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horrible lineage analysis hell

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This commit is contained in:
Tanushree Tunstall 2022-06-28 21:51:02 +01:00
parent ce0f12382e
commit 478df927cc
10 changed files with 1669 additions and 101 deletions
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33
scripts/functions/combining_dfs_plotting.R
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@ -185,9 +185,6 @@ combining_dfs_plotting <- function( my_df_u
}
# Quick formatting: ordering df and pretty labels
#------------------------------
@ -198,36 +195,12 @@ combining_dfs_plotting <- function( my_df_u
#-----------------------
# mutation_info_labels
#-----------------------
merged_df2$mutation_info_labels = ifelse(merged_df2$mutation_info == dr_muts_col
, "DM", "OM")
merged_df2$mutation_info_labels = factor(merged_df2$mutation_info_labels)
#merged_df2$mutation_info_labels = ifelse(merged_df2$mutation_info == dr_muts_col
# , "DM", "OM")
#merged_df2$mutation_info_labels = factor(merged_df2$mutation_info_labels)
#-----------------------
# lineage labels
#-----------------------
# merged_df2$lineage_labels = gsub("lineage", "L", merged_df2$lineage)
# 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)