Velma r

Minor fix to methanogenesis correlation fig

R_stats/mibipa_2hp_extended_data.Rmd

@@ -1640,7 +1640,7 @@ mgmt_2hp_met <- do.call("rbind", lapply(
     res <- subset_cors(df, "X2HP")
     colnames(res)[grep("Feature", colnames(res))] <- "KO"
     res <- merge(res, metgene_df)
-    res$Type <- x
+    res$Data <- x
     return(res)
   }))
 
@@ -1650,20 +1650,22 @@ mgmt_2hp_met$p_cat <- cut(mgmt_2hp_met$fdr,
                           include.lowest = TRUE)
 mgmt_2hp_met$p_cat <- factor(mgmt_2hp_met$p_cat,
                              levels = rev(levels(mgmt_2hp_met$p_cat)))
-mgmt_2hp_met_tab <- dcast(mgmt_2hp_met, Type + Subset ~ p_cat)
-mgmt_2hp_met_tab <- cbind(mgmt_2hp_met_tab[,1:2],
-                          prop.table(as.matrix(mgmt_2hp_met_tab[,3:7]), 1)*100)
+mgmt_2hp_met_tab <- dcast(mgmt_2hp_met, Type + Data + Subset ~ p_cat)
+mgmt_2hp_met_tab <- cbind(mgmt_2hp_met_tab[,1:3],
+                          prop.table(as.matrix(mgmt_2hp_met_tab[,4:8]), 1)*100)
 mgmt_2hp_met_tab <- melt(mgmt_2hp_met_tab)
 mgmt_2hp_met_tab <- subset(mgmt_2hp_met_tab, variable != "n.s.")
 mgmt_2hp_met_tab$Subset <- capitalize(mgmt_2hp_met_tab$Subset)
-
+mgmt_2hp_met_tab$Type <- capitalize(mgmt_2hp_met_tab$Type)
+mgmt_2hp_met_tab$Data_Type <- paste0(mgmt_2hp_met_tab$Data, " (", mgmt_2hp_met_tab$Type, ")")
+  
 metgene_cors_p <- ggplot(mgmt_2hp_met_tab,
        aes(x = Subset, y = value, fill = variable)) +
   geom_bar(stat = "identity", position = "stack",
            color = "black", size = 0.3) +
   scale_fill_manual(values = gray.colors(4, start = 0.95, end = 0.15),
                     name = "q-value\n(fdr-adjusted P)\nsignificance") +
-  facet_wrap(Type~., nrow = 1) +
+  facet_grid(.~Data_Type) +
   ylab("% of methanogenesis-related\ngenes correlated with 2-HP") +
   xlab("Data used for correlations") +
   custom_gg +