diff --git a/scripts/functions/combining_dfs_plotting.R b/scripts/functions/combining_dfs_plotting.R index 6016aea..88f62b6 100644 --- a/scripts/functions/combining_dfs_plotting.R +++ b/scripts/functions/combining_dfs_plotting.R @@ -204,29 +204,33 @@ combining_dfs_plotting <- function( my_df_u #----------------------- # lineage labels #----------------------- - merged_df2$lineage_labels = gsub("lineage", "L", merged_df2$lineage) + # merged_df2$lineage_labels = gsub("lineage", "L", merged_df2$lineage) - merged_df2$lineage_labels = factor(merged_df2$lineage_labels, c("L1" - , "L2" - , "L3" - , "L4" - , "L5" - , "L6" - , "L7" - , "LBOV" - , "L1;L2" - , "L1;L3" - , "L1;L4" - , "L2;L3" - , "L2;L3;L4" - , "L2;L4" - , "L2;L6" - , "L2;LBOV" - , "L3;L4" - , "L4;L6" - , "L4;L7" - , "")) + # Already solved upstream where lineage now contains L prefix + # merged_df2$lineage_labels = factor(merged_df2$lineage_labels, c("L1" + # , "L2" + # , "L3" + # , "L4" + # , "L5" + # , "L6" + # , "L7" + # , "LBOV" + # , "L1;L2" + # , "L1;L3" + # , "L1;L4" + # , "L2;L3" + # , "L2;L3;L4" + # , "L2;L4" + # , "L2;L6" + # , "L2;LBOV" + # , "L3;L4" + # , "L4;L6" + # , "L4;L7" + # , "")) + merged_df2$lineage_labels = merged_df2$lineage + #merged_df2$lineage_labels = as.factor(merged_df2$lineage_labels) + #merged_df2$lineage_labels = factor(merged_df2$lineage_labels) #================================================================= # Merge 2: merged_df3