Bug fixes; Update internal ggplot2 usage (#477)

ggobi · Nov 22, 2023 · 8131749 · 8131749
1 parent 9e7228c
commit 8131749
Show file tree

Hide file tree

Showing 228 changed files with 10,739 additions and 10,614 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -29,7 +29,7 @@ Description:
     plot networks.
 Depends:
     R (>= 3.1),
-    ggplot2 (>= 3.3.4)
+    ggplot2 (>= 3.4.4)
 Imports:
     dplyr (>= 1.0.0),
     tidyr (>= 1.3.0),

diff --git a/NAMESPACE b/NAMESPACE
@@ -134,6 +134,7 @@ import(RColorBrewer)
 import(ggplot2)
 import(utils)
 importFrom(dplyr,"%>%")
+importFrom(dplyr,all_of)
 importFrom(dplyr,group_by)
 importFrom(dplyr,rename)
 importFrom(dplyr,summarise)

diff --git a/R/deprecated.R b/R/deprecated.R
@@ -46,12 +46,12 @@ v1_ggmatrix_theme <- function() {
 #' p_ <- GGally::print_if_interactive
 #'
 #' data(tips)
-#' p_(ggally_cor_v1_5(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "tip")))
+#' p_(ggally_cor_v1_5(tips, mapping = ggplot2::aes(total_bill, tip)))
 #'
 #' # display with no grid
 #' p_(ggally_cor_v1_5(
 #'   tips,
-#'   mapping = ggplot2::aes_string(x = "total_bill", y = "tip"),
+#'   mapping = ggplot2::aes(total_bill, tip),
 #'   displayGrid = FALSE
 #' ))
 #'
@@ -66,26 +66,24 @@ v1_ggmatrix_theme <- function() {
 #' # split by a variable
 #' p_(ggally_cor_v1_5(
 #'   tips,
-#'   mapping = ggplot2::aes_string(x = "total_bill", y = "tip", color = "sex"),
+#'   mapping = ggplot2::aes(total_bill, tip, color = sex),
 #'   size = 5
 #' ))
 ggally_cor_v1_5 <- function(
-  data,
-  mapping,
-  alignPercent = 0.6,
-  method = "pearson", use = "complete.obs",
-  corAlignPercent = NULL, corMethod = NULL, corUse = NULL,
-  displayGrid = TRUE,
-  ...
-) {
-
-  if (! is.null(corAlignPercent)) {
+    data,
+    mapping,
+    alignPercent = 0.6,
+    method = "pearson", use = "complete.obs",
+    corAlignPercent = NULL, corMethod = NULL, corUse = NULL,
+    displayGrid = TRUE,
+    ...) {
+  if (!is.null(corAlignPercent)) {
     stop("'corAlignPercent' is deprecated.  Please use argument 'alignPercent'")
   }
-  if (! is.null(corMethod)) {
+  if (!is.null(corMethod)) {
     stop("'corMethod' is deprecated.  Please use argument 'method'")
   }
-  if (! is.null(corUse)) {
+  if (!is.null(corUse)) {
     stop("'corUse' is deprecated.  Please use argument 'use'")
   }
 
@@ -181,22 +179,22 @@ ggally_cor_v1_5 <- function(
       for (i in length(names(mapping)):1) {
         # find the last value of the aes, such as cyl of as.factor(cyl)
         tmp_map_val <- deparse(mapping[names(mapping)[i]][[1]])
-        if (tmp_map_val[length(tmp_map_val)] %in% colnames(data))
+        if (tmp_map_val[length(tmp_map_val)] %in% colnames(data)) {
           mapping[[names(mapping)[i]]] <- NULL
+        }
 
         if (length(names(mapping)) < 1) {
           mapping <- NULL
-          break;
+          break
         }
       }
     }
   }
 
   if (
     !is.null(colorData) &&
-    !inherits(colorData, "AsIs")
+      !inherits(colorData, "AsIs")
   ) {
-
     cord <- ddply(
       data.frame(x = xData, y = yData, color = colorData),
       "color",
@@ -248,7 +246,8 @@ ggally_cor_v1_5 <- function(
     yPos <- seq(
       from = 0.9,
       to = 0.2,
-      length.out = nrow(cord) + 1)
+      length.out = nrow(cord) + 1
+    )
     yPos <- yPos * diff(yrange) + min(yrange, na.rm = TRUE)
     yPos <- yPos[-1]
     # print(range(yVal))
@@ -269,7 +268,6 @@ ggally_cor_v1_5 <- function(
       ),
       hjust = 1,
       ...
-
     )
   } else {
     # calculate variable ranges so the gridlines line up

diff --git a/R/find-combo.R b/R/find-combo.R
@@ -6,8 +6,6 @@
 #' @author Barret Schloerke
 #' @keywords internal
 plot_types <- function(data, columnsX, columnsY, allowDiag = TRUE) {
-
-
   plotTypesX <- lapply(data[columnsX], plotting_data_type)
   plotTypesY <- lapply(data[columnsY], plotting_data_type)
 
@@ -26,7 +24,7 @@ plot_types <- function(data, columnsX, columnsY, allowDiag = TRUE) {
   posX <- integer(n)
   posY <- integer(n)
 
-  #horizontal then vertical
+  # horizontal then vertical
   for (yI in seq_len(lenY)) {
     yColName <- columnNamesY[yI]
     for (xI in seq_len(lenX)) {
@@ -78,7 +76,6 @@ plot_types <- function(data, columnsX, columnsY, allowDiag = TRUE) {
 #' @author Barret Schloerke
 #' @keywords internal
 find_plot_type <- function(col1Name, col2Name, type1, type2, isAllNa, allowDiag) {
-
   # diag calculations
   if (col1Name == col2Name && allowDiag) {
     if (type1 == "na") {
@@ -94,7 +91,7 @@ find_plot_type <- function(col1Name, col2Name, type1, type2, isAllNa, allowDiag)
     return("na")
   }
 
-  #cat(names(data)[col2Name],": ", type2,"\t",names(data)[col1Name],": ",type1,"\n")
+  # cat(names(data)[col2Name],": ", type2,"\t",names(data)[col1Name],": ",type1,"\n")
   isCats <- c(type1, type2) %in% "discrete"
   if (any(isCats)) {
     if (all(isCats)) {