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lineage labels gsub now redundant in combining_dfs_plotting.R

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Tanushree Tunstall 2022-05-05 19:31:00 +01:00
parent d61d11e020
commit 39566ceadd
1 changed files with 25 additions and 21 deletions
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46
scripts/functions/combining_dfs_plotting.R
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@ -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