#source("~/git/LSHTM_analysis/config/gid.R")
source("~/git/LSHTM_analysis/config/pnca.R")
#source("~/git/LSHTM_analysis/config/embb.R")
#source("~/git/LSHTM_analysis/config/katg.R")
#source("~/git/LSHTM_analysis/config/alr.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_or.R
################################
LP1<- 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 = 50
                            , rm_empty_y = F
                            , my_logo_col = 'chemistry'
                            , x_lab = "Wild-type position"
                            , y_lab = "Odds Ratio"
                            , x_ats = 10 # text size
                            , x_tangle = 90 # text angle
                            , y_ats = 15
                            , y_tangle = 0
                            , x_tts = 13 # title size
                            , y_tts = 13
                            #, 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
########################################
LP2<- 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 0,1, 2, etc.# DD
             , my_logo_col = "chemistry" #DD
             , x_lab = "Wild-type position"
             , y_lab = "nsSNP count"
             , x_ats = 10 
             , x_tangle = 90 
             , y_ats = 15
             , y_tangle = 0
             , x_tts = 13 
             , 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 = 14 
             , leg_tts = 16 
)

####################################################
# Logo plot MSA
# Mutant and wild-type
# Logo type: 
  # EDLogo
  # Bits/probability (PFM matrix)
  # Bits/probability (Raw MSA data)
# Can select active site residues
  # specify {plot_positions}
  # To plot entire MSA, simply don't specify {plot_positions}
# script: logoP_msa.R

# to select a small dataset: see test_ed_pfm_data.R
#####################################################
LP3<- LogoPlotMSA(unified_msa
                #msaSeq_mut = msa_seq
               #, msaSeq_wt = wt_seq
               , logo_type = c("EDLogo") # "EDLogo", bits_pfm", "probability_pfm", "bits_raw", "probability_raw")
               , EDScore_type =  c("log")
               , bg_prob = NULL
               , my_logo_col = "chemistry" 
               #, plot_positions = c(5:10, 92, 195, 118:119)
               , x_axis_offset = 0.02
               , x_axis_offset_filtered = 0.05
               , y_axis_offset = 0.05
               #, y_breaks = c(0, 2, 4, 6, 8, 10, 12)
               , x_lab_mut = "nsSNP-position"
               #, y_lab_mut
               , x_ats = 10
               , x_tangle = 90
               , y_ats = 12
               , y_tangle = 0
               , x_tts = 13
               , y_tts = 13
               , leg_pos = "top"
               , leg_dir = "horizontal" 
               , leg_ts = 16 
               , leg_tts = 16 
)



out_logoP = cowplot::plot_grid(LP3, LP1, LP2
                               , nrow = 3
                               , ncol = 1
                               , rel_width = c(1/3, 0.5/3, 1/3)
                               , rel_heights = c(0.8/2, 0.5/2, 0.7/2)
                               , align = "hv")

out_logoP
