Merge pull request #35 from hanneoberman/main

Update vignette with more info about the `ggmice()` function, fix issues #32 and #33

R/corr.R

@@ -32,7 +32,7 @@ plot_corr <- function(data, vrb = "all", label = FALSE, square = TRUE, diagonal
     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(low = ggplot2::alpha("deepskyblue", 0.6), mid = "lightyellow", high = ggplot2::alpha("orangered", 0.6), na.value = "white", limits = c(-1, 1)) +
+    ggplot2::scale_fill_gradient2(low = ggplot2::alpha("deepskyblue", 0.6), mid = "lightyellow", high = ggplot2::alpha("orangered", 0.6), na.value = "grey90", limits = c(-1, 1)) +
     ggplot2::labs(
       x = "Imputation model predictor",
       y = "Variable to impute",
@@ -45,7 +45,9 @@ plot_corr <- function(data, vrb = "all", label = FALSE, square = TRUE, diagonal
     gg <- gg + ggplot2::geom_text(color = "black", show.legend = FALSE, na.rm = TRUE)
   }
   if (square) {
-    gg <- gg + ggplot2::coord_fixed()
+    gg <- gg + ggplot2::coord_fixed(expand = FALSE)
+  } else {
+    gg <- gg + ggplot2::coord_cartesian(expand = FALSE)
   }
   if (rotate) {
     gg <- gg + ggplot2::theme(axis.text.x.top = ggplot2::element_text(angle = 90))

R/ggmice.R

@@ -1,6 +1,6 @@
 #' Plot incomplete or imputed data
 #'
-#' @param data An incomplete dataset (of class `data.frame` or `matrix`), or an object of class [`mice::mids`].
+#' @param data An incomplete dataset (of class `data.frame`), or an object of class [`mice::mids`].
 #' @param mapping A list of aesthetic mappings created with [ggplot2::aes()].
 #'
 #' @return An object of class [`ggplot2::ggplot`].

R/pattern.R

@@ -87,7 +87,9 @@ plot_pattern <- function(data, vrb = "all", square = FALSE, rotate = FALSE, clus
     ) +
     theme_minimice()
   if (square) {
-    gg <- gg + ggplot2::coord_fixed()
+    gg <- gg + ggplot2::coord_fixed(expand = FALSE)
+  } else {
+    gg <- gg + ggplot2::coord_cartesian(expand = FALSE)
   }
   if (rotate) {
     gg <- gg + ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90))

R/pred.R

@@ -8,10 +8,10 @@
 #' @return An object of class `ggplot2::ggplot`.
 #'
 #' @examples
-#' pred <- mice::make.predictorMatrix(mice::nhanes)
-#' plot_pred(pred, label = TRUE)
+#' pred <- mice::quickpred(mice::nhanes)
+#' plot_pred(pred)
 #' @export
-plot_pred <- function(data, label = FALSE, square = TRUE, rotate = FALSE) {
+plot_pred <- function(data, label = TRUE, square = TRUE, rotate = FALSE) {
   if (!is.matrix(data) | dim(data)[1] != dim(data)[2]) {
     stop("Predictor matrix should be a square matrix, try using mice::make.predictorMatrix() or mice::quickpred().")
   }
@@ -26,7 +26,7 @@ plot_pred <- function(data, label = FALSE, square = TRUE, rotate = FALSE) {
     ggplot2::geom_tile(color = "black", alpha = 0.6) +
     ggplot2::scale_x_discrete(limits = vrbs, position = "top") +
     ggplot2::scale_y_discrete(limits = rev(vrbs)) +
-    ggplot2::scale_fill_manual(values = c("yes" = "grey75", "no" = "white")) + ## 006CC2B3
+    ggplot2::scale_fill_manual(values = c("yes" = "grey50", "no" = "grey90")) + ## 006CC2B3
     ggplot2::labs(
       x = "Imputation model predictor",
       y = "Variable to impute",
@@ -38,7 +38,9 @@ plot_pred <- function(data, label = FALSE, square = TRUE, rotate = FALSE) {
     gg <- gg + ggplot2::geom_text(color = "black", show.legend = FALSE)
   }
   if (square) {
-    gg <- gg + ggplot2::coord_fixed()
+    gg <- gg + ggplot2::coord_fixed(expand = FALSE)
+  } else {
+    gg <- gg + ggplot2::coord_cartesian(expand = FALSE)
   }
   if (rotate) {
     gg <- gg + ggplot2::theme(axis.text.x.top = ggplot2::element_text(angle = 90))

R/theme.R

@@ -25,7 +25,8 @@ theme_minimice <- function() {
       legend.justification = "right",
       strip.placement = "outside",
       panel.grid.minor = ggplot2::element_blank(),
-      panel.grid.major = ggplot2::element_line(colour = "grey95"),
+      panel.grid.major = ggplot2::element_blank(),
+      axis.ticks = ggplot2::element_line(colour = "black"),
       axis.title.y.right = ggplot2::element_text(margin = ggplot2::margin(l = 6))
     )
 }

README.Rmd

@@ -30,7 +30,7 @@ Enhance a `mice` imputation workflow with visualizations for incomplete and/or i
 
 ## Installation
 
-You can install the latest `ggmice` release from [CRAN](https://cran.r-project.org/) with:
+You can install the latest `ggmice` release from [CRAN](https://CRAN.R-project.org/package=ggmice) with:
 
 ``` r
 install.packages("ggmice")

README.md

@@ -26,7 +26,7 @@ convergence, or compare observed versus imputed data.
 ## Installation
 
 You can install the latest `ggmice` release from
-[CRAN](https://cran.r-project.org/) with:
+[CRAN](https://CRAN.R-project.org/package=ggmice) with:
 
 ``` r
 install.packages("ggmice")