R/jjpiestats.b.R
In sbalci/ClinicoPathJamoviModule: Analysis for Clinicopathological Research
#' @title Pie Charts
#' @importFrom R6 R6Class
#' @import jmvcore
#'
jjpiestatsClass <- if (requireNamespace('jmvcore')) R6::R6Class(
"jjpiestatsClass",
inherit = jjpiestatsBase,
private = list(
# init ----
.init = function() {
self$results$plot1$setSize(650, 450)
self$results$plot2$setSize(650, 450)
# if (!is.null(self$options$dep) && !is.null(self$options$grvar)) {
#
# mydata <- self$data
#
# grvar <- self$options$grvar
#
# num_levels <- nlevels(
# as.factor(mydata[[grvar]])
# )
#
# self$results$plot3$setSize(num_levels * 600, 450)
#
# }
if (!is.null(self$options$grvar) && !is.null(self$options$group)) {
mydata <- self$data
group <- self$options$group
num_levels_group <- nlevels(
as.factor(mydata[[group]])
)
self$results$plot4$setSize(num_levels_group * 600, 450)
}
if (!is.null(self$options$group) && !is.null(self$options$grvar)) {
mydata <- self$data
grvar <- self$options$grvar
num_levels <- nlevels(
as.factor(mydata[[grvar]])
)
group <- self$options$group
num_levels_group <- nlevels(
as.factor(mydata[[group]])
)
# self$results$plot3$setSize((num_levels + num_levels_group) * 600, 450)
self$results$plot4$setSize((num_levels + num_levels_group) * 600, 450)
}
}
# run ----
,
.run = function() {
# Initial Message ----
if ( is.null(self$options$dep) ) {
# TODO ----
todo <- glue::glue(
"<br>Welcome to ClinicoPath
<br><br>
This tool will help you generate Pie Charts.
<br><br>
This function uses ggplot2 and ggstatsplot packages. See documentations <a href = 'https://indrajeetpatil.github.io/ggstatsplot/reference/ggpiestats.html' target='_blank'>ggpiestats</a> and <a href = 'https://indrajeetpatil.github.io/ggstatsplot/reference/grouped_ggpiestats.html' target='_blank'>grouped_ggpiestats</a>.
<br>
Please cite jamovi and the packages as given below.
<br><hr>"
)
self$results$todo$setContent(todo)
return()
} else {
# TODO ----
todo <- glue::glue(
"<br>You have selected to use Pie Charts.<br><hr>")
self$results$todo$setContent(todo)
if (nrow(self$data) == 0)
stop('Data contains no (complete) rows')
}
}
# the plot1 function ----
,
.plot1 = function(image, ggtheme, theme, ...) {
# Error messages ----
if ( is.null(self$options$dep) )
return()
if (nrow(self$data) == 0)
stop('Data contains no (complete) rows')
# Prepare Data ----
mydata <- self$data
# Exclude NA ----
mydata <- jmvcore::naOmit(mydata)
dep <- self$options$dep
# ggpiestats ----
# https://indrajeetpatil.github.io/ggstatsplot/reference/ggpiestats.html
plot1 <-
ggstatsplot::ggpiestats(
data = mydata,
x = !!rlang::sym(dep),
y = NULL,
counts = NULL,
ratio = NULL,
paired = FALSE,
label = "percentage",
perc.k = 0,
label.args = list(alpha = 1, fill = "white"),
bf.message = TRUE,
sampling.plan = "indepMulti",
fixed.margin = "rows",
prior.concentration = 1,
title = NULL,
subtitle = NULL,
caption = NULL,
conf.level = 0.95,
nboot = 100,
legend.title = NULL,
k = 2,
proportion.test = TRUE,
package = "RColorBrewer",
palette = "Dark2",
ggplot.component = NULL,
output = "plot",
messages = TRUE
, results.subtitle = self$options$resultssubtitle
)
originaltheme <- self$options$originaltheme
if (!originaltheme) {
plot1 <- plot1 + ggtheme
} else {
plot1 <- plot1 + ggstatsplot::theme_ggstatsplot()
# ggplot2::theme_bw()
}
# Print Plot1 ----
print(plot1)
TRUE
}
# the plot2 function ----
, .plot2 = function(image, ggtheme, theme, ...) {
# Error messages ----
if ( is.null(self$options$dep) || is.null(self$options$group) )
return()
if (nrow(self$data) == 0)
stop('Data contains no (complete) rows')
# Prepare Data ----
# # direction, paired ----
#
# direction <- self$options$direction
#
# if (direction == "repeated") {
#
# paired <- TRUE
#
# } else if (direction == "independent") {
#
# paired <- FALSE
#
# }
# distribution <-
# jmvcore::constructFormula(terms = self$options$distribution)
# pairw <- self$options$pairw
mydata <- self$data
# Exclude NA ----
mydata <- jmvcore::naOmit(mydata)
# mydep <- mydata[[self$options$dep]]
# mygroup <- mydata[[self$options$group]]
dep <- self$options$dep
group <- self$options$group
# originaltheme <- self$options$originaltheme
# dep <- jmvcore::composeTerm(components = dep)
# group <- jmvcore::composeTerm(components = group)
# ggpiestats ----
# https://indrajeetpatil.github.io/ggstatsplot/reference/ggpiestats.html
plot2 <-
ggstatsplot::ggpiestats(
data = mydata,
x = !!rlang::sym(dep),
y = !!rlang::sym(group),
counts = NULL,
ratio = NULL,
paired = FALSE,
label = "percentage",
perc.k = 0,
label.args = list(alpha = 1, fill = "white"),
bf.message = TRUE,
sampling.plan = "indepMulti",
fixed.margin = "rows",
prior.concentration = 1,
title = NULL,
subtitle = NULL,
caption = NULL,
conf.level = 0.95,
nboot = 100,
legend.title = NULL,
k = 2,
proportion.test = TRUE,
package = "RColorBrewer",
palette = "Dark2",
ggplot.component = NULL,
output = "plot",
messages = TRUE
, results.subtitle = self$options$resultssubtitle
)
originaltheme <- self$options$originaltheme
if (!originaltheme) {
plot2 <- plot2 + ggtheme
} else {
plot2 <- plot2 + ggstatsplot::theme_ggstatsplot()
# ggplot2::theme_bw()
}
# Print Plot2 ----
print(plot2)
TRUE
}
# # the plot3 function ----
#
#
#
# , .plot3 = function(image, ggtheme, theme, ...) {
#
# # Error messages ----
#
# if ( is.null(self$options$dep) || is.null(self$options$grvar) )
# return()
#
# if (nrow(self$data) == 0)
# stop('Data contains no (complete) rows')
#
#
# # Prepare Data ----
#
# mydata <- self$data
#
#
# # # direction, paired ----
# #
# # direction <- self$options$direction
# #
# # if (direction == "repeated") {
# #
# # paired <- TRUE
# #
# # } else if (direction == "independent") {
# #
# # paired <- FALSE
# #
# # }
#
# # Exclude NA ----
#
# excl <- self$options$excl
#
# if (excl) {mydata <- jmvcore::naOmit(mydata)}
#
#
# dep <- self$options$dep
#
# # group <- self$options$group
#
#
# # dep <- jmvcore::composeTerm(components = dep)
#
# # group <- jmvcore::composeTerm(components = group)
#
#
#
# # originaltheme <- self$options$originaltheme
#
#
# # grouped_ggpiestats ----
# # https://indrajeetpatil.github.io/ggstatsplot/reference/grouped_ggpiestats.html
#
#
# if ( !is.null(self$options$grvar) ) {
#
# grvar <- self$options$grvar
#
# # grvar <- jmvcore::composeTerm(components = grvar)
#
#
# plot3 <- ggstatsplot::grouped_ggpiestats(
# data = mydata,
# x = !!rlang::sym(dep),
# y = NULL,
# counts = NULL,
# grouping.var = !!rlang::sym(grvar),
# title.prefix = NULL,
# output = "plot",
# plotgrid.args = list(),
# title.text = NULL,
# title.args = list(size = 16, fontface = "bold"),
# caption.text = NULL,
# caption.args = list(size = 10),
# sub.text = NULL,
# sub.args = list(size = 12)
# , ggtheme = ggtheme
# , ggstatsplot.layer = originaltheme
#
# )
# }
#
#
# originaltheme <- self$options$originaltheme
#
# if (!originaltheme) {
# plot3 <- plot3 + ggtheme
# } else {
# plot3 <- plot3 + ggstatsplot::theme_ggstatsplot()
# # ggplot2::theme_bw()
# }
#
#
# # Print Plot3 ----
# print(plot3)
# TRUE
# }
#
#
# the plot4 function ----
, .plot4 = function(image, ggtheme, theme, ...) {
# Error messages ----
if ( is.null(self$options$dep) || is.null(self$options$group) || is.null(self$options$grvar) )
return()
if (nrow(self$data) == 0)
stop('Data contains no (complete) rows')
# Prepare Data ----
mydata <- self$data
# Exclude NA ----
mydata <- jmvcore::naOmit(mydata)
dep <- self$options$dep
group <- self$options$group
# originaltheme <- self$options$originaltheme
# dep <- jmvcore::composeTerm(components = dep)
# group <- jmvcore::composeTerm(components = group)
# grouped_ggpiestats ----
# https://indrajeetpatil.github.io/ggstatsplot/reference/grouped_ggpiestats.html
if ( !is.null(self$options$grvar) ) {
grvar <- self$options$grvar
originaltheme <- self$options$originaltheme
selected_theme <- if (!originaltheme) ggtheme else ggstatsplot::theme_ggstatsplot()
plot4 <- ggstatsplot::grouped_ggpiestats(
data = mydata,
x = !!rlang::sym(dep),
y = !!rlang::sym(group),
counts = NULL,
grouping.var = !!rlang::sym(grvar)
, ggtheme = selected_theme
, ggstatsplot.layer = originaltheme
)
}
# originaltheme <- self$options$originaltheme
#
# if (!originaltheme) {
# plot4 <- plot4 + ggtheme
# } else {
# plot4 <- plot4 + ggstatsplot::theme_ggstatsplot()
# # ggplot2::theme_bw()
# }
# Print Plot4 ----
print(plot4)
TRUE
}
)
)
sbalci/ClinicoPathJamoviModule documentation built on Feb. 25, 2025, 6:34 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
#' @title Pie Charts
#' @importFrom R6 R6Class
#' @import jmvcore
#'
jjpiestatsClass <- if (requireNamespace('jmvcore')) R6::R6Class(
"jjpiestatsClass",
inherit = jjpiestatsBase,
private = list(
# init ----
.init = function() {
self$results$plot1$setSize(650, 450)
self$results$plot2$setSize(650, 450)
# if (!is.null(self$options$dep) && !is.null(self$options$grvar)) {
#
# mydata <- self$data
#
# grvar <- self$options$grvar
#
# num_levels <- nlevels(
# as.factor(mydata[[grvar]])
# )
#
# self$results$plot3$setSize(num_levels * 600, 450)
#
# }
if (!is.null(self$options$grvar) && !is.null(self$options$group)) {
mydata <- self$data
group <- self$options$group
num_levels_group <- nlevels(
as.factor(mydata[[group]])
)
self$results$plot4$setSize(num_levels_group * 600, 450)
}
if (!is.null(self$options$group) && !is.null(self$options$grvar)) {
mydata <- self$data
grvar <- self$options$grvar
num_levels <- nlevels(
as.factor(mydata[[grvar]])
)
group <- self$options$group
num_levels_group <- nlevels(
as.factor(mydata[[group]])
)
# self$results$plot3$setSize((num_levels + num_levels_group) * 600, 450)
self$results$plot4$setSize((num_levels + num_levels_group) * 600, 450)
}
}
# run ----
,
.run = function() {
# Initial Message ----
if ( is.null(self$options$dep) ) {
# TODO ----
todo <- glue::glue(
"<br>Welcome to ClinicoPath
<br><br>
This tool will help you generate Pie Charts.
<br><br>
This function uses ggplot2 and ggstatsplot packages. See documentations <a href = 'https://indrajeetpatil.github.io/ggstatsplot/reference/ggpiestats.html' target='_blank'>ggpiestats</a> and <a href = 'https://indrajeetpatil.github.io/ggstatsplot/reference/grouped_ggpiestats.html' target='_blank'>grouped_ggpiestats</a>.
<br>
Please cite jamovi and the packages as given below.
<br><hr>"
)
self$results$todo$setContent(todo)
return()
} else {
# TODO ----
todo <- glue::glue(
"<br>You have selected to use Pie Charts.<br><hr>")
self$results$todo$setContent(todo)
if (nrow(self$data) == 0)
stop('Data contains no (complete) rows')
}
}
# the plot1 function ----
,
.plot1 = function(image, ggtheme, theme, ...) {
# Error messages ----
if ( is.null(self$options$dep) )
return()
if (nrow(self$data) == 0)
stop('Data contains no (complete) rows')
# Prepare Data ----
mydata <- self$data
# Exclude NA ----
mydata <- jmvcore::naOmit(mydata)
dep <- self$options$dep
# ggpiestats ----
# https://indrajeetpatil.github.io/ggstatsplot/reference/ggpiestats.html
plot1 <-
ggstatsplot::ggpiestats(
data = mydata,
x = !!rlang::sym(dep),
y = NULL,
counts = NULL,
ratio = NULL,
paired = FALSE,
label = "percentage",
perc.k = 0,
label.args = list(alpha = 1, fill = "white"),
bf.message = TRUE,
sampling.plan = "indepMulti",
fixed.margin = "rows",
prior.concentration = 1,
title = NULL,
subtitle = NULL,
caption = NULL,
conf.level = 0.95,
nboot = 100,
legend.title = NULL,
k = 2,
proportion.test = TRUE,
package = "RColorBrewer",
palette = "Dark2",
ggplot.component = NULL,
output = "plot",
messages = TRUE
, results.subtitle = self$options$resultssubtitle
)
originaltheme <- self$options$originaltheme
if (!originaltheme) {
plot1 <- plot1 + ggtheme
} else {
plot1 <- plot1 + ggstatsplot::theme_ggstatsplot()
# ggplot2::theme_bw()
}
# Print Plot1 ----
print(plot1)
TRUE
}
# the plot2 function ----
, .plot2 = function(image, ggtheme, theme, ...) {
# Error messages ----
if ( is.null(self$options$dep) || is.null(self$options$group) )
return()
if (nrow(self$data) == 0)
stop('Data contains no (complete) rows')
# Prepare Data ----
# # direction, paired ----
#
# direction <- self$options$direction
#
# if (direction == "repeated") {
#
# paired <- TRUE
#
# } else if (direction == "independent") {
#
# paired <- FALSE
#
# }
# distribution <-
# jmvcore::constructFormula(terms = self$options$distribution)
# pairw <- self$options$pairw
mydata <- self$data
# Exclude NA ----
mydata <- jmvcore::naOmit(mydata)
# mydep <- mydata[[self$options$dep]]
# mygroup <- mydata[[self$options$group]]
dep <- self$options$dep
group <- self$options$group
# originaltheme <- self$options$originaltheme
# dep <- jmvcore::composeTerm(components = dep)
# group <- jmvcore::composeTerm(components = group)
# ggpiestats ----
# https://indrajeetpatil.github.io/ggstatsplot/reference/ggpiestats.html
plot2 <-
ggstatsplot::ggpiestats(
data = mydata,
x = !!rlang::sym(dep),
y = !!rlang::sym(group),
counts = NULL,
ratio = NULL,
paired = FALSE,
label = "percentage",
perc.k = 0,
label.args = list(alpha = 1, fill = "white"),
bf.message = TRUE,
sampling.plan = "indepMulti",
fixed.margin = "rows",
prior.concentration = 1,
title = NULL,
subtitle = NULL,
caption = NULL,
conf.level = 0.95,
nboot = 100,
legend.title = NULL,
k = 2,
proportion.test = TRUE,
package = "RColorBrewer",
palette = "Dark2",
ggplot.component = NULL,
output = "plot",
messages = TRUE
, results.subtitle = self$options$resultssubtitle
)
originaltheme <- self$options$originaltheme
if (!originaltheme) {
plot2 <- plot2 + ggtheme
} else {
plot2 <- plot2 + ggstatsplot::theme_ggstatsplot()
# ggplot2::theme_bw()
}
# Print Plot2 ----
print(plot2)
TRUE
}
# # the plot3 function ----
#
#
#
# , .plot3 = function(image, ggtheme, theme, ...) {
#
# # Error messages ----
#
# if ( is.null(self$options$dep) || is.null(self$options$grvar) )
# return()
#
# if (nrow(self$data) == 0)
# stop('Data contains no (complete) rows')
#
#
# # Prepare Data ----
#
# mydata <- self$data
#
#
# # # direction, paired ----
# #
# # direction <- self$options$direction
# #
# # if (direction == "repeated") {
# #
# # paired <- TRUE
# #
# # } else if (direction == "independent") {
# #
# # paired <- FALSE
# #
# # }
#
# # Exclude NA ----
#
# excl <- self$options$excl
#
# if (excl) {mydata <- jmvcore::naOmit(mydata)}
#
#
# dep <- self$options$dep
#
# # group <- self$options$group
#
#
# # dep <- jmvcore::composeTerm(components = dep)
#
# # group <- jmvcore::composeTerm(components = group)
#
#
#
# # originaltheme <- self$options$originaltheme
#
#
# # grouped_ggpiestats ----
# # https://indrajeetpatil.github.io/ggstatsplot/reference/grouped_ggpiestats.html
#
#
# if ( !is.null(self$options$grvar) ) {
#
# grvar <- self$options$grvar
#
# # grvar <- jmvcore::composeTerm(components = grvar)
#
#
# plot3 <- ggstatsplot::grouped_ggpiestats(
# data = mydata,
# x = !!rlang::sym(dep),
# y = NULL,
# counts = NULL,
# grouping.var = !!rlang::sym(grvar),
# title.prefix = NULL,
# output = "plot",
# plotgrid.args = list(),
# title.text = NULL,
# title.args = list(size = 16, fontface = "bold"),
# caption.text = NULL,
# caption.args = list(size = 10),
# sub.text = NULL,
# sub.args = list(size = 12)
# , ggtheme = ggtheme
# , ggstatsplot.layer = originaltheme
#
# )
# }
#
#
# originaltheme <- self$options$originaltheme
#
# if (!originaltheme) {
# plot3 <- plot3 + ggtheme
# } else {
# plot3 <- plot3 + ggstatsplot::theme_ggstatsplot()
# # ggplot2::theme_bw()
# }
#
#
# # Print Plot3 ----
# print(plot3)
# TRUE
# }
#
#
# the plot4 function ----
, .plot4 = function(image, ggtheme, theme, ...) {
# Error messages ----
if ( is.null(self$options$dep) || is.null(self$options$group) || is.null(self$options$grvar) )
return()
if (nrow(self$data) == 0)
stop('Data contains no (complete) rows')
# Prepare Data ----
mydata <- self$data
# Exclude NA ----
mydata <- jmvcore::naOmit(mydata)
dep <- self$options$dep
group <- self$options$group
# originaltheme <- self$options$originaltheme
# dep <- jmvcore::composeTerm(components = dep)
# group <- jmvcore::composeTerm(components = group)
# grouped_ggpiestats ----
# https://indrajeetpatil.github.io/ggstatsplot/reference/grouped_ggpiestats.html
if ( !is.null(self$options$grvar) ) {
grvar <- self$options$grvar
originaltheme <- self$options$originaltheme
selected_theme <- if (!originaltheme) ggtheme else ggstatsplot::theme_ggstatsplot()
plot4 <- ggstatsplot::grouped_ggpiestats(
data = mydata,
x = !!rlang::sym(dep),
y = !!rlang::sym(group),
counts = NULL,
grouping.var = !!rlang::sym(grvar)
, ggtheme = selected_theme
, ggstatsplot.layer = originaltheme
)
}
# originaltheme <- self$options$originaltheme
#
# if (!originaltheme) {
# plot4 <- plot4 + ggtheme
# } else {
# plot4 <- plot4 + ggstatsplot::theme_ggstatsplot()
# # ggplot2::theme_bw()
# }
# Print Plot4 ----
print(plot4)
TRUE
}
)
)
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