b4b4", "#3c3c3c", "#00BFFF", "#1e24fc"))) +
`if`(analysis == "4arm_treat_tg" && orderlevelcond == "gtblock",
scale_color_manual(values=c("#b4b4b4", "#3c3c3c", "#00BFFF", "#1e24fc"))) +
`if`(analysis == "4arm_treat_ko" && orderlevelcond == "gtblock",
scale_fill_manual(values=c("#b4b4b4", "#3c3c3c", "#00BFFF", "#1e24fc"))) +
`if`(analysis == "4arm_treat_ko" && orderlevelcond == "gtblock",
scale_color_manual(values=c("#b4b4b4", "#3c3c3c", "#00BFFF", "#1e24fc"))) +
# choose colors (Condition first, than other factors)
`if`(analysis == "4arm_sd_tg" && orderlevelcond == "etblock",
scale_fill_manual(values=c("#b4b4b4", "#00BFFF", "#3c3c3c", "#1e24fc"))) +
`if`(analysis == "4arm_sd_tg" && orderlevelcond == "etblock",
scale_color_manual(values=c("#b4b4b4", "#00BFFF", "#3c3c3c", "#1e24fc"))) +
`if`(analysis == "4arm_sd_ko" && orderlevelcond == "etblock",
scale_fill_manual(values=c("#b4b4b4", "#00BFFF", "#3c3c3c", "#1e24fc"))) +
`if`(analysis == "4arm_sd_ko" && orderlevelcond == "etblock",
scale_color_manual(values=c("#b4b4b4", "#00BFFF", "#3c3c3c", "#1e24fc"))) +
`if`(analysis == "4arm_treat_tg" && orderlevelcond == "etblock",
scale_fill_manual(values=c("#b4b4b4", "#00BFFF", "#3c3c3c", "#1e24fc"))) +
`if`(analysis == "4arm_treat_tg" && orderlevelcond == "etblock",
scale_color_manual(values=c("#b4b4b4", "#00BFFF", "#3c3c3c", "#1e24fc"))) +
`if`(analysis == "4arm_treat_ko" && orderlevelcond == "etblock",
scale_fill_manual(values=c("#b4b4b4", "#00BFFF", "#3c3c3c", "#1e24fc"))) +
`if`(analysis == "4arm_treat_ko" && orderlevelcond == "etblock",
scale_color_manual(values=c("#b4b4b4", "#00BFFF", "#3c3c3c", "#1e24fc"))) +
# choose colors (alphabetical)
`if`(analysis == "4arm_sd_tg" && orderlevelcond == "other",
scale_fill_manual(values=c("#00BFFF", "#1e24fc", "#b4b4b4", "#3c3c3c"))) +
`if`(analysis == "4arm_sd_tg" && orderlevelcond == "other",
scale_color_manual(values=c("#00BFFF", "#1e24fc", "#b4b4b4", "#3c3c3c"))) +
`if`(analysis == "4arm_sd_ko" && orderlevelcond == "other",
scale_fill_manual(values=c("#00BFFF", "#1e24fc", "#b4b4b4", "#3c3c3c"))) +
`if`(analysis == "4arm_sd_ko" && orderlevelcond == "other",
scale_color_manual(values=c("#00BFFF", "#1e24fc", "#b4b4b4", "#3c3c3c"))) +
`if`(analysis == "4arm_treat_tg" && orderlevelcond == "other",
scale_fill_manual(values=c("#00BFFF", "#1e24fc", "#b4b4b4", "#3c3c3c"))) +
`if`(analysis == "4arm_treat_tg" && orderlevelcond == "other",
scale_color_manual(values=c("#00BFFF", "#1e24fc", "#b4b4b4", "#3c3c3c"))) +
`if`(analysis == "4arm_treat_ko" && orderlevelcond == "other",
scale_fill_manual(values=c("#00BFFF", "#1e24fc", "#b4b4b4", "#3c3c3c"))) +
`if`(analysis == "4arm_treat_ko" && orderlevelcond == "other",
scale_color_manual(values=c("#00BFFF", "#1e24fc", "#b4b4b4", "#3c3c3c"))) +
# choose colors (alphabetical order first, than other factors)
`if`(analysis == "2arm_tg", scale_fill_manual(values=c("#3c3c3c", "#1e24fc"))) +
`if`(analysis == "2arm_tg", scale_color_manual(values=c("#3c3c3c", "#1e24fc"))) +
`if`(analysis =="2arm_ko", scale_fill_manual(values=c("#3c3c3c", "#1e24fc"))) +
`if`(analysis == "2arm_ko", scale_color_manual(values=c("#3c3c3c", "#1e24fc"))) +
`if`(analysis == "2arm_sd", scale_fill_manual(values=c("#3c3c3c", "#1e24fc"))) +
`if`(analysis == "2arm_sd", scale_color_manual(values=c("#3c3c3c", "#1e24fc"))) +
`if`(analysis =="2arm_treat", scale_fill_manual(values=c("#3c3c3c", "#1e24fc"))) +
`if`(analysis == "2arm_treat", scale_color_manual(values=c("#3c3c3c", "#1e24fc"))) +
# add data points
geom_point(pch = 21, stroke=1.3, position = position_jitterdodge()) +
# title of axes
ylab(paste0(expname, "Score")) +
xlab("Condition") +
# range of y-axis
coord_cartesian(ylim = c(ymin, ymax)) +
# asterisks for significance
`if`(analysis == "4arm_sd_tg" || analysis == "4arm_sd_ko" ||
analysis == "4arm_treat_tg" || analysis == "4arm_treat_ko",
geom_signif(test = "t.test",
comparisons = list(c(1, 2),
c(3, 4),
c(2, 3),
c(2, 4)),
y=c(0.85*ymax, 0.85*ymax, 0.89*ymax, 0.95*ymax),
map_signif_level = c("***"=0.001, "**"=0.01, "*"=0.05),
textsize = 5, tip_length = 0.005)) +
`if`(analysis == "2arm_tg" || analysis == "2arm_ko" ||
analysis == "2arm_sd" || analysis == "2arm_treat",
geom_signif(test = "t.test",
comparisons = list(c(1, 2)),
y=0.89*ymax,
map_signif_level = c("***"=0.001, "**"=0.01, "*"=0.05),
textsize = 5, tip_length = 0.005)) +
# customize title
ggtitle(expname) +
# choose theme for layout (theme_choose)
theme_bw() +
# customize title position and size
theme(plot.title = element_text(hjust = 0.5)) +
theme(plot.title = element_text(size = 35)) +
# all elements blank
theme(panel.grid.major = element_blank(),
panel.border = element_blank(),
panel.grid.minor = element_blank(),
legend.key = element_blank(),
strip.background = element_blank(),
# customize axes
axis.line.y = element_line(colour = "black", size=1),
axis.ticks.x = element_blank(),
axis.text.x = element_text(angle=0, size=21),
axis.text.y = element_text(angle=0, size=18),
text = element_text(size=27),
# customize legend
legend.text = element_text(size=20),
legend.title = element_text(size=27))
# save pdf
`if`(!(saveplotdir =="FALSE"), ggsave(filename = paste0(saveplotdir, "/", "Boxplot_", expname, ".pdf"),
width = 7,
height = 5))
# return plot
return(outplot)
# turn warnings back on
options(warn=0)
}
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