add 'grid' argument for plot_pattern, plot_pred, and plot_corr

R/plot_corr.R

@@ -7,6 +7,7 @@
 #' @param diagonal Logical indicating whether the correlation of each variable with itself should be displayed.
 #' @param rotate Logical indicating whether the variable name labels should be rotated 90 degrees.
 #' @param caption Logical indicating whether the figure caption should be displayed.
+#' @param grid Logical indicating whether borders should be present between tiles.
 #'
 #' @return An object of class [ggplot2::ggplot].
 #'
@@ -20,7 +21,8 @@ plot_corr <-
            square = TRUE,
            diagonal = FALSE,
            rotate = FALSE,
-           caption = TRUE) {
+           caption = TRUE,
+           grid = TRUE) {
     if (is.matrix(data) && ncol(data) > 1) {
       data <- as.data.frame(data)
     }
@@ -73,7 +75,6 @@ plot_corr <-
                         label = .data$corr,
                         fill = .data$corr
                       )) +
-      ggplot2::geom_tile(color = "black", alpha = 0.6) +
       ggplot2::scale_x_discrete(limits = vrb, position = "top") +
       ggplot2::scale_y_discrete(limits = rev(vrb)) +
       ggplot2::scale_fill_gradient2(
@@ -84,6 +85,11 @@ plot_corr <-
         limits = c(-1, 1)
       )  +
       theme_minimice()
+    if (grid) {
+      gg <- gg + ggplot2::geom_tile(color = "black", alpha = 0.6)
+    } else {
+      gg <- gg + ggplot2::geom_tile(alpha = 0.6)
+    }
     if (caption) {
       gg <- gg +
         ggplot2::labs(

R/plot_pattern.R

@@ -7,6 +7,7 @@
 #' @param cluster Optional character string specifying which variable should be used for clustering (e.g., for multilevel data).
 #' @param npat Optional numeric input specifying the number of missing data patterns to be visualized, defaults to all patterns.
 #' @param caption Logical indicating whether the figure caption should be displayed.
+#' @param grid Logical indicating whether borders should be present between tiles.
 #'
 #' @return An object of class [ggplot2::ggplot].
 #'
@@ -20,7 +21,8 @@ plot_pattern <-
            rotate = FALSE,
            cluster = NULL,
            npat = NULL,
-           caption = TRUE) {
+           caption = TRUE,
+           grid = TRUE) {
     # input processing
     if (is.matrix(data) && ncol(data) > 1) {
       data <- as.data.frame(data)
@@ -150,7 +152,6 @@ plot_pattern <-
           alpha = 0.1 + .data$.opacity / 2
         )
       ) +
-      ggplot2::geom_tile(color = "black") +
       ggplot2::scale_fill_manual(values = c(
         "observed" = "#006CC2B3",
         "missing" = "#B61A51B3"
@@ -177,6 +178,11 @@ plot_pattern <-
       theme_minimice()
 
     # additional arguments
+    if (grid) {
+      gg <- gg + ggplot2::geom_tile(color = "black")
+    } else {
+      gg <- gg + ggplot2::geom_raster()
+    }
     if (square) {
       gg <- gg + ggplot2::coord_fixed(expand = FALSE)
     } else {
@@ -209,7 +215,6 @@ plot_pattern <-
                                          pat[rws, cls]))
       }
     }
-
     return(gg)
   }
 

R/plot_pred.R

@@ -6,6 +6,7 @@
 #' @param label Logical indicating whether predictor matrix values should be displayed.
 #' @param square Logical indicating whether the plot tiles should be squares.
 #' @param rotate Logical indicating whether the variable name labels should be rotated 90 degrees.
+#' @param grid Logical indicating whether borders should be present between tiles.
 #'
 #' @return An object of class `ggplot2::ggplot`.
 #'
@@ -19,7 +20,8 @@ plot_pred <-
            method = NULL,
            label = TRUE,
            square = TRUE,
-           rotate = FALSE) {
+           rotate = FALSE,
+           grid = TRUE) {
     verify_data(data, pred = TRUE)
     p <- nrow(data)
     if (!is.null(method) && is.character(method)) {
@@ -69,7 +71,6 @@ plot_pred <-
                         label = .data$ind,
                         fill = .data$clr
                       )) +
-      ggplot2::geom_tile(color = "black", alpha = 0.6) +
       ggplot2::scale_x_discrete(limits = vrbs, position = "top") +
       ggplot2::scale_y_reverse(
         breaks = 1:p,
@@ -92,7 +93,11 @@ plot_pred <-
         color = ""
       ) +
       theme_minimice()
-
+    if (grid) {
+      gg <- gg + ggplot2::geom_tile(color = "black", alpha = 0.6)
+    } else {
+      gg <- gg + ggplot2::geom_tile(alpha = 0.6)
+    }
     if (all(method == "")) {
       gg <-
         gg + ggplot2::theme(axis.ticks.y.right = ggplot2::element_blank())

tests/testthat/test-plot_corr.R

@@ -9,7 +9,8 @@ test_that("plot_corr creates ggplot object", {
     label = TRUE,
     square = FALSE,
     diagonal = TRUE,
-    rotate = TRUE
+    rotate = TRUE,
+    grid = FALSE
   ),
   "ggplot")
 })

tests/testthat/test-plot_pattern.R

@@ -4,7 +4,7 @@ dat <- mice::nhanes
 # tests
 test_that("plot_pattern produces plot", {
   expect_s3_class(plot_pattern(dat), "ggplot")
-  expect_s3_class(plot_pattern(dat, square = FALSE, rotate = TRUE, cluster = "age", npat = 2), "ggplot")
+  expect_s3_class(plot_pattern(dat, square = FALSE, rotate = TRUE, cluster = "age", grid = FALSE, npat = 2), "ggplot")
   expect_s3_class(plot_pattern(cbind(dat, "testvar" = NA), caption = FALSE), "ggplot")
 })
 

tests/testthat/test-plot_pred.R

@@ -10,7 +10,8 @@ test_that("plot_pred creates ggplot object", {
     method = c("pmm"),
     label = FALSE,
     square = FALSE,
-    rotate = TRUE
+    rotate = TRUE,
+    grid = FALSE
   ),
   "ggplot")
   expect_s3_class(plot_pred(pred, vrb = c("age", "bmi")), "ggplot")