added ggvenn package function to add venn plot

.gitignore

@@ -27,9 +27,9 @@ vignettes/*.pdf
 # R Environment Variables
 .Renviron
 .Rprofile
-
 ClinicoPath.Rproj
 build
 .Rbuildignore
 *.jmo
 .Rprofile
+.DS_Store

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: ClinicoPathDescriptives
 Title: Descriptives Functions for Clinicopathological Research
-Version: 0.0.2.0041
-Date: 2020-08-31
+Version: 0.0.2.0060
+Date: 2021-02-07
 Authors@R: 
     person(given = "Serdar",
            family = "Balci",
@@ -46,7 +46,8 @@ Imports:
 Remotes:
     spgarbet/tangram,
     mayoverse/arsenal,
-    carloscinelli/benford.analysis
+    carloscinelli/benford.analysis,
+    yanlinlin82/ggvenn
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)

R/00jmv.R

@@ -429,4 +429,11 @@
         `year`=2020, 
         `title`="bbplot: MAKING GGPLOT GRAPHICS IN BBC NEWS STYLE", 
         `publisher`="[R package]. Retrieved from https://github.com/bbc/bbplot", 
-        `url`="https://github.com/bbc/bbplot"))
+        `url`="https://github.com/bbc/bbplot"), 
+    `venn`=list(
+        `type`="software", 
+        `author`="Linlin Yan", 
+        `year`=2020, 
+        `title`=" Venn Diagram by ggplot2, with really easy-to-use API", 
+        `publisher`="[R package]. Retrieved from https://github.com/yanlinlin82/ggvenn", 
+        `url`="https://github.com/yanlinlin82/ggvenn"))

R/summarydata.b.R

@@ -98,6 +98,10 @@ summarydataClass <- if (requireNamespace("jmvcore")) R6::R6Class("summarydataCla
 
             self$results$text$setContent(results)
 
+            # ?ave
+
+
+
         }
 
 

R/venn.b.R

@@ -0,0 +1,142 @@
+#' @title Venn Diagram
+#'
+#'
+#'
+#'
+#' @importFrom R6 R6Class
+#' @import jmvcore
+#' @import ggvenn
+
+
+vennClass <- if (requireNamespace('jmvcore'))
+    R6::R6Class(
+        "vennClass",
+        inherit = vennBase,
+        private = list(
+            .run = function() {
+                # Error Message ----
+
+
+                if (is.null(self$options$var1)) {
+                    # ToDo Message ----
+                    todo <- "
+                <br>Welcome to ClinicoPath
+                <br><br>
+                This tool will help you form Venn Diagrams.
+                <hr><br>
+                "
+
+                    html <- self$results$todo
+                    html$setContent(todo)
+
+                } else {
+                    todo <- ""
+                    html <- self$results$todo
+                    html$setContent(todo)
+
+
+
+                    if (nrow(self$data) == 0)
+                        stop("Data contains no (complete) rows")
+
+
+                    # Read data ----
+
+                    mydata <- self$data
+
+                    var1 <- self$options$var1
+                    var1true <- self$options$var1true
+
+                    var2 <- self$options$var2
+                    var2true <- self$options$var2true
+
+                    var3 <- self$options$var3
+                    var3true <- self$options$var3true
+
+                    var4 <- self$options$var4
+                    var4true <- self$options$var4true
+
+                    # mydata <- jmvcore::select(df = mydata,
+                    #                           columnNames = c(var1, var2, var3, var4))
+
+                    mydata <- jmvcore::naOmit(mydata)
+
+
+                    if (!is.null(self$options$var1)) {
+                        mydata[[var1]] <-
+                            ifelse(test = mydata[[var1]] == var1true, TRUE, FALSE)
+                    }
+
+                    if (!is.null(self$options$var2)) {
+                        mydata[[var2]] <-
+                            ifelse(test = mydata[[var2]] == var2true, TRUE, FALSE)
+                    }
+
+                    if (!is.null(self$options$var3)) {
+                        mydata[[var3]] <-
+                            ifelse(test = mydata[[var3]] == var3true, TRUE, FALSE)
+                    }
+
+                    if (!is.null(self$options$var4)) {
+                        mydata[[var4]] <-
+                            ifelse(test = mydata[[var4]] == var4true, TRUE, FALSE)
+                    }
+
+                    myoutput1 <- list(
+                        "mydata" = head(mydata),
+                        "names" = names(mydata)
+                    )
+
+
+                    self$results$output1$setContent(myoutput1)
+
+
+                    plotData <- list("mydata" = mydata,
+                                     "names" = names(mydata)
+                                     )
+
+                    image <- self$results$plot
+                    image$setState(plotData)
+
+
+                }
+
+            }
+
+            ,
+
+            .plot = function(image, ggtheme, theme, ...) {
+                # the plot function ----
+
+
+                #Errors ----
+
+                if (is.null(self$options$var1))
+                    return()
+
+                if (nrow(self$data) == 0)
+                    stop('Data contains no (complete) rows')
+
+
+                # Prepare Data ----
+
+                results <- image$state
+
+                mydata2 <- results$mydata
+
+                namescolumn2 <- results$names
+
+                # Venn Diagram by ggplot2, with really easy-to-use API.
+                # https://github.com/yanlinlin82/ggvenn
+
+                plot <-
+                    ggvenn::ggvenn(data = mydata2,
+                                   columns = namescolumn2)
+
+
+                # Print Plot ----
+                print(plot)
+                TRUE
+            }
+        )
+    )