new attribute dpi for AssSpec2d

R/ass_spec_2d.R

@@ -61,6 +61,7 @@
 #' [`ggplot2::theme()`] or a complete ggplot2 theme like [`ggplot2::theme_light()`]). 
 #' The theme of the plot. Default is `NULL`, which means the default theme of ggplot2.
 #' @param units string. The units of `width` and `height`. Default is `"in"` (inches).
+#' @param dpi numeric. Plot resolution in dots per inch. Default is `300`.
 #' @return An AssSpec2d S3 object.
 #' @export
 AssSpec2d <- function(
@@ -93,7 +94,8 @@ AssSpec2d <- function(
     height = 4,
     colors = NULL,
     theme = NULL,
-    units = "in"
+    units = "in",
+    dpi = 300
 ){
     if(is.null(x_lab)){
         x_lab <- x_metric
@@ -134,6 +136,7 @@ AssSpec2d <- function(
     stopifnot(is.numeric(height) && height > 0)
     stopifnot((inherits(theme, "theme") && inherits(theme, "gg")) || is.null(theme))
     stopifnot(is.character(units))
+    stopifnot(is.numeric(dpi) && dpi > 0)
 
     ass_spec_2d <- list(
         "file" = file,
@@ -165,7 +168,8 @@ AssSpec2d <- function(
         "width" = width,
         "height" = height,
         "theme" = theme,
-        "units" = units
+        "units" = units,
+        "dpi" = dpi
     )
     return(structure(ass_spec_2d, class = "AssSpec2d"))
 }

R/plot.R

@@ -96,7 +96,8 @@ plot_2d_metric <- function(
         plt, 
         width = ass_spec_2d$width, 
         height = ass_spec_2d$height, 
-        units = ass_spec_2d$units
+        units = ass_spec_2d$units,
+        dpi = ass_spec_2d$dpi
     )
 
     # Save to csv (if wanted)

tests/testthat/test-assess_2d.R

@@ -46,15 +46,16 @@ test_that("assess_2d() works", {
     response_type = "binary"
   )
   ass_spec_2d <- AssSpec2d(
-    file = file.path(dir, "rpp.pdf"),
+    file = file.path(dir, "rpp.jpeg"),
     x_metric = "rpp",
     y_metric = "prec",
     pivot_time_cutoff = 2.,
     benchmark = "ipi",
     smooth_se = TRUE,
     show_plots = FALSE,
     text = list(ggplot2::aes(x = .5, y = .5, label = "this text"), 
-      color = "red", angle = 45)
+     color = "red", angle = 45),
+    dpi = 250
   )
 
   for(model_spec in list(model_spec_1, model_spec_2)){
@@ -79,7 +80,7 @@ test_that("assess_2d() works", {
 
 
   ass_spec_2d$benchmark <- "ipi"
-  ass_spec_2d$directory <- file.path(dir, "logrank.pdf")
+  ass_spec_2d$directory <- file.path(dir, "logrank.jpeg")
   ass_spec_2d$y_metric <- "logrank"
   ass_spec_2d$scale_y <- "log10"
   tbl <- assess_2d(
@@ -94,7 +95,7 @@ test_that("assess_2d() works", {
 
   ass_spec_2d$y_metric <- "precision_ci"
   ass_spec_2d$ci_level <- .95
-  ass_spec_2d$directory <- file.path(dir, "precision_ci.pdf")
+  ass_spec_2d$directory <- file.path(dir, "precision_ci.jpeg")
   ass_spec_2d$scale_y <- "identity"
   ass_spec_2d$title <- "Lower precision CI boundary (upper for ipi)"
   ass_spec_2d$show_plots <- FALSE

tests/testthat/test-assess_2d_center.R

@@ -60,7 +60,7 @@ test_that("assess_2d_center() works", {
 
   res_dir <- file.path(base_dir, "results")
   ass_spec_2d <- AssSpec2d(
-    file = file.path(model_dir, "perf_plot.pdf"),
+    file = file.path(model_dir, "perf_plot.jpeg"),
     x_metric = "rpp",
     y_metric = "prec",
     show_plots = FALSE,
@@ -72,7 +72,8 @@ test_that("assess_2d_center() works", {
     text = list(ggplot2::aes(x = .5, y = .5, label = "hello"), 
       color = "red", angle = 90),
     theme = ggplot2::theme_minimal() + 
-      ggplot2::theme(plot.background = ggplot2::element_rect(fill = "red"))
+      ggplot2::theme(plot.background = ggplot2::element_rect(fill = "red")),
+    dpi = 250
   )
 
   assess_2d_center(
@@ -83,13 +84,13 @@ test_that("assess_2d_center() works", {
     quiet = TRUE
   )
   expect_true(file.exists(ass_spec_2d$file))
-  expect_true(file.exists(file.path(res_dir, "logistic/2/scores.pdf")))
+  expect_true(file.exists(file.path(res_dir, "logistic/2/scores.jpeg")))
   expect_true(file.exists(file.path(res_dir, "cox/2/rpp_vs_prec.csv")))
 
   model_spec_1$split_index <- 1
   ass_spec_2d$y_metric <- "logrank"
   ass_spec_2d$scale_y <- "log10"
-  ass_spec_2d$file <- file.path(model_dir, "logrank.pdf")
+  ass_spec_2d$file <- file.path(model_dir, "logrank.jpeg")
   ass_spec_2d$benchmark <- NULL
   ass_spec_2d$text <- NULL
   ass_spec_2d$scores_plot <- FALSE
@@ -105,7 +106,7 @@ test_that("assess_2d_center() works", {
   model_spec_2$time_cutoffs <- 1.5
   ass_spec_2d$y_metric <- "precision_ci"
   ass_spec_2d$ci_level <- .95
-  ass_spec_2d$file <- file.path(model_dir, "precision_ci.pdf")
+  ass_spec_2d$file <- file.path(model_dir, "precision_ci.jpeg")
   ass_spec_2d$benchmark <- "ipi"
   assess_2d_center(
     model_spec_list = list(model_spec_2),
@@ -115,5 +116,5 @@ test_that("assess_2d_center() works", {
     cohorts = "train",
     quiet = TRUE
   )
-  expect_true(file.exists(file.path(model_dir, "logistic/1-5/rpp_vs_precision_ci.pdf")))
+  expect_true(file.exists(file.path(model_dir, "logistic/1-5/rpp_vs_precision_ci.jpeg")))
 })

tests/testthat/test-plot.R

@@ -6,7 +6,7 @@ test_that("plot_2d_metric() works", {
 
   dir <- withr::local_tempdir()
   ass_spec_2d <- AssSpec2d(
-    file = file.path(dir, "test.pdf"),
+    file = file.path(dir, "test.jpeg"),
     x_metric = "rpp",
     y_metric = "prec",
     pivot_time_cutoff = 2.,
@@ -24,7 +24,8 @@ test_that("plot_2d_metric() works", {
     text = list(ggplot2::aes(x = 0.5, y = 0.5, label = "this text")),
     colors = c("black", "blue", "yellow", "red"),
     theme = ggplot2::theme_dark() + 
-      ggplot2::theme(plot.background = ggplot2::element_rect(grDevices::rgb(1, 1, 1, .98)))
+      ggplot2::theme(plot.background = ggplot2::element_rect(grDevices::rgb(1, 1, 1, .98))),
+    dpi = 200
   )
   ass_spec_2d$data <- tibble::tibble(
     rpp = runif(n_row),
@@ -64,12 +65,13 @@ test_that("plot_risk_scores() works", {
   predicted <- l[[2]]
   dir <- withr::local_tempdir()
   ass_spec_2d <- AssSpec2d(
-    file = file.path(dir, "scores.pdf"),
+    file = file.path(dir, "scores.jpeg"),
     x_metric = "rank",
     y_metric = "scores",
     title = "this title",
     fellow_csv = TRUE,
-    show_plots = FALSE
+    show_plots = FALSE,
+    dpi = 250
   )
 
   expect_no_error(
@@ -81,7 +83,7 @@ test_that("plot_risk_scores() works", {
     )
   )
   expect_true(all(
-    file.exists(file.path(dir, "scores.pdf")),
+    file.exists(file.path(dir, "scores.jpeg")),
     file.exists(file.path(dir, "scores.csv"))
   ))
 })