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jjstatsplot functions working with defaluts
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‎.Rprofile‎

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@@ -1 +1,46 @@
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options(repos = c("https://cran.microsoft.com/snapshot/2020-05-01"))
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# source("renv/activate.R")
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# 'https://repo.jamovi.org'
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# "/Users/serdarbalciold/Library/R/3.6/library"
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# "/Library/Frameworks/R.framework/Versions/3.6/Resources/library"
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.libPaths(new = "~/histopathRprojects/ClinicoPathLibrary")
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# source(
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# "renv/activate.R"
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# "~/histopathRprojects/ClinicoPath/renv/activate.R"
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# # here::here("renv/activate.R")
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# )
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# https://stackoverflow.com/questions/2096473/r-determine-if-a-script-is-running-in-windows-or-linux
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# https://conjugateprior.org/2015/06/identifying-the-os-from-r/
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# if (.Platform$OS.type == "windows") {
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#
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# if (!requireNamespace('jmvtools')) install.packages('jmvtools', repos=c('https://repo.jamovi.org', 'https://cran.r-project.org'))
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#
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# library("jmvtools")
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#
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# jmvtools::check("C://Program Files//jamovi//bin")
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#
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# .libPaths(new = "C:\\ClinicoPathLibrary")
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#
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# Sys.setenv(TZ = "Europe/Istanbul")
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#
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# }
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.First <- function(){
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cat("\nWelcome to ClinicoPath", date(), "\n")
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}
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.Last <- function(){
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cat("\nGoodbye at ", date(), "\n")
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}
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‎DESCRIPTION‎

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@@ -1,8 +1,8 @@
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Type: Package
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Package: ClinicoPath
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Title: Analysis for Clinicopathological Research
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Version: 0.0.2.0011
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Date: 2020-06-05
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Version: 0.0.2.0012
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Date: 2020-06-09
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Authors@R:
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person(given = "Serdar",
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family = "Balci",
@@ -72,6 +72,11 @@ Suggests:
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gtsummary,
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vctrs,
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patchwork
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Remotes:
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ndphillips/FFTrees,
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easystats/report,
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spgarbet/tangram,
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cran/rmngb
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VignetteBuilder:
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knitr
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Encoding: UTF-8

‎R/jjbarstats.b.R‎

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@@ -24,7 +24,7 @@ jjbarstatsClass <- if (requireNamespace('jmvcore')) R6::R6Class(
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<br><br>
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This tool will help you generate Bar Charts.
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<br><br>
27-
This function uses ggplot2 and ggstatsplot packages. See documentations <a href = 'https://indrajeetpatil.github.io/ggstatsplot/reference/ggbarstats.html' target='_blank'>here</a> and <a href = 'https://indrajeetpatil.github.io/ggstatsplot/reference/grouped_ggbarstats.html' target='_blank'>here</a>.
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This function uses ggplot2 and ggstatsplot packages. See documentations <a href = 'https://indrajeetpatil.github.io/ggstatsplot/reference/ggbarstats.html' target='_blank'>ggbarstats</a> and <a href = 'https://indrajeetpatil.github.io/ggstatsplot/reference/grouped_ggbarstats.html' target='_blank'>grouped_ggbarstats</a>.
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<br>
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Please cite jamovi and the packages as given below.
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<br><hr>"

‎R/jjbetweenstats.b.R‎

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#' @title jjbetweenstats
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#' @title Violin Plots to Compare Between Groups
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#'
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#'
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#'

‎R/jjbetweenstats.h.R‎

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@@ -22,10 +22,9 @@ jjbetweenstatsOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
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"dep",
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dep,
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suggested=list(
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"ordinal",
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"nominal"),
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"continuous"),
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permitted=list(
28-
"factor"))
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"numeric"))
2928
private$..group <- jmvcore::OptionVariable$new(
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"group",
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group,
@@ -191,7 +190,6 @@ jjbetweenstats <- function(
191190
`if`( ! missing(group), group, NULL),
192191
`if`( ! missing(grvar), grvar, NULL))
193192

194-
for (v in dep) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
195193
for (v in group) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
196194
for (v in grvar) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
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‎R/jjcorrmat.b.R‎

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#' @title jjcorrmat
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#' @title Correlation Matrix
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#'
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#'
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#' @importFrom R6 R6Class
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1414
.run = function() {
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# Initial Message ----
17-
if ( is.null(self$options$dep) ) {
17+
if ( length(self$options$dep) <= 1 ) {
1818

1919
# TODO ----
2020

2121
todo <- glue::glue(
22-
"<br>Welcome to ClinicoPath
22+
"<br>Welcome to ClinicoPath
2323
<br><br>
2424
This tool will help you generate Bar Charts.
2525
<br><br>
26-
This function uses ggplot2 and ggstatsplot packages. See documentations <a href = 'https://indrajeetpatil.github.io/ggstatsplot/reference/ggbarstats.html' target='_blank'>here</a> and <a href = 'https://indrajeetpatil.github.io/ggstatsplot/reference/grouped_ggbarstats.html' target='_blank'>here</a>.
26+
This function uses ggplot2 and ggstatsplot packages. See documentations <a href = 'https://indrajeetpatil.github.io/ggstatsplot/reference/ggcorrmat.html' target='_blank'>ggcorrmat</a> and <a href = 'https://indrajeetpatil.github.io/ggstatsplot/reference/grouped_ggcorrmat.html' target='_blank'>grouped_ggcorrmat</a>.
2727
<br>
2828
Please cite jamovi and the packages as given below.
2929
<br><hr>"
@@ -54,7 +54,7 @@ jjcorrmatClass <- if (requireNamespace('jmvcore')) R6::R6Class(
5454
# the plot function ----
5555
# Error messages ----
5656

57-
if ( is.null(self$options$dep) )
57+
if ( length(self$options$dep) <= 1 )
5858
return()
5959

6060
if (nrow(self$data) == 0)
@@ -74,6 +74,7 @@ jjcorrmatClass <- if (requireNamespace('jmvcore')) R6::R6Class(
7474
if (excl) {mydata <- jmvcore::naOmit(mydata)}
7575

7676

77+
# define main arguments ----
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7879
myvars <- jmvcore::constructFormula(terms = self$options$dep)
7980

@@ -123,97 +124,90 @@ jjcorrmatClass <- if (requireNamespace('jmvcore')) R6::R6Class(
123124

124125
}
125126

126-
#
127-
# ,
128-
#
129-
# .plot2 = function(image, ...) {
130-
# # the plot function ----
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# # Error messages ----
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#
133-
# if ( is.null(self$options$dep) || is.null(self$options$grvar))
134-
# return()
135-
#
136-
# if (nrow(self$data) == 0)
137-
# stop('Data contains no (complete) rows')
138-
#
139-
#
140-
# # Prepare Data ----
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#
142-
# mydata <- self$data
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#
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#
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# # direction, paired ----
146-
#
147-
# direction <- self$options$direction
148-
#
149-
# if (direction == "repeated") {
150-
#
151-
# paired <- TRUE
152-
#
153-
# } else if (direction == "independent") {
154-
#
155-
# paired <- FALSE
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#
157-
# }
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#
159-
# # Exclude NA ----
160-
#
161-
# excl <- self$options$excl
162-
#
163-
# if (excl) {mydata <- jmvcore::naOmit(mydata)}
164-
#
165-
#
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#
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# dep <- self$options$dep
168-
#
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#
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#
171-
# dep <- jmvcore::composeTerm(components = dep)
172-
#
173-
#
174-
#
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#
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#
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#
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# # grouped_ggcorrmat
179-
# # https://indrajeetpatil.github.io/ggstatsplot/reference/grouped_ggcorrmat.html
180-
#
181-
#
182-
#
183-
# if ( !is.null(self$options$grvar) ) {
184-
# grvar <- self$options$grvar
185-
#
186-
# plot2 <- ggstatsplot::grouped_ggcorrmat(
187-
# data,
188-
# cor.vars = NULL,
189-
# cor.vars.names = NULL,
190-
# grouping.var,
191-
# title.prefix = NULL,
192-
# output = "plot",
193-
# ...,
194-
# plotgrid.args = list(),
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# title.text = NULL,
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# title.args = list(size = 16, fontface = "bold"),
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# caption.text = NULL,
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# caption.args = list(size = 10),
199-
# sub.text = NULL,
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# sub.args = list(size = 12)
201-
# )
202-
#
203-
#
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# }
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#
206-
# # Print Plot ----
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#
208-
# print(plot2)
209-
# TRUE
210-
#
211-
# }
212-
#
213127

128+
,
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130+
.plot2 = function(image, ...) {
131+
# the plot function ----
132+
# Error messages ----
133+
134+
if ( is.null(self$options$dep) || is.null(self$options$grvar))
135+
return()
136+
137+
if (nrow(self$data) == 0)
138+
stop('Data contains no (complete) rows')
139+
140+
141+
# Prepare Data ----
142+
143+
mydata <- self$data
144+
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146+
# direction, paired ----
147+
148+
direction <- self$options$direction
149+
150+
if (direction == "repeated") {
151+
152+
paired <- TRUE
153+
154+
} else if (direction == "independent") {
155+
156+
paired <- FALSE
157+
158+
}
159+
160+
# Exclude NA ----
161+
162+
excl <- self$options$excl
163+
164+
if (excl) {mydata <- jmvcore::naOmit(mydata)}
165+
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167+
# define main arguments ----
168+
169+
myvars <- jmvcore::constructFormula(terms = self$options$dep)
170+
171+
myvars <- jmvcore::decomposeFormula(formula = myvars)
172+
173+
myvars <- unlist(myvars)
174+
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176+
# grouped_ggcorrmat ----
177+
# https://indrajeetpatil.github.io/ggstatsplot/reference/grouped_ggcorrmat.html
214178

215179

216180

181+
if ( !is.null(self$options$grvar) ) {
182+
183+
grvar <- self$options$grvar
184+
185+
plot2 <- ggstatsplot::grouped_ggcorrmat(
186+
data = mydata,
187+
cor.vars = myvars,
188+
cor.vars.names = NULL,
189+
grouping.var = !!grvar,
190+
title.prefix = NULL,
191+
output = "plot",
192+
plotgrid.args = list(),
193+
title.text = NULL,
194+
title.args = list(size = 16, fontface = "bold"),
195+
caption.text = NULL,
196+
caption.args = list(size = 10),
197+
sub.text = NULL,
198+
sub.args = list(size = 12)
199+
)
200+
201+
202+
}
203+
204+
# Print Plot ----
205+
206+
print(plot2)
207+
TRUE
208+
209+
}
210+
217211
)
218212
)
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‎R/jjcorrmat.h.R‎

Lines changed: 18 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -65,14 +65,15 @@ jjcorrmatResults <- if (requireNamespace('jmvcore')) R6::R6Class(
6565
inherit = jmvcore::Group,
6666
active = list(
6767
todo = function() private$.items[["todo"]],
68+
plot2 = function() private$.items[["plot2"]],
6869
plot = function() private$.items[["plot"]]),
6970
private = list(),
7071
public=list(
7172
initialize=function(options) {
7273
super$initialize(
7374
options=options,
7475
name="",
75-
title="jjcorrmat",
76+
title="Correlation Matrix",
7677
refs=list(
7778
"ggplot2",
7879
"ggstatsplot"))
@@ -84,10 +85,23 @@ jjcorrmatResults <- if (requireNamespace('jmvcore')) R6::R6Class(
8485
"dep",
8586
"grvar",
8687
"direction")))
88+
self$add(jmvcore::Image$new(
89+
options=options,
90+
name="plot2",
91+
title="Chart",
92+
width=800,
93+
height=600,
94+
renderFun=".plot2",
95+
requiresData=TRUE,
96+
clearWith=list(
97+
"dep",
98+
"grvar",
99+
"direction"),
100+
visible="(grvar)"))
87101
self$add(jmvcore::Image$new(
88102
options=options,
89103
name="plot",
90-
title="`Bar Chart ${group} - {dep}`",
104+
title="Chart",
91105
width=800,
92106
height=600,
93107
renderFun=".plot",
@@ -117,7 +131,7 @@ jjcorrmatBase <- if (requireNamespace('jmvcore')) R6::R6Class(
117131
requiresMissings = FALSE)
118132
}))
119133

120-
#' jjcorrmat
134+
#' Correlation Matrix
121135
#'
122136
#' 'Wrapper Function for ggstatsplot::ggbarstats and
123137
#' ggstatsplot::grouped_ggbarstats to generate Bar Charts.'
@@ -135,6 +149,7 @@ jjcorrmatBase <- if (requireNamespace('jmvcore')) R6::R6Class(
135149
#' @return A results object containing:
136150
#' \tabular{llllll}{
137151
#' \code{results$todo} \tab \tab \tab \tab \tab a html \cr
152+
#' \code{results$plot2} \tab \tab \tab \tab \tab an image \cr
138153
#' \code{results$plot} \tab \tab \tab \tab \tab an image \cr
139154
#' }
140155
#'

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