#source("~/git/LSHTM_analysis/config/gid.R")
#source("~/git/LSHTM_analysis/config/pnca.R") # YES
source("~/git/LSHTM_analysis/config/embb.R")
#---------------------------------------------------
# FIXME
# source("~/git/LSHTM_analysis/config/alr.R")
# source("~/git/LSHTM_analysis/config/embb.R")
# source("~/git/LSHTM_analysis/config/katg.R")
# source("~/git/LSHTM_analysis/config/rpob.R")
#---------------------------------------------------
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
# 
# ################################
# # Logo plot with custom Y axis
# # mainly OR
# # script: logoP.R
# ################################
# LogoPlotCustomH (plot_df = merged_df3
#                             , x_axis_colname = "position"
#                             , y_axis_colname = "or_mychisq"
#                             , symbol_colname = "mutant_type"
#                             , y_axis_log  = F
#                             , log_value = log10
#                             , y_axis_increment = 5
#                             , rm_empty_y = F
#                             , my_logo_col = 'chemistry'
#                             , x_lab = "Wild-type position"
#                             , y_lab = "Odds Ratio"
#                             , x_ats = 12 # text size
#                             , x_tangle = 90 # text angle
#                             , y_ats = 22
#                             , y_tangle = 0
#                             , x_tts = 19 # title size
#                             , y_tts = 22
#                             #, leg_pos = c(0.05,-0.12)
#                             , leg_pos = "top"
#                             , leg_dir = "horizontal"
#                             , leg_ts = 15 # leg text size
#                             , leg_tts = 16 # leg title size
# )
# 
# 
# # ########################################
# # # Logo plot showing nsSNPs by positions
# # # wild-type and mutant aa
# # # script: logoP_snp.R
# # ########################################
# LogoPlotSnps(plot_df = merged_df3
#              , x_axis_colname = "position"
#              , symbol_mut_colname = "mutant_type"
#              , symbol_wt_colname = "wild_type"
#              , omit_snp_count = c(0)# can be 1, 2, etc.
#              , my_logo_col = "chemistry"
#              , x_lab = "Wild-type position"
#              , y_lab = ""
#              , x_ats = 13 # text size
#              , x_tangle = 90 # text angle
#              , y_ats = 20
#              , y_tangle = 0
#              , x_tts = 18 # title size
#              , y_tts = 18
#              , leg_pos = "top" # can be top, left, right and bottom or c(0.8, 0.9)
#              , leg_dir = "horizontal" # can be vertical or horizontal
#              , leg_ts = 14 # leg text size
#              , leg_tts = 16 # leg title size
# )
# 
# 

########################################
# Logo plot MSA
# Mutant and wild-type
# wild-type and mutant aa
# Can select active site residues
  # specify {plot_positions}
  # To plot entire MSA, simply don't specify {plot_positions}
# script: logoP_msa.R
# TODO perhaps: ED logo from Logolas

########################################
LogoPlotMSA(msaSeq_mut = msa_seq
            , msaSeq_wt = wt_seq
            , msa_method = 'bits' # or probability
            , my_logo_col = "taylor" 
            #, plot_positions = active_aa_pos
            , x_lab = "nsSNP position"
            , y_lab = ""
            , x_ats = 10 # text size
            , x_tangle = 90 # text angle
            , y_ats = 13
            , y_tangle = 0
            , x_tts = 13 # title size
            , y_tts = 13
            , leg_pos = "top" # can be top, left, right and bottom or c(0.8, 0.9)
            , leg_dir = "horizontal" #can be vertical or horizontal
            , leg_ts = 16 # leg text size
            , leg_tts = 16 # leg title size
)