Updated scipts to create worse versions of the figures with no riskta…

…bles. Simplicity.

R/plot_one_survfit_no_risktable.R

@@ -0,0 +1,55 @@
+
+plot_one_survfit_no_risktable <- function(
+    dat,
+    surv_form,
+    pal = c('#bb5566', '#004488', '#ddaa33'),
+    plot_title = NULL,
+    plot_subtitle = NULL,
+    x_title = "Years",
+    x_exp = 0.15,
+    x_breaks = seq(0, 100, by = 2.5),
+    force_color = NULL
+) {
+
+  gg <- survfit2(surv_form, data = dat) 
+
+  # couldn't figure out how to do this without an if/else, sadly.
+  if (!is.null(force_color)) {
+    gg %<>% ggsurvfit(color = force_color)
+  } else {
+    gg %<>% ggsurvfit()
+  }
+
+  gg <- gg + 
+    scale_y_continuous(
+      expand = c(0,0),
+      label = scales::label_percent(),
+      name = "Survival"
+    ) +
+    scale_x_continuous(
+      name = x_title,
+      expand = expansion(add = 0, mult = c(0, x_exp)), # needed to prevent clipping
+      breaks = x_breaks
+    ) +
+    scale_color_manual(
+      values = pal
+    ) + 
+    coord_cartesian(
+      xlim = c(0, NA),
+      ylim = c(0,1.01),
+      expand = T
+    ) +
+    labs(
+      title = plot_title,
+      subtitle = plot_subtitle
+    ) +
+    theme(
+      axis.title.y = element_blank(),
+      plot.title.position = "plot",
+      title = element_markdown(),
+      # prevents the axis tick label clipping:
+      plot.margin=unit(c(.2,.2,.2,.2),"cm")
+    )
+
+  return(gg)
+}

analysis/script/create_2025_asco_gu_abtract_figures.R

@@ -0,0 +1,57 @@
+# Creates an output versions of figures for GU ASCO 2025 submission poster.
+
+library(purrr); library(fs); library(here);
+purrr::walk(.x = fs::dir_ls(here('R')), .f = source)
+
+dir_out <- here('output', 'fig', 'manu')
+
+os_by_stage <- readr::read_rds(
+    file = here('data', 'survival', 'os_dx_by_stage_manu.rds')
+)
+
+first_line_platinum <- readr::read_rds(
+  file = here('data', 'survival', 'first_line_platinum', 'gg_first_line_platinum.rds')
+)
+
+first_line_by_ddr <- readr::read_rds(
+  file = here('data', 'survival', 'ddr_onco', 
+              'gg_met_ddr_manu.rds')
+)
+
+first_line_by_ddr_plat <- readr::read_rds(
+  file = here('data', 'survival', 'ddr_onco', 
+              'gg_met_ddr_plat_split.rds')
+)
+
+second_line_by_ddr_io <- readr::read_rds(
+  file = here('data', 'survival', 'ddr_onco', 
+              'gg_os_2l_io_ddr.rds')
+)
+
+
+
+fig1_comb <- plot_grid(
+  ggsurvfit_build(os_by_stage),
+  ggsurvfit_build(first_line_platinum),
+  ggsurvfit_build(first_line_by_ddr),
+  ggsurvfit_build(first_line_by_ddr_plat),
+  ggsurvfit_build(second_line_by_ddr_io),
+  labels = "AUTO",
+  align = 'hv',
+  axis = 't',
+  ncol = 2
+)
+
+
+
+ggsave(
+  plot = fig1_comb,
+  filename = here(dir_out, 'fig1.pdf'),
+  height = 7.5, width = 7, scale = 1.8
+)
+
+ggsave(
+  plot = fig1_comb,
+  filename = here(dir_out, 'fig1.png'),
+  height = 7.5, width = 7, scale = 1.8
+)

analysis/script/surv_ddr_asco_2025_io.R

@@ -300,6 +300,16 @@ dft_cohort_ddr %>%
   select(-record_id) %>%
   gtsummary::tbl_summary(.)
 
+dft_met_ddr_surv_grouped %>%
+  mutate(
+    pt_counts = purrr::map(
+      .x = data,
+      .f = \(x) count(x, ddr_before_entry)
+    )
+  ) %>%
+  select(analysis_group, pt_counts) %>%
+  unnest(pt_counts)
+
 dft_met_ddr_surv_grouped %>%
   select(analysis_group, cox_ddr) %>%
   unnest(cox_ddr) %>%
@@ -377,7 +387,24 @@ gg_os_2l_io_ddr <- plot_one_survfit(
   x_exp = 0.05
 )
 
+# A no-risktable version for the poster.
+gg_os_2l_io_ddr_no_rt <- plot_one_survfit_no_risktable(
+  dat = dft_met_ddr_surv,
+  surv_form = surv_obj_os_fmr ~ ddr_disp,
+  plot_title = "OS from second line pembrolizumab or atezolizumab",
+  plot_subtitle = "Adjusted for (independent) delayed entry",
+  x_breaks = seq(0, 10, by = 0.5),
+  x_exp = 0.05
+)
+
+
 readr::write_rds(
   gg_os_2l_io_ddr,
   here('data', 'survival', 'ddr_onco', 'gg_os_2l_io_ddr.rds')
 )
+
+readr::write_rds(
+  gg_os_2l_io_ddr_no_rt,
+  here('data', 'survival', 'ddr_onco', 'gg_os_2l_io_ddr_no_rt.rds')
+)
+

analysis/script/surv_ddr_onco_plat.R

@@ -295,11 +295,25 @@ gg_os_fmr_ddr_manu <- plot_one_survfit(
   coord_cartesian(xlim = c(0,5)) +
   theme(plot.title.position = 'panel')
 
+gg_os_fmr_ddr_manu_no_rt <- plot_one_survfit_no_risktable(
+  dat = dft_met_ddr_surv,
+  surv_form = surv_obj_os_fmr ~ ddr_disp,
+  plot_title = "OS from first line platinum chemo",
+  x_breaks = seq(0, 100, by = 0.5)
+) + 
+  coord_cartesian(xlim = c(0,5)) +
+  theme(plot.title.position = 'panel')
+
 readr::write_rds(
   gg_os_fmr_ddr_manu,
   file = here(dir_out, "gg_met_ddr_manu.rds")
 )
 
+readr::write_rds(
+  gg_os_fmr_ddr_manu_no_rt,
+  file = here(dir_out, "gg_met_ddr_manu_no_rt.rds")
+)
+
 ggsave(
   plot = gg_os_fmr_ddr_manu,
   height = 4, width = 7,
@@ -351,13 +365,30 @@ gg_os_fmr_ddr_manu_plat_split <- plot_one_survfit(
   coord_cartesian(xlim = c(0,5)) +
   theme(plot.title.position = 'panel')
 
-gg_os_fmr_ddr_manu_plat_split
+gg_os_fmr_ddr_manu_plat_split_no_rt <- plot_one_survfit_no_risktable(
+  dat = dft_met_ddr_surv,
+  surv_form = surv_obj_os_fmr ~ ddr_plat_comb,
+  plot_title = "OS from first line platinum chemo",
+  x_breaks = seq(0, 100, by = 0.5),
+  pal = c("#ee99aa", "#994455", "#6699cc", "#004488")
+) + 
+  coord_cartesian(xlim = c(0,5)) +
+  theme(plot.title.position = 'panel')
+
+gg_os_fmr_ddr_manu_plat_split_no_rt
+
 
 readr::write_rds(
   gg_os_fmr_ddr_manu_plat_split,
   file = here(dir_out, "gg_met_ddr_plat_split.rds")
 )
 
+readr::write_rds(
+  gg_os_fmr_ddr_manu_plat_split_no_rt,
+  file = here(dir_out, "gg_met_ddr_plat_split_no_rt.rds")
+)
+
+