Merge pull request #67 from d3b-center/rjcorb/65-format-survival-numbers

Update survival plots number formatting (4/N)
d3b-center · May 13, 2024 · 0ec3ddb · 0ec3ddb
2 parents becc6bf + 3cd15d4
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diff --git a/analyses/braf-fusions/03-survival-by-braf-breakpoints.html b/analyses/braf-fusions/03-survival-by-braf-breakpoints.html
diff --git a/...ses/braf-fusions/plots/pbta_ancestry_forest_efs_add_breakpoint15_9_resection_ancestry.pdf b/...ses/braf-fusions/plots/pbta_ancestry_forest_efs_add_breakpoint15_9_resection_ancestry.pdf
diff --git a/...ses/braf-fusions/plots/pbta_ancestry_forest_efs_add_breakpoint16_9_resection_ancestry.pdf b/...ses/braf-fusions/plots/pbta_ancestry_forest_efs_add_breakpoint16_9_resection_ancestry.pdf
diff --git a/...s/braf-fusions/plots/pbta_ancestry_forest_efs_add_resection_ancestry_breakpoint_group.pdf b/...s/braf-fusions/plots/pbta_ancestry_forest_efs_add_resection_ancestry_breakpoint_group.pdf
diff --git a/...es/braf-fusions/plots/pbta_ancestry_forest_efs_add_resection_ancestry_breakpoint_type.pdf b/...es/braf-fusions/plots/pbta_ancestry_forest_efs_add_resection_ancestry_breakpoint_type.pdf
diff --git a/analyses/braf-fusions/plots/pbta_ancestry_forest_efs_add_resection_breakpoint_group.pdf b/analyses/braf-fusions/plots/pbta_ancestry_forest_efs_add_resection_breakpoint_group.pdf
diff --git a/analyses/braf-fusions/plots/pbta_ancestry_forest_efs_add_resection_breakpoint_type.pdf b/analyses/braf-fusions/plots/pbta_ancestry_forest_efs_add_resection_breakpoint_type.pdf
diff --git a/analyses/braf-fusions/plots/pbta_ancestry_forest_efs_int_resection_breakpoint_group.pdf b/analyses/braf-fusions/plots/pbta_ancestry_forest_efs_int_resection_breakpoint_group.pdf
diff --git a/analyses/braf-fusions/plots/pbta_ancestry_forest_efs_int_resection_breakpoint_type.pdf b/analyses/braf-fusions/plots/pbta_ancestry_forest_efs_int_resection_breakpoint_type.pdf
diff --git a/analyses/braf-fusions/plots/pbta_ancestry_km_efs_15_9_predicted_ancestry.pdf b/analyses/braf-fusions/plots/pbta_ancestry_km_efs_15_9_predicted_ancestry.pdf
diff --git a/analyses/braf-fusions/plots/pbta_ancestry_km_efs_16_9_predicted_ancestry.pdf b/analyses/braf-fusions/plots/pbta_ancestry_km_efs_16_9_predicted_ancestry.pdf
diff --git a/analyses/braf-fusions/plots/pbta_ancestry_km_efs_breakpoint_group.pdf b/analyses/braf-fusions/plots/pbta_ancestry_km_efs_breakpoint_group.pdf
diff --git a/analyses/braf-fusions/plots/pbta_ancestry_km_efs_breakpoint_type.pdf b/analyses/braf-fusions/plots/pbta_ancestry_km_efs_breakpoint_type.pdf
diff --git a/analyses/braf-fusions/results/coxph_braf_efs_add_15_9_resection_ancestry_breakpoint.RDS b/analyses/braf-fusions/results/coxph_braf_efs_add_15_9_resection_ancestry_breakpoint.RDS
diff --git a/analyses/braf-fusions/results/coxph_braf_efs_add_16_9_resection_ancestry_breakpoint.RDS b/analyses/braf-fusions/results/coxph_braf_efs_add_16_9_resection_ancestry_breakpoint.RDS
diff --git a/analyses/braf-fusions/results/coxph_braf_efs_add_resection_ancestry_breakpoint_group.RDS b/analyses/braf-fusions/results/coxph_braf_efs_add_resection_ancestry_breakpoint_group.RDS
diff --git a/analyses/braf-fusions/results/coxph_braf_efs_add_resection_ancestry_breakpoint_type.RDS b/analyses/braf-fusions/results/coxph_braf_efs_add_resection_ancestry_breakpoint_type.RDS
diff --git a/analyses/braf-fusions/results/coxph_braf_efs_add_resection_breakpoint_group.RDS b/analyses/braf-fusions/results/coxph_braf_efs_add_resection_breakpoint_group.RDS
diff --git a/analyses/braf-fusions/results/coxph_braf_efs_add_resection_breakpoint_type.RDS b/analyses/braf-fusions/results/coxph_braf_efs_add_resection_breakpoint_type.RDS
diff --git a/analyses/braf-fusions/results/coxph_braf_efs_int_resection_breakpoint_group.RDS b/analyses/braf-fusions/results/coxph_braf_efs_int_resection_breakpoint_group.RDS
diff --git a/analyses/braf-fusions/results/coxph_braf_efs_int_resection_breakpoint_type.RDS b/analyses/braf-fusions/results/coxph_braf_efs_int_resection_breakpoint_type.RDS
diff --git a/analyses/survival/01-prepare-survival.nb.html b/analyses/survival/01-prepare-survival.nb.html
diff --git a/analyses/survival/02-run-survival.nb.html b/analyses/survival/02-run-survival.nb.html
diff --git a/analyses/survival/03-plot-survival.R b/analyses/survival/03-plot-survival.R
@@ -128,13 +128,17 @@ for (var in variables){
         ))
     }
 
-    forest_pdf <- file.path(plots_dir, 
-                            glue::glue("forest_{group_df$subtype[i]}_OS_subtype_{var}.pdf"))
+    if (sum(is.na(broom::tidy(os_survival_result)$estimate)) != nrow(broom::tidy(os_survival_result))) {
 
+      forest_pdf <- file.path(plots_dir, 
+                              glue::glue("forest_{group_df$subtype[i]}_OS_subtype_{var}.pdf"))
+
+
+      forest_plot <- try(plotForest(os_survival_result), silent = TRUE)
+
+      ggsave(forest_pdf, forest_plot, width = 8, height = 3)
 
-    forest_plot <- plotForest(os_survival_result)
-
-    ggsave(forest_pdf, forest_plot, width = 8, height = 3)
+    }
 
 
     if (grepl("Low-grade glioma|LGG", group_df$group[i])){
@@ -149,14 +153,17 @@ for (var in variables){
         ))
     }
 
-    forest_pdf <- file.path(plots_dir, 
-                            glue::glue("forest_{group_df$subtype[i]}_EFS_subtype_{var}.pdf"))
-
-
-    forest_plot <- plotForest(efs_survival_result)
-
-    ggsave(forest_pdf, forest_plot, width = 8, height = 3)
-
+    if (sum(is.na(broom::tidy(efs_survival_result)$estimate)) != nrow(broom::tidy(efs_survival_result))) {
+
+      forest_pdf <- file.path(plots_dir, 
+                              glue::glue("forest_{group_df$subtype[i]}_EFS_subtype_{var}.pdf"))
+
+
+      forest_plot <- plotForest(efs_survival_result)
+
+      ggsave(forest_pdf, forest_plot, width = 8, height = 3)
+
+    }
 
   }
 

diff --git a/analyses/survival/plots/CPT/forest_CPT_EFS_subtype_EUR_status.pdf b/analyses/survival/plots/CPT/forest_CPT_EFS_subtype_EUR_status.pdf
diff --git a/analyses/survival/plots/CPT/forest_CPT_EFS_subtype_ethnicity.pdf b/analyses/survival/plots/CPT/forest_CPT_EFS_subtype_ethnicity.pdf
diff --git a/analyses/survival/plots/CPT/forest_CPT_EFS_subtype_predicted_ancestry.pdf b/analyses/survival/plots/CPT/forest_CPT_EFS_subtype_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/CPT/forest_CPT_EFS_subtype_race.pdf b/analyses/survival/plots/CPT/forest_CPT_EFS_subtype_race.pdf
diff --git a/analyses/survival/plots/CPT/forest_CPT_OS_subtype_EUR_status.pdf b/analyses/survival/plots/CPT/forest_CPT_OS_subtype_EUR_status.pdf
diff --git a/analyses/survival/plots/CPT/forest_CPT_OS_subtype_ethnicity.pdf b/analyses/survival/plots/CPT/forest_CPT_OS_subtype_ethnicity.pdf
diff --git a/analyses/survival/plots/CPT/forest_CPT_OS_subtype_predicted_ancestry.pdf b/analyses/survival/plots/CPT/forest_CPT_OS_subtype_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/CPT/forest_CPT_OS_subtype_race.pdf b/analyses/survival/plots/CPT/forest_CPT_OS_subtype_race.pdf
diff --git a/analyses/survival/plots/CPT/km_CPT_EFS_EUR_status.pdf b/analyses/survival/plots/CPT/km_CPT_EFS_EUR_status.pdf
diff --git a/analyses/survival/plots/CPT/km_CPT_EFS_ethnicity.pdf b/analyses/survival/plots/CPT/km_CPT_EFS_ethnicity.pdf
diff --git a/analyses/survival/plots/CPT/km_CPT_EFS_predicted_ancestry.pdf b/analyses/survival/plots/CPT/km_CPT_EFS_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/CPT/km_CPT_EFS_race.pdf b/analyses/survival/plots/CPT/km_CPT_EFS_race.pdf
diff --git a/analyses/survival/plots/CPT/km_CPT_OS_EUR_status.pdf b/analyses/survival/plots/CPT/km_CPT_OS_EUR_status.pdf
diff --git a/analyses/survival/plots/CPT/km_CPT_OS_ethnicity.pdf b/analyses/survival/plots/CPT/km_CPT_OS_ethnicity.pdf
diff --git a/analyses/survival/plots/CPT/km_CPT_OS_predicted_ancestry.pdf b/analyses/survival/plots/CPT/km_CPT_OS_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/CPT/km_CPT_OS_race.pdf b/analyses/survival/plots/CPT/km_CPT_OS_race.pdf
diff --git a/analyses/survival/plots/GERM/forest_GERM_EFS_subtype_EUR_status.pdf b/analyses/survival/plots/GERM/forest_GERM_EFS_subtype_EUR_status.pdf
diff --git a/analyses/survival/plots/GERM/forest_GERM_EFS_subtype_ethnicity.pdf b/analyses/survival/plots/GERM/forest_GERM_EFS_subtype_ethnicity.pdf
diff --git a/analyses/survival/plots/GERM/forest_GERM_EFS_subtype_predicted_ancestry.pdf b/analyses/survival/plots/GERM/forest_GERM_EFS_subtype_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/GERM/forest_GERM_EFS_subtype_race.pdf b/analyses/survival/plots/GERM/forest_GERM_EFS_subtype_race.pdf
diff --git a/analyses/survival/plots/GERM/forest_GERM_OS_subtype_EUR_status.pdf b/analyses/survival/plots/GERM/forest_GERM_OS_subtype_EUR_status.pdf
diff --git a/analyses/survival/plots/GERM/forest_GERM_OS_subtype_ethnicity.pdf b/analyses/survival/plots/GERM/forest_GERM_OS_subtype_ethnicity.pdf
diff --git a/analyses/survival/plots/GERM/forest_GERM_OS_subtype_predicted_ancestry.pdf b/analyses/survival/plots/GERM/forest_GERM_OS_subtype_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/GERM/forest_GERM_OS_subtype_race.pdf b/analyses/survival/plots/GERM/forest_GERM_OS_subtype_race.pdf
diff --git a/analyses/survival/plots/GERM/km_GERM_EFS_EUR_status.pdf b/analyses/survival/plots/GERM/km_GERM_EFS_EUR_status.pdf
diff --git a/analyses/survival/plots/GERM/km_GERM_EFS_ethnicity.pdf b/analyses/survival/plots/GERM/km_GERM_EFS_ethnicity.pdf
diff --git a/analyses/survival/plots/GERM/km_GERM_EFS_predicted_ancestry.pdf b/analyses/survival/plots/GERM/km_GERM_EFS_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/GERM/km_GERM_EFS_race.pdf b/analyses/survival/plots/GERM/km_GERM_EFS_race.pdf
diff --git a/analyses/survival/plots/GERM/km_GERM_OS_EUR_status.pdf b/analyses/survival/plots/GERM/km_GERM_OS_EUR_status.pdf
diff --git a/analyses/survival/plots/GERM/km_GERM_OS_ethnicity.pdf b/analyses/survival/plots/GERM/km_GERM_OS_ethnicity.pdf
diff --git a/analyses/survival/plots/GERM/km_GERM_OS_predicted_ancestry.pdf b/analyses/survival/plots/GERM/km_GERM_OS_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/GERM/km_GERM_OS_race.pdf b/analyses/survival/plots/GERM/km_GERM_OS_race.pdf
diff --git a/analyses/survival/plots/GNG/forest_GNG_BRAF-V600E_EFS_subtype_EUR_status.pdf b/analyses/survival/plots/GNG/forest_GNG_BRAF-V600E_EFS_subtype_EUR_status.pdf
diff --git a/analyses/survival/plots/GNG/forest_GNG_BRAF-V600E_EFS_subtype_ethnicity.pdf b/analyses/survival/plots/GNG/forest_GNG_BRAF-V600E_EFS_subtype_ethnicity.pdf
diff --git a/analyses/survival/plots/GNG/forest_GNG_BRAF-V600E_EFS_subtype_predicted_ancestry.pdf b/analyses/survival/plots/GNG/forest_GNG_BRAF-V600E_EFS_subtype_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/GNG/forest_GNG_BRAF-V600E_EFS_subtype_race.pdf b/analyses/survival/plots/GNG/forest_GNG_BRAF-V600E_EFS_subtype_race.pdf
diff --git a/analyses/survival/plots/GNG/forest_GNG_BRAF-V600E_OS_subtype_EUR_status.pdf b/analyses/survival/plots/GNG/forest_GNG_BRAF-V600E_OS_subtype_EUR_status.pdf
diff --git a/analyses/survival/plots/GNG/forest_GNG_BRAF-V600E_OS_subtype_ethnicity.pdf b/analyses/survival/plots/GNG/forest_GNG_BRAF-V600E_OS_subtype_ethnicity.pdf
diff --git a/analyses/survival/plots/GNG/forest_GNG_BRAF-V600E_OS_subtype_predicted_ancestry.pdf b/analyses/survival/plots/GNG/forest_GNG_BRAF-V600E_OS_subtype_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/GNG/forest_GNG_BRAF-V600E_OS_subtype_race.pdf b/analyses/survival/plots/GNG/forest_GNG_BRAF-V600E_OS_subtype_race.pdf
diff --git a/analyses/survival/plots/GNG/forest_GNG_EFS_subtype_EUR_status.pdf b/analyses/survival/plots/GNG/forest_GNG_EFS_subtype_EUR_status.pdf
diff --git a/analyses/survival/plots/GNG/forest_GNG_EFS_subtype_ethnicity.pdf b/analyses/survival/plots/GNG/forest_GNG_EFS_subtype_ethnicity.pdf
diff --git a/analyses/survival/plots/GNG/forest_GNG_EFS_subtype_predicted_ancestry.pdf b/analyses/survival/plots/GNG/forest_GNG_EFS_subtype_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/GNG/forest_GNG_EFS_subtype_race.pdf b/analyses/survival/plots/GNG/forest_GNG_EFS_subtype_race.pdf
diff --git a/analyses/survival/plots/GNG/forest_GNG_OS_subtype_EUR_status.pdf b/analyses/survival/plots/GNG/forest_GNG_OS_subtype_EUR_status.pdf
diff --git a/analyses/survival/plots/GNG/forest_GNG_OS_subtype_ethnicity.pdf b/analyses/survival/plots/GNG/forest_GNG_OS_subtype_ethnicity.pdf
diff --git a/analyses/survival/plots/GNG/forest_GNG_OS_subtype_predicted_ancestry.pdf b/analyses/survival/plots/GNG/forest_GNG_OS_subtype_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/GNG/forest_GNG_OS_subtype_race.pdf b/analyses/survival/plots/GNG/forest_GNG_OS_subtype_race.pdf
diff --git a/analyses/survival/plots/GNG/forest_GNG_Other-alteration_EFS_subtype_EUR_status.pdf b/analyses/survival/plots/GNG/forest_GNG_Other-alteration_EFS_subtype_EUR_status.pdf
diff --git a/analyses/survival/plots/GNG/forest_GNG_Other-alteration_EFS_subtype_ethnicity.pdf b/analyses/survival/plots/GNG/forest_GNG_Other-alteration_EFS_subtype_ethnicity.pdf
diff --git a/analyses/survival/plots/GNG/forest_GNG_Other-alteration_EFS_subtype_predicted_ancestry.pdf b/analyses/survival/plots/GNG/forest_GNG_Other-alteration_EFS_subtype_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/GNG/forest_GNG_Other-alteration_EFS_subtype_race.pdf b/analyses/survival/plots/GNG/forest_GNG_Other-alteration_EFS_subtype_race.pdf
diff --git a/analyses/survival/plots/GNG/forest_GNG_Other-alteration_OS_subtype_EUR_status.pdf b/analyses/survival/plots/GNG/forest_GNG_Other-alteration_OS_subtype_EUR_status.pdf
diff --git a/analyses/survival/plots/GNG/forest_GNG_Other-alteration_OS_subtype_ethnicity.pdf b/analyses/survival/plots/GNG/forest_GNG_Other-alteration_OS_subtype_ethnicity.pdf
diff --git a/analyses/survival/plots/GNG/forest_GNG_Other-alteration_OS_subtype_predicted_ancestry.pdf b/analyses/survival/plots/GNG/forest_GNG_Other-alteration_OS_subtype_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/GNG/forest_GNG_Other-alteration_OS_subtype_race.pdf b/analyses/survival/plots/GNG/forest_GNG_Other-alteration_OS_subtype_race.pdf
diff --git a/analyses/survival/plots/GNG/km_GNG_BRAF-V600E_EFS_EUR_status.pdf b/analyses/survival/plots/GNG/km_GNG_BRAF-V600E_EFS_EUR_status.pdf
diff --git a/analyses/survival/plots/GNG/km_GNG_BRAF-V600E_EFS_ethnicity.pdf b/analyses/survival/plots/GNG/km_GNG_BRAF-V600E_EFS_ethnicity.pdf
diff --git a/analyses/survival/plots/GNG/km_GNG_BRAF-V600E_EFS_predicted_ancestry.pdf b/analyses/survival/plots/GNG/km_GNG_BRAF-V600E_EFS_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/GNG/km_GNG_BRAF-V600E_EFS_race.pdf b/analyses/survival/plots/GNG/km_GNG_BRAF-V600E_EFS_race.pdf
diff --git a/analyses/survival/plots/GNG/km_GNG_BRAF-V600E_OS_EUR_status.pdf b/analyses/survival/plots/GNG/km_GNG_BRAF-V600E_OS_EUR_status.pdf
diff --git a/analyses/survival/plots/GNG/km_GNG_BRAF-V600E_OS_ethnicity.pdf b/analyses/survival/plots/GNG/km_GNG_BRAF-V600E_OS_ethnicity.pdf
diff --git a/analyses/survival/plots/GNG/km_GNG_BRAF-V600E_OS_predicted_ancestry.pdf b/analyses/survival/plots/GNG/km_GNG_BRAF-V600E_OS_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/GNG/km_GNG_BRAF-V600E_OS_race.pdf b/analyses/survival/plots/GNG/km_GNG_BRAF-V600E_OS_race.pdf
diff --git a/analyses/survival/plots/GNG/km_GNG_EFS_EUR_status.pdf b/analyses/survival/plots/GNG/km_GNG_EFS_EUR_status.pdf
diff --git a/analyses/survival/plots/GNG/km_GNG_EFS_ethnicity.pdf b/analyses/survival/plots/GNG/km_GNG_EFS_ethnicity.pdf
diff --git a/analyses/survival/plots/GNG/km_GNG_EFS_predicted_ancestry.pdf b/analyses/survival/plots/GNG/km_GNG_EFS_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/GNG/km_GNG_EFS_race.pdf b/analyses/survival/plots/GNG/km_GNG_EFS_race.pdf
diff --git a/analyses/survival/plots/GNG/km_GNG_OS_EUR_status.pdf b/analyses/survival/plots/GNG/km_GNG_OS_EUR_status.pdf
diff --git a/analyses/survival/plots/GNG/km_GNG_OS_ethnicity.pdf b/analyses/survival/plots/GNG/km_GNG_OS_ethnicity.pdf
diff --git a/analyses/survival/plots/GNG/km_GNG_OS_predicted_ancestry.pdf b/analyses/survival/plots/GNG/km_GNG_OS_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/GNG/km_GNG_OS_race.pdf b/analyses/survival/plots/GNG/km_GNG_OS_race.pdf
diff --git a/analyses/survival/plots/GNG/km_GNG_Other-alteration_EFS_EUR_status.pdf b/analyses/survival/plots/GNG/km_GNG_Other-alteration_EFS_EUR_status.pdf
diff --git a/analyses/survival/plots/GNG/km_GNG_Other-alteration_EFS_ethnicity.pdf b/analyses/survival/plots/GNG/km_GNG_Other-alteration_EFS_ethnicity.pdf
diff --git a/analyses/survival/plots/GNG/km_GNG_Other-alteration_EFS_predicted_ancestry.pdf b/analyses/survival/plots/GNG/km_GNG_Other-alteration_EFS_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/GNG/km_GNG_Other-alteration_EFS_race.pdf b/analyses/survival/plots/GNG/km_GNG_Other-alteration_EFS_race.pdf
diff --git a/analyses/survival/plots/GNG/km_GNG_Other-alteration_OS_EUR_status.pdf b/analyses/survival/plots/GNG/km_GNG_Other-alteration_OS_EUR_status.pdf
diff --git a/analyses/survival/plots/GNG/km_GNG_Other-alteration_OS_ethnicity.pdf b/analyses/survival/plots/GNG/km_GNG_Other-alteration_OS_ethnicity.pdf
diff --git a/analyses/survival/plots/GNG/km_GNG_Other-alteration_OS_predicted_ancestry.pdf b/analyses/survival/plots/GNG/km_GNG_Other-alteration_OS_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/GNG/km_GNG_Other-alteration_OS_race.pdf b/analyses/survival/plots/GNG/km_GNG_Other-alteration_OS_race.pdf
diff --git a/analyses/survival/plots/HGG/forest_HGG_EFS_subtype_EUR_status.pdf b/analyses/survival/plots/HGG/forest_HGG_EFS_subtype_EUR_status.pdf
diff --git a/analyses/survival/plots/HGG/forest_HGG_EFS_subtype_ethnicity.pdf b/analyses/survival/plots/HGG/forest_HGG_EFS_subtype_ethnicity.pdf
diff --git a/analyses/survival/plots/HGG/forest_HGG_EFS_subtype_predicted_ancestry.pdf b/analyses/survival/plots/HGG/forest_HGG_EFS_subtype_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/HGG/forest_HGG_EFS_subtype_race.pdf b/analyses/survival/plots/HGG/forest_HGG_EFS_subtype_race.pdf
diff --git a/analyses/survival/plots/HGG/forest_HGG_H3-WT_EFS_subtype_EUR_status.pdf b/analyses/survival/plots/HGG/forest_HGG_H3-WT_EFS_subtype_EUR_status.pdf
diff --git a/analyses/survival/plots/HGG/forest_HGG_H3-WT_EFS_subtype_ethnicity.pdf b/analyses/survival/plots/HGG/forest_HGG_H3-WT_EFS_subtype_ethnicity.pdf
diff --git a/analyses/survival/plots/HGG/forest_HGG_H3-WT_EFS_subtype_predicted_ancestry.pdf b/analyses/survival/plots/HGG/forest_HGG_H3-WT_EFS_subtype_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/HGG/forest_HGG_H3-WT_EFS_subtype_race.pdf b/analyses/survival/plots/HGG/forest_HGG_H3-WT_EFS_subtype_race.pdf
diff --git a/analyses/survival/plots/HGG/forest_HGG_H3-WT_OS_subtype_EUR_status.pdf b/analyses/survival/plots/HGG/forest_HGG_H3-WT_OS_subtype_EUR_status.pdf
diff --git a/analyses/survival/plots/HGG/forest_HGG_H3-WT_OS_subtype_ethnicity.pdf b/analyses/survival/plots/HGG/forest_HGG_H3-WT_OS_subtype_ethnicity.pdf
diff --git a/analyses/survival/plots/HGG/forest_HGG_H3-WT_OS_subtype_predicted_ancestry.pdf b/analyses/survival/plots/HGG/forest_HGG_H3-WT_OS_subtype_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/HGG/forest_HGG_H3-WT_OS_subtype_race.pdf b/analyses/survival/plots/HGG/forest_HGG_H3-WT_OS_subtype_race.pdf
diff --git a/analyses/survival/plots/HGG/forest_HGG_OS_subtype_EUR_status.pdf b/analyses/survival/plots/HGG/forest_HGG_OS_subtype_EUR_status.pdf
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diff --git a/analyses/survival/plots/HGG/forest_HGG_OS_subtype_predicted_ancestry.pdf b/analyses/survival/plots/HGG/forest_HGG_OS_subtype_predicted_ancestry.pdf
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diff --git a/analyses/survival/plots/HGG/km_HGG_EFS_EUR_status.pdf b/analyses/survival/plots/HGG/km_HGG_EFS_EUR_status.pdf
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diff --git a/analyses/survival/plots/LGG/forest_LGG_BRAF-V600E_EFS_subtype_EUR_status.pdf b/analyses/survival/plots/LGG/forest_LGG_BRAF-V600E_EFS_subtype_EUR_status.pdf
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diff --git a/analyses/survival/plots/LGG/forest_LGG_Other-alteration_EFS_subtype_EUR_status.pdf b/analyses/survival/plots/LGG/forest_LGG_Other-alteration_EFS_subtype_EUR_status.pdf
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diff --git a/analyses/survival/plots/MB/forest_MB_SHH_OS_subtype_EUR_status.pdf b/analyses/survival/plots/MB/forest_MB_SHH_OS_subtype_EUR_status.pdf
diff --git a/analyses/survival/plots/MB/forest_MB_SHH_OS_subtype_ethnicity.pdf b/analyses/survival/plots/MB/forest_MB_SHH_OS_subtype_ethnicity.pdf
diff --git a/analyses/survival/plots/MB/forest_MB_SHH_OS_subtype_predicted_ancestry.pdf b/analyses/survival/plots/MB/forest_MB_SHH_OS_subtype_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/MB/forest_MB_SHH_OS_subtype_race.pdf b/analyses/survival/plots/MB/forest_MB_SHH_OS_subtype_race.pdf
diff --git a/analyses/survival/plots/MB/forest_MB_WNT_EFS_subtype_EUR_status.pdf b/analyses/survival/plots/MB/forest_MB_WNT_EFS_subtype_EUR_status.pdf
diff --git a/analyses/survival/plots/MB/forest_MB_WNT_EFS_subtype_ethnicity.pdf b/analyses/survival/plots/MB/forest_MB_WNT_EFS_subtype_ethnicity.pdf
diff --git a/analyses/survival/plots/MB/forest_MB_WNT_EFS_subtype_predicted_ancestry.pdf b/analyses/survival/plots/MB/forest_MB_WNT_EFS_subtype_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/MB/forest_MB_WNT_EFS_subtype_race.pdf b/analyses/survival/plots/MB/forest_MB_WNT_EFS_subtype_race.pdf
diff --git a/analyses/survival/plots/MB/forest_MB_WNT_OS_subtype_EUR_status.pdf b/analyses/survival/plots/MB/forest_MB_WNT_OS_subtype_EUR_status.pdf
diff --git a/analyses/survival/plots/MB/forest_MB_WNT_OS_subtype_ethnicity.pdf b/analyses/survival/plots/MB/forest_MB_WNT_OS_subtype_ethnicity.pdf
diff --git a/analyses/survival/plots/MB/forest_MB_WNT_OS_subtype_predicted_ancestry.pdf b/analyses/survival/plots/MB/forest_MB_WNT_OS_subtype_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/MB/forest_MB_WNT_OS_subtype_race.pdf b/analyses/survival/plots/MB/forest_MB_WNT_OS_subtype_race.pdf
diff --git a/analyses/survival/plots/MB/km_MB_EFS_EUR_status.pdf b/analyses/survival/plots/MB/km_MB_EFS_EUR_status.pdf
diff --git a/analyses/survival/plots/MB/km_MB_EFS_ethnicity.pdf b/analyses/survival/plots/MB/km_MB_EFS_ethnicity.pdf
diff --git a/analyses/survival/plots/MB/km_MB_EFS_predicted_ancestry.pdf b/analyses/survival/plots/MB/km_MB_EFS_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/MB/km_MB_EFS_race.pdf b/analyses/survival/plots/MB/km_MB_EFS_race.pdf
diff --git a/analyses/survival/plots/MB/km_MB_Group3_EFS_EUR_status.pdf b/analyses/survival/plots/MB/km_MB_Group3_EFS_EUR_status.pdf
diff --git a/analyses/survival/plots/MB/km_MB_Group3_EFS_ethnicity.pdf b/analyses/survival/plots/MB/km_MB_Group3_EFS_ethnicity.pdf
diff --git a/analyses/survival/plots/MB/km_MB_Group3_EFS_predicted_ancestry.pdf b/analyses/survival/plots/MB/km_MB_Group3_EFS_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/MB/km_MB_Group3_EFS_race.pdf b/analyses/survival/plots/MB/km_MB_Group3_EFS_race.pdf
diff --git a/analyses/survival/plots/MB/km_MB_Group3_OS_EUR_status.pdf b/analyses/survival/plots/MB/km_MB_Group3_OS_EUR_status.pdf
diff --git a/analyses/survival/plots/MB/km_MB_Group3_OS_ethnicity.pdf b/analyses/survival/plots/MB/km_MB_Group3_OS_ethnicity.pdf
diff --git a/analyses/survival/plots/MB/km_MB_Group3_OS_predicted_ancestry.pdf b/analyses/survival/plots/MB/km_MB_Group3_OS_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/MB/km_MB_Group3_OS_race.pdf b/analyses/survival/plots/MB/km_MB_Group3_OS_race.pdf
diff --git a/analyses/survival/plots/MB/km_MB_Group4_EFS_EUR_status.pdf b/analyses/survival/plots/MB/km_MB_Group4_EFS_EUR_status.pdf
diff --git a/analyses/survival/plots/MB/km_MB_Group4_EFS_ethnicity.pdf b/analyses/survival/plots/MB/km_MB_Group4_EFS_ethnicity.pdf
diff --git a/analyses/survival/plots/MB/km_MB_Group4_EFS_predicted_ancestry.pdf b/analyses/survival/plots/MB/km_MB_Group4_EFS_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/MB/km_MB_Group4_EFS_race.pdf b/analyses/survival/plots/MB/km_MB_Group4_EFS_race.pdf
diff --git a/analyses/survival/plots/MB/km_MB_Group4_OS_EUR_status.pdf b/analyses/survival/plots/MB/km_MB_Group4_OS_EUR_status.pdf
diff --git a/analyses/survival/plots/MB/km_MB_Group4_OS_ethnicity.pdf b/analyses/survival/plots/MB/km_MB_Group4_OS_ethnicity.pdf
diff --git a/analyses/survival/plots/MB/km_MB_Group4_OS_predicted_ancestry.pdf b/analyses/survival/plots/MB/km_MB_Group4_OS_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/MB/km_MB_Group4_OS_race.pdf b/analyses/survival/plots/MB/km_MB_Group4_OS_race.pdf
diff --git a/analyses/survival/plots/MB/km_MB_OS_EUR_status.pdf b/analyses/survival/plots/MB/km_MB_OS_EUR_status.pdf
diff --git a/analyses/survival/plots/MB/km_MB_OS_ethnicity.pdf b/analyses/survival/plots/MB/km_MB_OS_ethnicity.pdf
diff --git a/analyses/survival/plots/MB/km_MB_OS_predicted_ancestry.pdf b/analyses/survival/plots/MB/km_MB_OS_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/MB/km_MB_OS_race.pdf b/analyses/survival/plots/MB/km_MB_OS_race.pdf
diff --git a/analyses/survival/plots/MB/km_MB_SHH_EFS_EUR_status.pdf b/analyses/survival/plots/MB/km_MB_SHH_EFS_EUR_status.pdf
diff --git a/analyses/survival/plots/MB/km_MB_SHH_EFS_ethnicity.pdf b/analyses/survival/plots/MB/km_MB_SHH_EFS_ethnicity.pdf
diff --git a/analyses/survival/plots/MB/km_MB_SHH_EFS_predicted_ancestry.pdf b/analyses/survival/plots/MB/km_MB_SHH_EFS_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/MB/km_MB_SHH_EFS_race.pdf b/analyses/survival/plots/MB/km_MB_SHH_EFS_race.pdf
diff --git a/analyses/survival/plots/MB/km_MB_SHH_OS_EUR_status.pdf b/analyses/survival/plots/MB/km_MB_SHH_OS_EUR_status.pdf
diff --git a/analyses/survival/plots/MB/km_MB_SHH_OS_ethnicity.pdf b/analyses/survival/plots/MB/km_MB_SHH_OS_ethnicity.pdf
diff --git a/analyses/survival/plots/MB/km_MB_SHH_OS_predicted_ancestry.pdf b/analyses/survival/plots/MB/km_MB_SHH_OS_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/MB/km_MB_SHH_OS_race.pdf b/analyses/survival/plots/MB/km_MB_SHH_OS_race.pdf
diff --git a/analyses/survival/plots/MB/km_MB_WNT_EFS_EUR_status.pdf b/analyses/survival/plots/MB/km_MB_WNT_EFS_EUR_status.pdf
diff --git a/analyses/survival/plots/MB/km_MB_WNT_EFS_ethnicity.pdf b/analyses/survival/plots/MB/km_MB_WNT_EFS_ethnicity.pdf
diff --git a/analyses/survival/plots/MB/km_MB_WNT_EFS_predicted_ancestry.pdf b/analyses/survival/plots/MB/km_MB_WNT_EFS_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/MB/km_MB_WNT_EFS_race.pdf b/analyses/survival/plots/MB/km_MB_WNT_EFS_race.pdf
diff --git a/analyses/survival/plots/MB/km_MB_WNT_OS_EUR_status.pdf b/analyses/survival/plots/MB/km_MB_WNT_OS_EUR_status.pdf
diff --git a/analyses/survival/plots/MB/km_MB_WNT_OS_ethnicity.pdf b/analyses/survival/plots/MB/km_MB_WNT_OS_ethnicity.pdf
diff --git a/analyses/survival/plots/MB/km_MB_WNT_OS_predicted_ancestry.pdf b/analyses/survival/plots/MB/km_MB_WNT_OS_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/MB/km_MB_WNT_OS_race.pdf b/analyses/survival/plots/MB/km_MB_WNT_OS_race.pdf
diff --git a/analyses/survival/plots/MES/forest_MES_EFS_subtype_EUR_status.pdf b/analyses/survival/plots/MES/forest_MES_EFS_subtype_EUR_status.pdf
diff --git a/analyses/survival/plots/MES/forest_MES_EFS_subtype_ethnicity.pdf b/analyses/survival/plots/MES/forest_MES_EFS_subtype_ethnicity.pdf
diff --git a/analyses/survival/plots/MES/forest_MES_EFS_subtype_predicted_ancestry.pdf b/analyses/survival/plots/MES/forest_MES_EFS_subtype_predicted_ancestry.pdf
diff --git a/analyses/survival/plots/MES/forest_MES_EFS_subtype_race.pdf b/analyses/survival/plots/MES/forest_MES_EFS_subtype_race.pdf