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renamed files for lineage_diff_sensitivites.R

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This commit is contained in:
Tanushree Tunstall 2022-09-05 13:19:06 +01:00
parent 69a0da0a59
commit 1dacebbaf6
5 changed files with 179 additions and 39 deletions
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28
scripts/plotting/plotting_thesis/gid/lineage_diff_sensitivities.R → scripts/plotting/plotting_thesis/gid/gid_lineage_diff_sensitivities.R
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@ -45,20 +45,10 @@ lef_snps_df = df2[df2$mutationinformation%in%left_snps,]
table(lef_snps_df$lineage)
##################################
# selected lineage plos
cols_to_subset = c("mutationinformation"
, "lineage"
, "dst2"
, "sens2")
# selected lineage plots
##################################
#-----------------------------------------------
# step 0: Subset a smaller df
#-----------------------------------------------
plot_df_gene = df2_lin[, cols_to_subset]
#-----------------------------------------------
# step 1: Select muts for each target
# step 0: Select muts for each target
#-----------------------------------------------
# embb
#sel_mutsP = c("D354N", "Y319D", "Y319D", "A962P", "S651N", "A201S")
@ -69,6 +59,17 @@ sel_mutsP = c("P75R", "A19G", "A133P", "R154W", "R118L") #G30D)
# rpob
#sel_mutsP = c("")
#-----------------------------------------------
# step 1: Subset a smaller df
#-----------------------------------------------
cols_to_subset = c("mutationinformation"
, "lineage"
, "dst2"
, "sens2")
plot_df_gene = df2_lin[, cols_to_subset]
#-----------------------------------------------
# step 2: Subset data with just those genes
#-----------------------------------------------
plot_df_gene = plot_df_gene[plot_df_gene$mutationinformation%in%sel_mutsP,]
@ -82,6 +83,7 @@ plot_df = plot_df_gene
#-----------------------------------------------
# step 4: Add p-value
# NOT NEEDED, get it from lineage_diff_sensitivities.R if needed
#-----------------------------------------------