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git trimmed downthe dm_om_data.R

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Tanushree Tunstall 2022-08-05 14:36:02 +01:00
parent fae846395d
commit 05ab89ec09
5 changed files with 168 additions and 351 deletions
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43
scripts/plotting/plotting_thesis/preformatting.R
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@ -10,8 +10,10 @@ source("~/git/LSHTM_analysis/config/embb.R")
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
###################################################################
# FIXME: ADD distance to NA when SP replies
# DONE: plotting_globals.R
dist_columns = c("ligand_distance", "interface_dist")
DistCutOff = 10
common_cols = c("mutationinformation"
, "X5uhc_position"
, "X5uhc_offset"
@ -98,22 +100,24 @@ df3 = merged_df3
#=================
# PREFORMATTING: for consistency
#=================
df3$sensitivity = ifelse(df3$dst_mode == 1, "R", "S")
table(df3$sensitivity)
# DONE: combining_dfs.R
# df3$sensitivity = ifelse(df3$dst_mode == 1, "R", "S")
# table(df3$sensitivity)
# ConSurf labels
consurf_colOld = "consurf_colour_rev"
consurf_colNew = "consurf_outcome"
df3[[consurf_colNew]] = df3[[consurf_colOld]]
df3[[consurf_colNew]] = as.factor(df3[[consurf_colNew]])
df3[[consurf_colNew]]
#consurf_colOld = "consurf_colour_rev"
#consurf_colNew = "consurf_outcome"
#df3[[consurf_colNew]] = df3[[consurf_colOld]]
#df3[[consurf_colNew]] = as.factor(df3[[consurf_colNew]])
#df3[[consurf_colNew]]
# not this bit
levels(df3$consurf_outcome) = c( "nsd", 1, 2, 3, 4, 5, 6, 7, 8, 9)
levels(df3$consurf_outcome)
#levels(df3$consurf_outcome)
# SNAP2 labels
snap2_colname = "snap2_outcome"
df3[[snap2_colname]] <- str_replace(df3[[snap2_colname]], "effect", "Effect")
df3[[snap2_colname]] <- str_replace(df3[[snap2_colname]], "neutral", "Neutral")
#snap2_colname = "snap2_outcome"
#df3[[snap2_colname]] <- str_replace(df3[[snap2_colname]], "effect", "Effect")
#df3[[snap2_colname]] <- str_replace(df3[[snap2_colname]], "neutral", "Neutral")
# for ref: not needed perse as function already does this and assigns labels for barplots
# labels_duet = levels(as.factor(df3$duet_outcome))
@ -138,14 +142,16 @@ df2 = merged_df2
#=================
# PREFORMATTING: for consistency
#=================
df2$sensitivity = ifelse(df2$dst_mode == 1, "R", "S")
table(df2$sensitivity)
# DONE: combining_dfs.R
# df2$sensitivity = ifelse(df2$dst_mode == 1, "R", "S")
# table(df2$sensitivity)
#----------------------------------------------------
# Create dst2: fill na in dst with value of dst_mode
# for epistasis
#----------------------------------------------------
df2$dst2 = ifelse(is.na(df2$dst), df2$dst_mode, df2f$dst)
# DONE: combining_dfs.R
# df2$dst2 = ifelse(is.na(df2$dst), df2$dst_mode, df2f$dst)
#----------------------------------------------------
# reverse signs for foldx scaled values for
@ -168,10 +174,11 @@ scaled_cols_stab_revised = c(scaled_cols_stab_revised, "foldx_scaled_signC")
######################################################
# Affinity related variables
DistCutOff = 10
LigDist_colname # = "ligand_distance" # from globals
ppi2Dist_colname = "interface_dist"
naDist_colname = "TBC"
# DONE:in plotting_globals.R
# DistCutOff = 10
# LigDist_colname # = "ligand_distance" # from globals
# ppi2Dist_colname = "interface_dist"
# naDist_colname = "TBC"
######################################################
# corr colnames