#################
# Numbers
##################
all_dm_om_df = dm_om_wf_lf_data(df = merged_df3, gene = gene)
# 
# lf_duet   = all_dm_om_df[['lf_duet']]
# table(lf_duet$param_type)
################################################################

#======================
# Data: Dist+genomics
#======================
lf_dist_genP   = all_dm_om_df[['lf_dist_gen']]
wf_dist_genP   = all_dm_om_df[['wf_dist_gen']]

levels(lf_dist_genP$param_type)
#lf_dist_genP$param_type <- factor(lf_dist_genP$param_type, levels=c("Log10(MAF)", "Lig Dist(Å)", "PPI Dist(Å)"))
table(lf_dist_genP$param_type)

genomics_param = c("Log10(MAF)")

dist_genP = lf_bp2(lf_dist_genP
               #, p_title
               , violin_quantiles = c(0.5), monochrome = F)

#-------------------
# Genomics data plot
#-------------------
genomics_dataP = lf_dist_genP[lf_dist_genP$param_type%in%genomics_param,]
genomics_dataP$param_type = factor(genomics_dataP$param_type)
table(genomics_dataP$param_type)

genomicsP = lf_bp2(genomics_dataP
                   #, p_title = ""
                   , violin_quantiles = c(0.5), monochrome = F)

genomicsP

#check
wilcox.test(wf_dist_genP$`Log10(MAF)`[wf_dist_genP$mutation_info_labels=="R"]
            , wf_dist_genP$`Log10(MAF)`[wf_dist_genP$mutation_info_labels=="S"], paired = FALSE)

tapply(wf_dist_genP$`Log10(MAF)`, wf_dist_genP$mutation_info_labels, summary)

#-------------------
# Distance data plot: not genomics data
#-------------------
dist_dataP = lf_dist_genP[!lf_dist_genP$param_type%in%genomics_param,]
#dist_dataP$param_type = factor(dist_dataP$param_type)
table(dist_dataP$param_type)

distanceP = lf_bp2(dist_dataP
                   #, p_title = ""
                   , violin_quantiles = c(0.5), monochrome = F)

distanceP

# check
wilcox.test(wf_dist_genP$`PPI Dist(Å)`[wf_dist_genP$mutation_info_labels=="R"]
, wf_dist_genP$`PPI Dist(Å)`[wf_dist_genP$mutation_info_labels=="S"], paired = FALSE)

wilcox.test(wf_dist_genP$`Lig Dist(Å)`[wf_dist_genP$mutation_info_labels=="R"]
            , wf_dist_genP$`Lig Dist(Å)`[wf_dist_genP$mutation_info_labels=="S"], paired = FALSE)

tapply(wf_dist_genP$`PPI Dist(Å)`, wf_dist_genP$mutation_info_labels, summary)

tapply(wf_dist_genP$`Lig Dist(Å)`, wf_dist_genP$mutation_info_labels, summary)

#==============
# Plot:DUET
#==============
lf_duetP   = all_dm_om_df[['lf_duet']]
#lf_duetP  = lf_duet[!lf_duet$param_type%in%c(static_colsP),]
table(lf_duetP$param_type)
lf_duetP$param_type = factor(lf_duetP$param_type)
table(lf_duetP$param_type)

duetP = lf_bp2(lf_duetP
               #, p_title = ""
               , violin_quantiles = c(0.5), monochrome = F
               , dot_transparency = 0.2)

#==============
# Plot:FoldX
#==============
lf_foldxP   = all_dm_om_df[['lf_foldx']]
#lf_foldxP  = lf_foldx[!lf_foldx$param_type%in%c(static_colsP),]
table(lf_foldxP$param_type)
lf_foldxP$param_type = factor(lf_foldxP$param_type)
table(lf_foldxP$param_type)

foldxP = lf_bp2(lf_foldxP
                #, p_title = ""
                , violin_quantiles = c(0.5), monochrome = F
                , dot_transparency = 0.1)

#==============
# Plot:DeepDDG
#==============
lf_deepddgP   = all_dm_om_df[['lf_deepddg']]
#lf_deepddgP  = lf_deepddg[!lf_deepddg$param_type%in%c(static_colsP),]
table(lf_deepddgP$param_type)
lf_deepddgP$param_type = factor(lf_deepddgP$param_type)
table(lf_deepddgP$param_type)

deepddgP = lf_bp2(lf_deepddgP
                  #, p_title = ""
                  , violin_quantiles = c(0.5), monochrome = F
                  , dot_transparency = 0.2)

deepddgP

#==============
# Plot: Dynamut2
#==============
lf_dynamut2P   = all_dm_om_df[['lf_dynamut2']]
#lf_dynamut2P  = lf_dynamut2[!lf_dynamut2$param_type%in%c(static_colsP),]
table(lf_dynamut2P$param_type)
lf_dynamut2P$param_type = factor(lf_dynamut2P$param_type)
table(lf_dynamut2P$param_type)

dynamut2P = lf_bp2(lf_dynamut2P
                   #, p_title = ""
                   , violin_quantiles = c(0.5), monochrome = F
                   , dot_transparency = 0.2)


#==============
# Plot:ConSurf
#==============
lf_consurfP   = all_dm_om_df[['lf_consurf']]
#lf_consurfP  = lf_consurf[!lf_consurf$param_type%in%c(static_colsP),]
table(lf_consurfP$param_type)
lf_consurfP$param_type = factor(lf_consurfP$param_type)
table(lf_consurfP$param_type)

consurfP = lf_bp2(lf_consurfP
                  #, p_title = ""
                  , violin_quantiles = c(0.5), monochrome = F)

#==============
# Plot:PROVEAN
#==============
lf_proveanP   = all_dm_om_df[['lf_provean']]
#lf_proveanP  = lf_provean[!lf_provean$param_type%in%c(static_colsP),]
table(lf_proveanP$param_type)
lf_proveanP$param_type = factor(lf_proveanP$param_type)
table(lf_proveanP$param_type)

proveanP = lf_bp2(lf_proveanP
                  #, p_title = ""
                  , violin_quantiles = c(0.5), monochrome = F)

#==============
# Plot:SNAP2
#==============
lf_snap2P  = all_dm_om_df[['lf_snap2']]
#lf_snap2P  = lf_snap2[!lf_snap2$param_type%in%c(static_colsP),]
table(lf_snap2P$param_type)
lf_snap2P$param_type = factor(lf_snap2P$param_type)
table(lf_snap2P$param_type)

snap2P = lf_bp2(lf_snap2P
                #, p_title = ""
                , violin_quantiles = c(0.5), monochrome = F)


############################################################################
#================
# Plot: mCSM-lig
#================
lf_mcsm_ligP   = all_dm_om_df[['lf_mcsm_lig']]
#lf_mcsm_ligP  = lf_mcsm_lig[!lf_mcsm_lig$param_type%in%c(static_colsP),]
table(lf_mcsm_ligP$param_type)
lf_mcsm_ligP$param_type = factor(lf_mcsm_ligP$param_type)
table(lf_mcsm_ligP$param_type)

mcsmligP = lf_bp2(lf_mcsm_ligP
                  #, p_title = ""
                  , violin_quantiles = c(0.5), monochrome = F
                  , dot_transparency = 1)


#=================
# Plot: mmCSM-lig2
#=================
lf_mmcsm_lig2P   = all_dm_om_df[['lf_mmcsm_lig2']]
#lf_mmcsm_lig2P  = lf_mmcsm_lig2P[!lf_mmcsm_lig2P$param_type%in%c(static_colsP),]
table(lf_mmcsm_lig2P$param_type)
lf_mmcsm_lig2P$param_type = factor(lf_mmcsm_lig2P$param_type)
table(lf_mmcsm_lig2P$param_type)

mcsmlig2P = lf_bp2(lf_mmcsm_lig2P
                   #, p_title = ""
                   , violin_quantiles = c(0.5), monochrome = F
                   , dot_transparency = 1)

mcsmlig2P

#================
# Plot: mCSM-ppi2
#================
if (tolower(gene)%in%geneL_ppi2){
  lf_mcsm_ppi2P   = all_dm_om_df[['lf_mcsm_ppi2']]
  #lf_mcsm_ppi2P  = lf_mcsm_ppi2[!lf_mcsm_ppi2$param_type%in%c(static_colsP),]
  table(lf_mcsm_ppi2P$param_type)
  lf_mcsm_ppi2P$param_type = factor(lf_mcsm_ppi2P$param_type)
  table(lf_mcsm_ppi2P$param_type)
  
  mcsmppi2P = lf_bp2(lf_mcsm_ppi2P
                     #, p_title = ""
                     , violin_quantiles = c(0.5), monochrome = F
                     , dot_transparency = 1)
  
}

#==============
# Plot: mCSM-NA
#==============
if (tolower(gene)%in%geneL_na){
  lf_mcsm_naP   = all_dm_om_df[['lf_mcsm_na']]
  #lf_mcsm_naP  = lf_mcsm_na[!lf_mcsm_na$param_type%in%c(static_colsP),]
  table(lf_mcsm_naP$param_type)
  lf_mcsm_naP$param_type = factor(lf_mcsm_naP$param_type)
  table(lf_mcsm_naP$param_type)
  
  mcsmnaP = lf_bp2(lf_mcsm_naP
                   #, p_title = ""
                   , violin_quantiles = c(0.5), monochrome = F
                   , dot_transparency = 1)
  
}

######################################
# Outplot  with stats
######################################
outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene), "/")

dm_om_combinedP =  paste0(outdir_images
                   ,tolower(gene)
                   ,"_dm_om_all.svg" )

cat("DM OM plots with stats:", dm_om_combinedP)
svg(dm_om_combinedP, width = 32, height = 18)
cowplot::plot_grid(
  cowplot::plot_grid(duetP, foldxP, deepddgP, dynamut2P, genomicsP, distanceP
                   , nrow=1
                   , rel_widths = c(1/7, 1/7,1/7,1/7, 1/7, 1.75/7)),
                   #, rel_widths = c(1/8, 1/8,1/8,1/8, 1/8, 2.75/8)), # for 3 distances
  cowplot::plot_grid(consurfP, proveanP, snap2P
                   , mcsmligP
                   , mcsmlig2P
                   , mcsmppi2P
                   #, mcsmnaP
                   , nrow=1),
  nrow=2)

dev.off()

#foo = lf_consurfP

# proveanP = lf_bp2(lf_proveanP, colour_categ = "mutation_info_labels"
#                   , p_title = paste0("Evolutionary conservation")
#                   , dot_transparency = 1
#                   , violin_quantiles = c(0.5), monochrome = F)
# 
# proveanP