jjstatsplot functions working with defaluts

sbalci · Jun 9, 2020 · 94e1eaf · 94e1eaf
1 parent f20ac2a
commit 94e1eaf
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diff --git a/.Rprofile b/.Rprofile
@@ -1 +1,46 @@
 options(repos = c("https://cran.microsoft.com/snapshot/2020-05-01"))
+# source("renv/activate.R")
+
+# 'https://repo.jamovi.org'
+
+# "/Users/serdarbalciold/Library/R/3.6/library"
+# "/Library/Frameworks/R.framework/Versions/3.6/Resources/library"
+
+.libPaths(new = "~/histopathRprojects/ClinicoPathLibrary")
+
+# source(
+#     "renv/activate.R"
+# "~/histopathRprojects/ClinicoPath/renv/activate.R"
+#     # here::here("renv/activate.R")
+# )
+
+
+# https://stackoverflow.com/questions/2096473/r-determine-if-a-script-is-running-in-windows-or-linux
+
+# https://conjugateprior.org/2015/06/identifying-the-os-from-r/
+
+
+# if (.Platform$OS.type == "windows") {
+#
+#     if (!requireNamespace('jmvtools')) install.packages('jmvtools', repos=c('https://repo.jamovi.org', 'https://cran.r-project.org'))
+#
+#     library("jmvtools")
+#
+#     jmvtools::check("C://Program Files//jamovi//bin")
+#
+#     .libPaths(new = "C:\\ClinicoPathLibrary")
+#
+#     Sys.setenv(TZ = "Europe/Istanbul")
+#
+# }
+
+
+.First <- function(){
+    cat("\nWelcome to ClinicoPath", date(), "\n")
+}
+
+
+.Last <- function(){
+    cat("\nGoodbye at ", date(), "\n")
+}
+
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: ClinicoPath
 Title: Analysis for Clinicopathological Research
-Version: 0.0.2.0011
-Date: 2020-06-05
+Version: 0.0.2.0012
+Date: 2020-06-09
 Authors@R: 
     person(given = "Serdar",
            family = "Balci",
@@ -72,6 +72,11 @@ Suggests:
     gtsummary,
     vctrs,
     patchwork
+Remotes:
+    ndphillips/FFTrees,
+    easystats/report,
+    spgarbet/tangram,
+    cran/rmngb
 VignetteBuilder:
     knitr
 Encoding: UTF-8

diff --git a/R/jjbarstats.b.R b/R/jjbarstats.b.R
@@ -24,7 +24,7 @@ jjbarstatsClass <- if (requireNamespace('jmvcore')) R6::R6Class(
                 <br><br>
                 This tool will help you generate Bar Charts.
                 <br><br>
-                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>.
+                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>.
                 <br>
                 Please cite jamovi and the packages as given below.
                 <br><hr>"

diff --git a/R/jjbetweenstats.b.R b/R/jjbetweenstats.b.R
@@ -1,4 +1,4 @@
-#' @title jjbetweenstats
+#' @title Violin Plots to Compare Between Groups
 #'
 #'
 #'

diff --git a/R/jjbetweenstats.h.R b/R/jjbetweenstats.h.R
@@ -22,10 +22,9 @@ jjbetweenstatsOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
                 "dep",
                 dep,
                 suggested=list(
-                    "ordinal",
-                    "nominal"),
+                    "continuous"),
                 permitted=list(
-                    "factor"))
+                    "numeric"))
             private$..group <- jmvcore::OptionVariable$new(
                 "group",
                 group,
@@ -191,7 +190,6 @@ jjbetweenstats <- function(
             `if`( ! missing(group), group, NULL),
             `if`( ! missing(grvar), grvar, NULL))
 
-    for (v in dep) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
     for (v in group) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
     for (v in grvar) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
 

diff --git a/R/jjcorrmat.b.R b/R/jjcorrmat.b.R
@@ -1,4 +1,4 @@
-#' @title jjcorrmat
+#' @title Correlation Matrix
 #'
 #'
 #' @importFrom R6 R6Class
@@ -14,16 +14,16 @@ jjcorrmatClass <- if (requireNamespace('jmvcore')) R6::R6Class(
         .run = function() {
 
             # Initial Message ----
-            if ( is.null(self$options$dep) ) {
+            if ( length(self$options$dep) <= 1 ) {
 
                 # TODO ----
 
                 todo <- glue::glue(
-                    "<br>Welcome to ClinicoPath
+                "<br>Welcome to ClinicoPath
                 <br><br>
                 This tool will help you generate Bar Charts.
                 <br><br>
-                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>.
+                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>.
                 <br>
                 Please cite jamovi and the packages as given below.
                 <br><hr>"
@@ -54,7 +54,7 @@ jjcorrmatClass <- if (requireNamespace('jmvcore')) R6::R6Class(
             # the plot function ----
             # Error messages ----
 
-            if ( is.null(self$options$dep) )
+            if ( length(self$options$dep) <= 1 )
                 return()
 
             if (nrow(self$data) == 0)
@@ -74,6 +74,7 @@ jjcorrmatClass <- if (requireNamespace('jmvcore')) R6::R6Class(
             if (excl) {mydata <- jmvcore::naOmit(mydata)}
 
 
+            # define main arguments ----
 
             myvars <- jmvcore::constructFormula(terms = self$options$dep)
 
@@ -123,97 +124,90 @@ jjcorrmatClass <- if (requireNamespace('jmvcore')) R6::R6Class(
 
         }
 
-#
-#         ,
-#
-#         .plot2 = function(image, ...) {
-#             # the plot function ----
-#             # 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
-#
-#
-#
-#             dep <- jmvcore::composeTerm(components = dep)
-#
-#
-#
-#
-#
-#
-#             # grouped_ggcorrmat
-#             # https://indrajeetpatil.github.io/ggstatsplot/reference/grouped_ggcorrmat.html
-#
-#
-#
-#             if ( !is.null(self$options$grvar) ) {
-#                 grvar <- self$options$grvar
-#
-#                 plot2 <- ggstatsplot::grouped_ggcorrmat(
-#                     data,
-#                     cor.vars = NULL,
-#                     cor.vars.names = NULL,
-#                     grouping.var,
-#                     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)
-#                 )
-#
-#
-#             }
-#
-#             # Print Plot ----
-#
-#             print(plot2)
-#             TRUE
-#
-#         }
-#
 
+        ,
+
+        .plot2 = function(image, ...) {
+            # the plot function ----
+            # 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)}
+
+
+            # define main arguments ----
+
+            myvars <- jmvcore::constructFormula(terms = self$options$dep)
+
+            myvars <- jmvcore::decomposeFormula(formula = myvars)
+
+            myvars <- unlist(myvars)
+
+
+            # grouped_ggcorrmat ----
+            # https://indrajeetpatil.github.io/ggstatsplot/reference/grouped_ggcorrmat.html
 
 
 
+            if ( !is.null(self$options$grvar) ) {
+
+                grvar <- self$options$grvar
+
+                plot2 <- ggstatsplot::grouped_ggcorrmat(
+                    data = mydata,
+                    cor.vars = myvars,
+                    cor.vars.names = NULL,
+                    grouping.var = !!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)
+                )
+
+
+            }
+
+            # Print Plot ----
+
+            print(plot2)
+            TRUE
+
+        }
+
     )
 )
 

diff --git a/R/jjcorrmat.h.R b/R/jjcorrmat.h.R
@@ -65,14 +65,15 @@ jjcorrmatResults <- if (requireNamespace('jmvcore')) R6::R6Class(
     inherit = jmvcore::Group,
     active = list(
         todo = function() private$.items[["todo"]],
+        plot2 = function() private$.items[["plot2"]],
         plot = function() private$.items[["plot"]]),
     private = list(),
     public=list(
         initialize=function(options) {
             super$initialize(
                 options=options,
                 name="",
-                title="jjcorrmat",
+                title="Correlation Matrix",
                 refs=list(
                     "ggplot2",
                     "ggstatsplot"))
@@ -84,10 +85,23 @@ jjcorrmatResults <- if (requireNamespace('jmvcore')) R6::R6Class(
                     "dep",
                     "grvar",
                     "direction")))
+            self$add(jmvcore::Image$new(
+                options=options,
+                name="plot2",
+                title="Chart",
+                width=800,
+                height=600,
+                renderFun=".plot2",
+                requiresData=TRUE,
+                clearWith=list(
+                    "dep",
+                    "grvar",
+                    "direction"),
+                visible="(grvar)"))
             self$add(jmvcore::Image$new(
                 options=options,
                 name="plot",
-                title="`Bar Chart ${group} - {dep}`",
+                title="Chart",
                 width=800,
                 height=600,
                 renderFun=".plot",
@@ -117,7 +131,7 @@ jjcorrmatBase <- if (requireNamespace('jmvcore')) R6::R6Class(
                 requiresMissings = FALSE)
         }))
 
-#' jjcorrmat
+#' Correlation Matrix
 #'
 #' 'Wrapper Function for ggstatsplot::ggbarstats and
 #' ggstatsplot::grouped_ggbarstats to generate Bar Charts.'
@@ -135,6 +149,7 @@ jjcorrmatBase <- if (requireNamespace('jmvcore')) R6::R6Class(
 #' @return A results object containing:
 #' \tabular{llllll}{
 #'   \code{results$todo} \tab \tab \tab \tab \tab a html \cr
+#'   \code{results$plot2} \tab \tab \tab \tab \tab an image \cr
 #'   \code{results$plot} \tab \tab \tab \tab \tab an image \cr
 #' }
 #'