Merge pull request #10 from parmsam-pfizer/4-update-km-plot-code

Switch over to ggsurvfit for KM plot
RConsortium · May 3, 2024 · cbd578a · cbd578a
2 parents b5df29c + 9901d9e
commit cbd578a
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Showing 2 changed files with 62 additions and 15 deletions.
diff --git a/app/views/km_plot.R b/app/views/km_plot.R
@@ -1,12 +1,16 @@
 box::use(
   dplyr[filter, inner_join, mutate, select],
-  ggplot2[element_text, geom_hline, rel, theme, theme_bw, theme_set],
+  ggplot2[element_text, geom_hline, rel, theme, theme_bw, theme_set, labs],
   shiny[
     NS, observeEvent, p, plotOutput, reactiveValues, renderPlot, renderUI, selectInput,
     tagAppendAttributes, tagList, tags, uiOutput, updateSelectInput,
     fluidRow, column
   ],
-  visR[add_CI, add_CNSR, estimate_KM, visr]
+  ggsurvfit[
+    Surv, survfit2, ggsurvfit, add_confidence_interval, add_risktable,
+    add_censor_mark, scale_ggsurvfit
+  ],
+  scales[breaks_width]
 )
 
 box::use(
@@ -107,17 +111,20 @@ server <- function(input, output, session, datasets) {
         AVAL = AVAL / 30.4167
       )
 
-    surv_mod <- estimate_KM(data = anl, strata = "TRT01A")
+    surv_mod <- survfit2(Surv(AVAL, 1 - CNSR) ~ TRT01A, data = anl)
     theme_set(theme_bw())
 
-    km_plot <- visr(surv_mod,
-      y_label = "Survival Probability (%)",
-      x_label = "Time (Months)",
-      fun = "pct",
-      legend_position = "bottom"
-    ) |>
-      add_CNSR() |>
-      add_CI()
+    km_plot <- ggsurvfit(surv_mod) +
+      add_censor_mark() +
+      add_confidence_interval() +
+      add_risktable(
+        risktable_stats = "n.risk",
+        size = rel(5)
+      ) +
+      labs(
+        y = "Survival Probability",
+        x = "Time (Months)",
+      )
 
     km_plot <- km_plot +
       theme(
@@ -126,10 +133,12 @@ server <- function(input, output, session, datasets) {
         legend.text = element_text(size = rel(1.3)),
         legend.title = element_text(size = rel(1.4))
       ) +
-      geom_hline(yintercept = 0.5, linetype = "dashed")
-
-    km_plot <- km_plot |>
-      add_risktable2(group = "statlist")
+      scale_ggsurvfit(
+        x_scales = list(
+          breaks = scales::breaks_width(0.5)
+        )
+      ) +
+      geom_hline(yintercept = 0.05, linetype = "dashed")
 
     output$plot_title <- renderUI({
       tags$div(

diff --git a/renv.lock b/renv.lock
@@ -689,6 +689,26 @@
       ],
       "Hash": "3a147ee02e85a8941aad9909f1b43b7b"
     },
+    "ggsurvfit": {
+      "Package": "ggsurvfit",
+      "Version": "1.0.0",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "broom",
+        "cli",
+        "dplyr",
+        "ggplot2",
+        "glue",
+        "gtable",
+        "patchwork",
+        "rlang",
+        "survival",
+        "tidyr"
+      ],
+      "Hash": "42d3b3206360e4fb840a7c9311b975cc"
+    },
     "glue": {
       "Package": "glue",
       "Version": "1.6.2",
@@ -1233,6 +1253,24 @@
       ],
       "Hash": "2a0dc8c6adfb6f032e4d4af82d258ab5"
     },
+    "patchwork": {
+      "Package": "patchwork",
+      "Version": "1.2.0",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "cli",
+        "ggplot2",
+        "grDevices",
+        "graphics",
+        "grid",
+        "gtable",
+        "rlang",
+        "stats",
+        "utils"
+      ],
+      "Hash": "9c8ab14c00ac07e9e04d1664c0b74486"
+    },
     "pillar": {
       "Package": "pillar",
       "Version": "1.9.0",