adding miss_vis graph

NAMESPACE

@@ -7,6 +7,7 @@ export(label_breaks)
 export(plot_epicurve)
 export(plot_pyramid)
 export(plot_stacked_bar)
+export(miss_vis)
 import(ggplot2)
 import(gt)
 importFrom(magrittr,"%<>%")

R/miss_vis.R

@@ -0,0 +1,147 @@
+#' Title
+#'
+#' @param x a dataframe
+#' @param facet a character value of variable to facet the graph
+#' @param col_vec a vector of length 2 specifying the color for Missing and Present values respectively
+#' @param y_axis_text_size a nuemric value for the size of the y axis text
+#'
+#' @return a ggplot tile graph displaying the missing/present values for all variables of the dataframe
+#' @export
+#'
+#' @examples
+#' #Use fake data from Epidemiologist R handbook
+#'
+#' suppressMessages(c(library(dplyr), library(readr)))
+#' linelist <- read_rds("https://github.com/appliedepi/epirhandbook/raw/master/inst/extdata/case_linelists/linelist_cleaned.rds")
+#'
+#' plot_stacked_bar(
+#'   linelist,
+#'   cols = c( "fever", "vomit", "chills", "cough", "aches"),
+#'   levels_value = c("yes"),
+#'   keep_na = FALSE,
+#'   use_counts = TRUE,
+#'   flip = FALSE
+#' )
+#'
+miss_vis <- function(
+  x,
+  facet = NULL,
+  col_vec = c("#6a040f", "#cce3de"),
+  y_axis_text_size = 8
+) {
+  if (is.null(facet)) {
+    tile_dat <- x |>
+      dplyr::mutate(across(everything(), ~ case_when(
+        is.na(.x) ~ "Missing",
+        !is.na(.x) ~ "Present"
+      ))) |>
+      dplyr::mutate(
+        observations = row_number()
+      ) |>
+      dplyr::relocate(observations, .before = 1) |>
+      tidyr::pivot_longer(
+        cols = !observations,
+        names_to = "variable_name",
+        values_to = "status"
+      ) |>
+      dplyr::mutate(
+        .by = observations,
+        pct_missing = sum(status == "Missing") / n()
+      ) |>
+      dplyr::mutate(
+        order = as.numeric(forcats::fct_reorder(as.factor(observations), pct_missing, .desc = TRUE))
+      )
+  } else {
+    tile_dat <- x |>
+      dplyr::mutate(across(!.data[[facet]], ~ dplyr::case_when(
+        is.na(.x) ~ "Missing",
+        !is.na(.x) ~ "Present"
+      ))) |>
+      dplyr::mutate(
+        .by = .data[[facet]],
+        observations = row_number()
+      ) |>
+      dplyr::relocate(observations, .before = 1) |>
+      dplyr::pivot_longer(
+        cols = !observations & !.data[[facet]],
+        names_to = "variable_name",
+        values_to = "status"
+      ) |>
+      dplyr::mutate(
+        .by = observations,
+        pct_missing = sum(status == "Missing") / n()
+      ) |>
+      dplyr::mutate(
+        .by = .data[[facet]],
+        order = as.numeric(forcats::fct_reorder(as.factor(observations), pct_missing, .desc = TRUE))
+      )
+  }
+
+  pct_df <- tile_dat |>
+    dplyr::count(status) |>
+    dplyr::mutate(pct = round(digits = 1, n / sum(n) * 100))
+
+  pct_var_df <- tile_dat |>
+    dplyr::count(variable_name, status) |>
+    dplyr::mutate(
+      .by = variable_name,
+      pct = dplyr::if_else(status == "Present", 100 - (n / sum(n) * 100), n / sum(n) * 100)
+    ) |>
+    dplyr::filter(status == "Missing" & pct != 0 | status == "Present" & pct == 0) |>
+    dplyr::mutate(
+      variable_name_label = paste0(variable_name, " (", round(digits = 1, pct), "%)")
+    ) |>
+    dplyr::select(variable_name, variable_name_label, pct)
+
+  tile_dat <- tile_dat |>
+    dplyr::left_join(pct_var_df, dplyr::join_by(variable_name)) |>
+    dplyr::mutate(variable_name_label = forcats::fct_reorder(variable_name_label, pct))
+
+  gg <- tile_dat |>
+    ggplot2::ggplot() +
+    ggplot2::geom_tile(
+      ggplot2::aes(
+        x = order,
+        y = variable_name_label,
+        fill = status
+      ),
+      height = .9,
+      width = .8
+    ) +
+
+    ggplot2::scale_fill_manual(
+      "Assessment",
+      values = c(
+        "Missing" = col_vec[1],
+        "Present" = col_vec[2]
+      ),
+      labels = c(
+        glue::glue("Missing ({filter(pct_df, status=='Missing')$pct}%)"),
+        glue::glue("Present ({filter(pct_df, status=='Present')$pct}%)")
+      )
+    ) +
+    ggplot2::labs(
+      y = "Variable Name",
+      x = "Observations"
+    ) +
+    ggplot2::theme_minimal() +
+    ggplot2::theme(
+      strip.text = ggplot2::element_text(face = "bold"),
+      strip.clip = "off",
+      axis.text.x = ggplot2::element_blank(),
+      axis.text.y = ggplot2::element_text(size = y_axis_text_size),
+      panel.grid.major = ggplot2::element_blank(),
+      panel.grid.minor = ggplot2::element_blank()
+    )
+
+  if (is.null(facet)) {
+    gg
+  } else {
+    gg +
+      ggplot2::facet_grid(
+        ~ .data[[facet]],
+        scales = "free",
+        space = "free"
+      )
+  }
+}