added cfr funnel plot

mrc-ide · Aug 30, 2024 · be0ae32 · be0ae32
1 parent 06e694d
commit be0ae32
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Showing 2 changed files with 27 additions and 8 deletions.
diff --git a/src/lassa_collate/orderly.R b/src/lassa_collate/orderly.R
@@ -7,9 +7,9 @@ orderly_dependency("lassa_serology", "latest(parameter:pathogen == this:pathogen
                    files = c("figure_2.png","figure_2.pdf"))
 orderly_dependency("lassa_severity", "latest(parameter:pathogen == this:pathogen)",
                    files = c("figure_3.png","figure_S7.png","figure_S8.png",
-                             "figure_S9.png","figure_S10.png","figure_S11.png","figure_S12.png","figure_S13.png",
+                             "figure_S9.png","figure_S10.png","figure_S11.png","figure_S12.png","figure_S13.png","figure_S14.png",
                              "figure_3.pdf","figure_S7.pdf","figure_S8.pdf",
-                             "figure_S9.pdf","figure_S10.pdf","figure_S11.pdf","figure_S12.pdf","figure_S13.pdf"))
+                             "figure_S9.pdf","figure_S10.pdf","figure_S11.pdf","figure_S12.pdf","figure_S13.pdf","figure_S14.pdf"))
 orderly_dependency("lassa_delays", "latest(parameter:pathogen == this:pathogen)",
                    files = c("figure_4.png","figure_S5.png","figure_S6.png","figure_4.pdf","figure_S5.pdf","figure_S6.pdf"))
 orderly_dependency("lassa_transmission", "latest(parameter:pathogen == this:pathogen)",
@@ -27,9 +27,11 @@ orderly_artefact("lassa-specific outputs",
                    "supp/figure_S2.png","supp/figure_S3.png","supp/figure_S4.png",
                    "supp/figure_S5.png","supp/figure_S6.png","supp/figure_S7.png","supp/figure_S8.png",
                    "supp/figure_S9.png","supp/figure_S10.png","supp/figure_S11.png","supp/figure_S12.png","supp/figure_S13.png",
+                   "supp/figure_S14.png",
                    "supp/figure_S2.pdf","supp/figure_S3.pdf","supp/figure_S4.pdf",
                    "supp/figure_S5.pdf","supp/figure_S6.pdf","supp/figure_S7.pdf","supp/figure_S8.pdf",
                    "supp/figure_S9.pdf","supp/figure_S10.pdf","supp/figure_S11.pdf","supp/figure_S12.pdf","supp/figure_S13.pdf",
+                   "supp/figure_S14.pdf",
                    "supp/latex_outbreaks.csv","supp/latex_models.csv",
                    "supp/latex_transmission.csv","supp/latex_delays.csv","supp/latex_severity.csv",
                    "supp/latex_seroprevalence.csv","supp/latex_riskfactors.csv"))
@@ -88,6 +90,8 @@ file.copy(from = "figure_S12.png",
           to = "supp/figure_S12.png")
 file.copy(from = "figure_S13.png",
           to = "supp/figure_S13.png")
+file.copy(from = "figure_S14.png",
+          to = "supp/figure_S14.png")
 
 file.copy(from = "figure_S2.pdf",
           to = "supp/figure_S2.pdf")
@@ -113,6 +117,8 @@ file.copy(from = "figure_S12.pdf",
           to = "supp/figure_S12.pdf")
 file.copy(from = "figure_S13.pdf",
           to = "supp/figure_S13.pdf")
+file.copy(from = "figure_S14.pdf",
+          to = "supp/figure_S14.pdf")
 
 file.copy(from = "latex_outbreaks.csv",
           to = "supp/latex_outbreaks.csv")

diff --git a/src/lassa_severity/orderly.R b/src/lassa_severity/orderly.R
@@ -30,10 +30,10 @@ orderly_shared_resource("lassa_functions.R" = "lassa_functions.R")
 source("lassa_functions.R")
 orderly_artefact("lassa-specific figures",c("figure_3.png","figure_S7.png",
                                             "figure_S8.png","figure_S9.png","figure_S10.png",
-                                            "figure_S11.png","figure_S12.png","figure_S13.png",
+                                            "figure_S11.png","figure_S12.png","figure_S13.png","figure_S14.png",
                                             "figure_3.pdf","figure_S7.pdf",
                                             "figure_S8.pdf","figure_S9.pdf","figure_S10.pdf",
-                                            "figure_S11.pdf","figure_S12.pdf","figure_S13.pdf"))
+                                            "figure_S11.pdf","figure_S12.pdf","figure_S13.pdf","figure_S14.pdf"))
 
 ###################
 ## DATA CURATION ##
@@ -183,7 +183,7 @@ patchwork <- patchwork + plot_annotation(tag_levels = 'A')
 ggsave("figure_3.png", plot = patchwork, width = 18, height = 12)
 ggsave("figure_3.pdf", plot = patchwork, width = 18, height = 12)
 
-#figure_S6-S10: meta-analysis with all estimates plotted
+#figure_S7-S11: meta-analysis with all estimates plotted
 m1 <- metaprop_wrap(dataframe = da %>% arrange(-central), subgroup = "lineage", 
                     plot_pooled = TRUE, sort_by_subg = TRUE, plot_study = TRUE, digits = 3, colour = "red", 
                     width = 1200, height = 1600, resolution = 115)
@@ -217,7 +217,7 @@ ggsave("figure_S10.pdf", plot = p4, width = 12, height = 16)
 ggsave("figure_S11.png", plot = p5, width = 12, height = 16)
 ggsave("figure_S11.pdf", plot = p5, width = 12, height = 16)
 
-#figure_S11: meta-analysis with only known duplicates excluded
+#figure_S12: meta-analysis with only known duplicates excluded
 db <- d1 %>% filter(duplicate_cfr %in% c("False","Assumed"))
 
 m1 <- metaprop_wrap(dataframe = db, subgroup = "lineage", 
@@ -243,7 +243,7 @@ patchwork <- patchwork + plot_annotation(tag_levels = 'A')
 ggsave("figure_S12.png", plot = patchwork, width = 12, height = 12)
 ggsave("figure_S12.pdf", plot = patchwork, width = 12, height = 12)
 
-#figure_S12: meta-analysis without de-duplication
+#figure_S13: meta-analysis without de-duplication
 dc <- d1
 
 m1 <- metaprop_wrap(dataframe = dc, subgroup = "lineage", 
@@ -267,4 +267,17 @@ p4 <- m4$plot
 patchwork <- (p1 + p2 + p3 + p4) + plot_layout(ncol = 2, widths = c(1,1))
 patchwork <- patchwork + plot_annotation(tag_levels = 'A') 
 ggsave("figure_S13.png", plot = patchwork, width = 12, height = 12)
-ggsave("figure_S13.pdf", plot = patchwork, width = 12, height = 12)
+ggsave("figure_S13.pdf", plot = patchwork, width = 12, height = 12)
+
+#figure_S14: meta-analysis funnel plot
+png(file = "temp.png", width = 9500, height = 6500, res = 1000)
+funnel(m5$result, xlim = c(-3,2), ylim = c(0,1), common = FALSE,#only plots funnel for either common or random for some reason
+       pch = 22, bg = "red", level = 0.95, 
+       studlab = TRUE, cex.studlab = 0.75, pos.studlab = 2)
+dev.off()
+gg <- png::readPNG("temp.png", native = TRUE)
+file.remove("temp.png")
+gg <- wrap_elements(plot = rasterGrob(gg, interpolate = TRUE))
+
+ggsave("figure_S14.png", plot = gg, width = 12, height = 8)
+ggsave("figure_S14.pdf", plot = gg, width = 12, height = 8)