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box_plot.R
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box_plot.R
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#' @title Box plot support two levels and multiple groups with P value.
#' @description Box plot support two levels and multiple groups with P value.
#' @author benben-miao
#'
#' @return Plot: box plot support two levels and multiple groups with P value.
#' @param data Dataframe: Length, Width, Weight, and Sex traits dataframe (1st-col: Value, 2nd-col: Traits, 3rd-col: Sex).
#' @param test_method Character: test methods of P value. Default: "t.test", options: "wilcox.test", "t.test", "anova", "kruskal.test".
#' @param test_label Character: test label of P value. Default: "p.format", options: "p.signif", "p.format". c(0, 0.0001, 0.001, 0.01, 0.05, 1).
#' @param notch Logical: Box notch or none. Default: TRUE, options: TRUE, FALSE.
#' @param group_level Character: group levels. Default: "Three_Column", options: "Two_Column", "Three_Column".
#' @param add_element Character: add new plot. Default: "jitter", options: "none", "dotplot", "jitter", "boxplot", "point", "mean", "mean_se", "mean_sd", "mean_ci", "mean_range", "median", "median_iqr", "median_hilow", "median_q1q3", "median_mad", "median_range".
#' @param my_shape Character: box scatter shape. Default: "fill_circle", options: "border_square", "border_circle", "border_triangle", "plus", "times", "border_diamond", "border_triangle_down", "square_times", "plus_times", "diamond_plus", "circle_plus", "di_triangle", "square_plus", "circle_times","square_triangle", "fill_square", "fill_circle", "fill_triangle", "fill_diamond", "large_circle", "small_circle", "fill_border_circle", "fill_border_square", "fill_border_diamond", "fill_border_triangle".
#' @param sci_fill_color Character: ggsci color pallet. Default: "Sci_AAAS", options: "Sci_AAAS", "Sci_NPG", "Sci_Simpsons", "Sci_JAMA", "Sci_GSEA", "Sci_Lancet", "Sci_Futurama", "Sci_JCO", "Sci_NEJM", "Sci_IGV", "Sci_UCSC", "Sci_D3", "Sci_Material".
#' @param sci_fill_alpha Numeric: ggsci fill color alpha. Default: 0.50, min: 0.00, max: 1.00.
#' @param sci_color_alpha Numeric: ggsci border color alpha. Default: 1.00, min: 0.00, max: 1.00.
#' @param legend_pos Character: legend position. Default: "right", options: "none", "left", "right", "bottom", "top".
#' @param legend_dir Character: legend direction. Default: "vertical", options: "horizontal", "vertical".
#' @param ggTheme Character: ggplot2 themes. Default: "theme_light", options: "theme_default", "theme_bw", "theme_gray", "theme_light", "theme_linedraw", "theme_dark", "theme_minimal", "theme_classic", "theme_void"
#'
#' @import ggplot2
#' @import ggsci
#' @importFrom ggpubr ggboxplot stat_compare_means
#' @importFrom utils combn
#' @export
#'
#' @examples
#' # 1. Library TOmicsVis package
#' library(TOmicsVis)
#'
#' # 2. Use example dataset
#' data(traits_sex)
#' head(traits_sex)
#'
#' # 3. Default parameters
#' box_plot(traits_sex)
#'
#' # 4. Set test_label = "p.signif",
#' box_plot(traits_sex, test_label = "p.signif")
#'
#' # 5. Set notch = FALSE
#' box_plot(traits_sex, notch = FALSE)
#'
#' # 6. Set group_level = "Two_Column"
#' box_plot(traits_sex, group_level = "Two_Column")
#'
#' # 7. Set add_element = "point"
#' box_plot(traits_sex, add_element = "point")
#'
box_plot <- function(data,
test_method = "t.test",
test_label = "p.format",
notch = TRUE,
group_level = "Three_Column",
add_element = "jitter",
my_shape = "fill_circle",
sci_fill_color = "Sci_AAAS",
sci_fill_alpha = 0.50,
sci_color_alpha = 1.00,
legend_pos = "right",
legend_dir = "vertical",
ggTheme = "theme_light"
){
# -> 2. Data Operation
# set.seed(123)
# wdata = data.frame(
# sex = factor(rep(c("F", "M"), each=200)),
# weight = c(rnorm(200, 55), rnorm(200, 58)))
# <- 2. Data Operation
# -> 3. Plot Parameters
# fonts <- "Times"
# ChoiceBox: "Times", "Palatino", "Bookman", "Courier", "Helvetica", "URWGothic", "NimbusMon", "NimbusSan"
# ggTheme <- "theme_light"
# ChoiceBox: "theme_default", "theme_bw", "theme_gray", "theme_light", "theme_linedraw", "theme_dark", "theme_minimal", "theme_classic", "theme_void"
if (ggTheme == "theme_default") {
gg_theme <- theme()
} else if (ggTheme == "theme_bw") {
gg_theme <- theme_bw()
} else if (ggTheme == "theme_gray") {
gg_theme <- theme_gray()
} else if (ggTheme == "theme_light") {
gg_theme <- theme_light()
} else if (ggTheme == "theme_linedraw") {
gg_theme <- theme_linedraw()
} else if (ggTheme == "theme_dark") {
gg_theme <- theme_dark()
} else if (ggTheme == "theme_minimal") {
gg_theme <- theme_minimal()
} else if (ggTheme == "theme_classic") {
gg_theme <- theme_classic()
} else if (ggTheme == "theme_void") {
gg_theme <- theme_void()
} else if (ggTheme == "theme_test") {
gg_theme <- theme_test()
}
# sci_fill_alpha <- 0.5
# sci_color_alpha <- 1.00
# sci_fill_color <- "Sci_AAAS"
# ChoiceBox: "Sci_AAAS", "Sci_NPG", "Sci_Simpsons", "Sci_JAMA", "Sci_GSEA", "Sci_Lancet", "Sci_Futurama", "Sci_JCO", "Sci_NEJM", "Sci_IGV", "Sci_UCSC", "Sci_D3", "Sci_Material"
if (sci_fill_color == "Default") {
sci_fill <- NULL
sci_color <- NULL
} else if (sci_fill_color == "Sci_AAAS") {
sci_fill <- scale_fill_aaas(alpha = sci_fill_alpha)
sci_color <- scale_color_aaas(alpha = sci_color_alpha)
# Science and Science Translational Medicine:
} else if (sci_fill_color == "Sci_NPG") {
sci_fill <- scale_fill_npg(alpha = sci_fill_alpha)
sci_color <- scale_color_npg(alpha = sci_color_alpha)
} else if (sci_fill_color == "Sci_Simpsons") {
sci_fill <- scale_fill_simpsons(alpha = sci_fill_alpha)
sci_color <- scale_color_simpsons(alpha = sci_color_alpha)
# The Simpsons
} else if (sci_fill_color == "Sci_JAMA") {
sci_fill <- scale_fill_jama(alpha = sci_fill_alpha)
sci_color <- scale_color_jama(alpha = sci_color_alpha)
# The Journal of the American Medical Association
} else if (sci_fill_color == "Sci_Lancet") {
sci_fill <- scale_fill_lancet(alpha = sci_fill_alpha)
sci_color <- scale_color_lancet(alpha = sci_color_alpha)
# Lancet Oncology
} else if (sci_fill_color == "Sci_Futurama") {
sci_fill <- scale_fill_futurama(alpha = sci_fill_alpha)
sci_color <- scale_color_futurama(alpha = sci_color_alpha)
# Futurama
} else if (sci_fill_color == "Sci_JCO") {
sci_fill <- scale_fill_jco(alpha = sci_fill_alpha)
sci_color <- scale_color_jco(alpha = sci_color_alpha)
# Journal of Clinical Oncology:
} else if (sci_fill_color == "Sci_NEJM") {
sci_fill <- scale_fill_nejm(alpha = sci_fill_alpha)
sci_color <- scale_color_nejm(alpha = sci_color_alpha)
# The New England Journal of Medicine
} else if (sci_fill_color == "Sci_IGV") {
sci_fill <- scale_fill_igv(alpha = sci_fill_alpha)
sci_color <- scale_color_igv(alpha = sci_color_alpha)
# Integrative Genomics Viewer (IGV)
} else if (sci_fill_color == "Sci_UCSC") {
sci_fill <- scale_fill_ucscgb(alpha = sci_fill_alpha)
sci_color <- scale_color_ucscgb(alpha = sci_color_alpha)
# UCSC Genome Browser chromosome sci_fill
} else if (sci_fill_color == "Sci_D3") {
sci_fill <- scale_fill_d3(alpha = sci_fill_alpha)
sci_color <- scale_color_d3(alpha = sci_color_alpha)
# D3.JS
} else if (sci_fill_color == "Sci_Material") {
sci_fill <- scale_fill_material(alpha = sci_fill_alpha)
sci_color <- scale_color_material(alpha = sci_color_alpha)
# The Material Design color palettes
}
# my_shape <- "fill_circle"
# ChoiceBox: "border_square", "border_circle", "border_triangle", "plus", "times", "border_diamond", "border_triangle_down", "square_times", "plus_times", "diamond_plus", "circle_plus", "di_triangle", "square_plus", "circle_times","square_triangle", "fill_square", "fill_circle", "fill_triangle", "fill_diamond", "large_circle", "small_circle", "fill_border_circle", "fill_border_square", "fill_border_diamond", "fill_border_triangle"
if (my_shape == "border_square") {
shape <- 0
} else if (my_shape == "border_circle") {
shape <- 1
} else if (my_shape == "border_triangle") {
shape <- 2
} else if (my_shape == "plus") {
shape <- 3
} else if (my_shape == "times") {
shape <- 4
} else if (my_shape == "border_diamond") {
shape <- 5
} else if (my_shape == "border_triangle_down") {
shape <- 6
} else if (my_shape == "square_times") {
shape <- 7
} else if (my_shape == "plus_times") {
shape <- 8
} else if (my_shape == "diamond_plus") {
shape <- 9
} else if (my_shape == "circle_plus") {
shape <- 10
} else if (my_shape == "di_triangle") {
shape <- 11
} else if (my_shape == "square_plus") {
shape <- 12
} else if (my_shape == "circle_times") {
shape <- 13
} else if (my_shape == "square_triangle") {
shape <- 14
} else if (my_shape == "fill_square") {
shape <- 15
} else if (my_shape == "fill_circle") {
shape <- 16
} else if (my_shape == "fill_triangle") {
shape <- 17
} else if (my_shape == "fill_diamond") {
shape <- 18
} else if (my_shape == "large_circle") {
shape <- 19
} else if (my_shape == "small_circle") {
shape <- 20
} else if (my_shape == "fill_border_circle") {
shape <- 21
} else if (my_shape == "fill_border_square") {
shape <- 22
} else if (my_shape == "fill_border_diamond") {
shape <- 23
} else if (my_shape == "fill_border_triangle") {
shape <- 24
}
# title <- "BoxPlot with Test"
# TextField
xlab <- colnames(data)[2]
ylab <- colnames(data)[1]
# group_level <- "Three_Column"
# ChoiceBox: "Two_Column", "Three_Column"
lineType <- "solid"
# ChoiceBox: "blank", "solid", "dashed", "dotted", "dotdash", "longdash", "twodash"
lineSize <- 1.0
# ChoiceBox: 1.0, 0.0, 10.0, 0.1
boxWidth <- 0.8
# Slider: 0.8, 0.0, 1.0, 0.1
# boxNotch <- "Notch_Show"
# # ChoiceBox: "Notch_Show", "Notch_Hidden"
# if (boxNotch == "Notch_Show") {
# notch <- TRUE
# } else if (boxNotch == "Notch_Hidden") {
# notch <- FALSE
# }
# add_element <- "dotplot"
# ChoiceBox: "none", "dotplot", "jitter", "boxplot", "point", "mean", "mean_se", "mean_sd", "mean_ci", "mean_range", "median", "median_iqr", "median_hilow", "median_q1q3", "median_mad", "median_range"
boxError <- "errorbar"
# ChoiceBox: "pointrange", "linerange", "crossbar", "errorbar", "upper_errorbar", "lower_errorbar", "upper_pointrange", "lower_pointrange", "upper_linerange", "lower_linerange"
# test_method <- "wilcox.test"
# ChoiceBox: "wilcox.test", "t.test", "anova", "kruskal.test"
nsShow <- "NS_Show"
# ChoiceBox: "NS_Show", "NS_Hidden"
if (nsShow == "NS_Show") {
hide_ns <- FALSE
} else if (nsShow == "NS_Hidden") {
hide_ns <- TRUE
}
# test_label <- "p.format"
# ChoiceBox: "p.signif", "p.format"
bracketSize <- 1.0
# Slider: 1.0, 0.0, 10.0, 0.1
plotTitleFace <- "bold"
# ChoiceBox: "plain", "italic", "bold", "bold.italic"
plotTitleSize <- 18
# Slider: 18, 0, 50, 1
plotTitleHjust <- 0.5
# Slider: 0.5, 0.0, 1.0, 0.1
axisTitleFace <- "plain"
# ChoiceBox: "plain", "italic", "bold", "bold.italic"
axisTitleSize <- 16
# Slider: 16, 0, 50, 1
axisTextSize <- 10
# Slider: 10, 0, 50, 1
legendTitleSize <- 12
# Slider: 12, 0, 50, 1
# legend_pos <- "right"
# ChoiceBox: "none", "left", "right", "bottom", "top"
# legend_dir <- "vertical"
# ChoiceBox: "horizontal", "vertical"
groups <- unique(data[[2]])
my_comparisons <- combn(groups, 2, simplify = FALSE)
my_comparisons <- lapply(my_comparisons, as.character)
symnum_args <- list(cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05, 1),
symbols = c("****", "***", "**", "*", "ns"))
# <- 3. Plot Parameters
# # -> 4. Plot
if (group_level == "Two_Column") {
p <- ggboxplot(data,
x = colnames(data)[2],
y = colnames(data)[1],
combine = FALSE,
merge = FALSE,
color = colnames(data)[2],
fill = colnames(data)[2],
# title = title,
xlab = xlab,
ylab = ylab,
bxp.errorbar = FALSE,
bxp.errorbar.width = 0.3,
# facet.by = colnames(data)[3],
# panel.labs = NULL,
# short.panel.labs = FALSE,
linetype = lineType,
# "blank", "solid", "dashed", "dotted", "dotdash", "longdash", "twodash"
size = lineSize, # Numeric value (e.g.: size = 1). change the size of points and outlines
width = boxWidth, # numeric value between 0 and 1 specifying box width
notch = notch,
add = add_element,
# "none", "dotplot", "jitter", "boxplot", "point", "mean", "mean_se", "mean_sd", "mean_ci", "mean_range", "median", "median_iqr", "median_hilow", "median_q1q3", "median_mad", "median_range"
outlier.shape = shape,
error.plot = boxError
# "pointrange", "linerange", "crossbar", "errorbar", "upper_errorbar", "lower_errorbar", "upper_pointrange", "lower_pointrange", "upper_linerange", "lower_linerange"
) +
stat_compare_means(
comparisons = my_comparisons,
method = test_method, # "wilcox.test", "t.test", "anova", "kruskal.test"
hide.ns = hide_ns,
label = test_label, # "p.signif", "p.format"
tip.length = 0.03,
bracket.size = bracketSize,
# symnum.args = symnum_args,
show.legend = FALSE
) +
sci_color +
sci_fill +
gg_theme +
theme(plot.title = element_text(face = plotTitleFace,
# "plain", "italic", "bold", "bold.italic"
size = plotTitleSize,
hjust = plotTitleHjust
),
axis.title = element_text(face = axisTitleFace,
# "plain", "italic", "bold", "bold.italic"
size = axisTitleSize
),
axis.text = element_text(face = "plain",
size = axisTextSize
),
legend.title = element_text(face = "plain",
size = legendTitleSize
),
legend.position = legend_pos,
# "none", "left", "right", "bottom", "top"
legend.direction = legend_dir,
# "horizontal" or "vertical"
strip.background = element_rect(fill = "#cdcdcd", color = "#cdcdcd"),
strip.text = element_text(color = "#333333", size = 10, face = "bold")
)
} else if (group_level == "Three_Column") {
p <- ggboxplot(data,
x = colnames(data)[2],
y = colnames(data)[1],
combine = FALSE,
merge = FALSE,
color = colnames(data)[2],
fill = colnames(data)[2],
# title = title,
xlab = xlab,
ylab = ylab,
bxp.errorbar = FALSE,
bxp.errorbar.width = 0.3,
facet.by = colnames(data)[3],
panel.labs = NULL,
short.panel.labs = FALSE,
linetype = lineType,
# "blank", "solid", "dashed", "dotted", "dotdash", "longdash", "twodash"
size = lineSize, # Numeric value (e.g.: size = 1). change the size of points and outlines
width = boxWidth, # numeric value between 0 and 1 specifying box width
notch = notch,
add = add_element,
# "none", "dotplot", "jitter", "boxplot", "point", "mean", "mean_se", "mean_sd", "mean_ci", "mean_range", "median", "median_iqr", "median_hilow", "median_q1q3", "median_mad", "median_range"
outlier.shape = shape,
error.plot = boxError
# "pointrange", "linerange", "crossbar", "errorbar", "upper_errorbar", "lower_errorbar", "upper_pointrange", "lower_pointrange", "upper_linerange", "lower_linerange"
) +
stat_compare_means(
comparisons = my_comparisons,
method = test_method, # "wilcox.test", "t.test", "anova", "kruskal.test"
hide.ns = hide_ns,
label = test_label, # "p.signif", "p.format"
tip.length = 0.03,
bracket.size = bracketSize,
# symnum.args = symnum_args,
show.legend = FALSE
) +
sci_color +
sci_fill +
gg_theme +
theme(plot.title = element_text(face = plotTitleFace,
# "plain", "italic", "bold", "bold.italic"
size = plotTitleSize,
hjust = plotTitleHjust
),
axis.title = element_text(face = axisTitleFace,
# "plain", "italic", "bold", "bold.italic"
size = axisTitleSize
),
axis.text = element_text(face = "plain",
size = axisTextSize
),
legend.title = element_text(face = "plain",
size = legendTitleSize
),
legend.position = legend_pos,
# "none", "left", "right", "bottom", "top"
legend.direction = legend_dir,
# "horizontal" or "vertical"
strip.background = element_rect(fill = "#cdcdcd", color = "#cdcdcd"),
strip.text = element_text(color = "#333333", size = 10, face = "bold")
)
}
# # <- 4. Plot
return(p)
invisible()
}