LSHTM_analysis/scripts/plotting/plotting_thesis/thesis-figs-alr.R

#
# small_df3 = merged_df3[merged_df3['position'] <= 670 & merged_df3['position'] >= 300,]
# 
# small_df3 = merged_df3[merged_df3['position'] <= 451 & merged_df3['position'] >= 300,]
# 
# 
# mutable_df3  = cbind(small_df3)
# plot_df = cbind(small_df3)

source("~/git/LSHTM_analysis/config/alr.R")
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
#outdir="/home/pub/Work/LSHTM/Thesis_Plots/"
outdir="~/git/Writing/thesis/tex/images-corrected/alr/"


# add "pos_count" position count column
merged_df3=merged_df3 %>% dplyr::add_count(position)
merged_df3$pos_count=merged_df3$n
merged_df3$n=NULL

# re-sort the dataframe according to position count
sorted_df = cbind(merged_df3)
sorted_df = sorted_df %>% arrange(pos_count)

# determine some split points

# further split up our sorted dataframe into low/mid/high for stability plotting
#snpcount_high_df = sorted_df[mid_snpcount:nrow(sorted_df),]
#snpcount_mid_df = sorted_df[low_snpcount:mid_snpcount,]
#snpcount_low_df = sorted_df[1:low_snpcount,]

snpcount_high_df = sorted_df[sorted_df$pos_count>1,]
snpcount_low_df  = sorted_df[sorted_df$pos_count<2,]

low_half_snpcount = round(nrow(snpcount_low_df)/2)

snpcount_low_low_df = snpcount_low_df[1:low_half_snpcount,]
snpcount_low_high_df = snpcount_low_df[low_half_snpcount:nrow(snpcount_low_df),]

#### Put sorted-by-pos_count bp_stability_hmaps here ####
#...if they look better :-)

length(merged_df3$position)

# manually picked numbers due to irregular position distribution
low = 170
centre=300
#low=round(max(merged_df3$position)/3)
#centre=low*2

# Generate heat bar for whole DF
heatbar_df = generate_distance_colour_map(merged_df3)

heat_bar_legend = get_legend(
  ggplot(merged_df3, aes(factor(ligand_distance), y=0)) +
    theme(legend.direction="horizontal",
          legend.title = element_text(size=10),
          #legend.text = element_text(size=10),
          #legend.key.size = unit(10, "pt")
    )+
    geom_point(aes(
      colour = ligand_distance,
      
    )
    ) +
    scale_colour_gradientn(
      name="Ligand\nDistance (Å)", 
      colours = magma(5, direction = -1))
)
# Position Tile Legend
# STR #00ff00
tile_colour_map = c("DCS"  = "#00ff00"
                    ,"PLP"  = "#000080")

tile_legend=get_legend(
  ggplot(tile_map, aes(factor(tile),y=0
                       , colour=tile_colour
                       , fill=tile_colour))+
    geom_tile() +
    theme(
      legend.direction="horizontal",
      legend.text = element_text(size=10),
      legend.key.size = unit(10, "pt")) +
    scale_colour_manual(name="Active Site:"
                        , values=tile_colour_map) +
    scale_fill_manual(name="Active Site:" 
                      , values = tile_colour_map)
)

# SAV Tile Red/Blue Legend

temp_snp_df=merged_df3%>%dplyr::add_count(position)

snp_tile_legend = get_legend(
  ggplot(temp_snp_df, aes(factor(avg_stability_scaled), y=0)) +
    theme(#legend.title = element_blank(),
      legend.direction="horizontal",
      legend.title = element_text(size=10),
      #legend.text = element_text(size=10),
      #legend.key.size = unit(10, "pt")
    )+
    geom_point(aes(
      colour = avg_stability_scaled,
      
    )
    ) +
    scale_colour_gradientn(
      name="Protein Stability\n(ΔΔG Kcal/mol)", colours = rev(
        c("#007ba4", # rev() because FUCK
          "#00bfc4",
          "#ffffff",
          "#ffd9d0",
          "#f8766d",
          "#ae3121")
      )
    )
)
# Logop Chemistry Colours
temp_logo_p_snp=cbind(merged_df3)
tab_mt = table(temp_logo_p_snp[["mutant_type"]], temp_logo_p_snp[["position"]])
tab_mt = unclass(tab_mt)
logoplot_chemistry_legend=get_legend(
  ggplot() +
    geom_logo(
      tab_mt
      , method = 'custom'
      , col_scheme = "chemistry"
      , seq_type = 'aa') + theme(
        legend.title = element_blank(),
        legend.direction="horizontal",
        legend.text = element_text(size=10),
        legend.key.size = unit(10, "pt")
      )
)

stab=function(...){bp_stability_hmap(
  small_df3,
  p_title = NULL,
  yvar_colname = 'avg_stability_scaled',
  stability_colname = "avg_stability_scaled",
  stability_outcome_colname = "avg_stability_outcome",
  my_ylab = "",
  my_xaxls = 6, # x-axis label size
  my_yaxls = 8, # y-axis label size
  drug_colour = tile_map$tile_colour[1],
  lig1_colour = tile_map$tile_colour[2],
  lig2_colour = tile_map$tile_colour[3],
  lig3_colour = tile_map$tile_colour[4],
  y_max_override=max(merged_df3$pos_count),
  aa_pos_drug=aa_pos_drug,
  active_aa_pos=active_aa_pos,
  aa_pos_lig1=aa_pos_lig1,
  aa_pos_lig2=aa_pos_lig2,
  aa_pos_lig3=aa_pos_lig3,
  ...
)
}



# LOW
small_df3 = merged_df3[merged_df3['position'] < low,]
mutable_df3  = cbind(small_df3)
print(paste0("Plotting LOW Rows: ", nrow(small_df3)))


logo_p_snps_low = LogoPlotSnps(
  mutable_df3,
  y_lab="SAV Diversity",
  aa_pos_drug=aa_pos_drug,
  active_aa_pos=active_aa_pos,
  aa_pos_lig1=aa_pos_lig1,
  aa_pos_lig2=aa_pos_lig2,
  aa_pos_lig3=aa_pos_lig3,
  drug_colour = tile_map$tile_colour[1],
  lig1_colour = tile_map$tile_colour[2],
  lig2_colour = tile_map$tile_colour[3],
  lig3_colour = tile_map$tile_colour[4]
)

# needs to be: active_aa_pos AND odds ratio >10
logo_or_low = LogoPlotCustomH(
  small_df3,
  y_axis_increment=10,
  y_lab="",
  aa_pos_drug=aa_pos_drug,
  active_aa_pos=active_aa_pos,
  aa_pos_lig1=aa_pos_lig1,
  aa_pos_lig2=aa_pos_lig2,
  aa_pos_lig3=aa_pos_lig3,
  rm_empty_y=FALSE,
  drug_colour = tile_map$tile_colour[1],
  lig1_colour = tile_map$tile_colour[2],
  lig2_colour = tile_map$tile_colour[3],
  lig3_colour = tile_map$tile_colour[4]
)

stability_low    = stab()+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3)


# MID
small_df3 = merged_df3[merged_df3['position'] <= centre & merged_df3['position'] >= low,]
mutable_df3  = cbind(small_df3)
print(paste0("Plotting MID Rows: ", nrow(small_df3)))

logo_p_snps_centre = LogoPlotSnps(
  mutable_df3,
  y_lab = "SAV Diversity",
  aa_pos_drug=aa_pos_drug,
  active_aa_pos=active_aa_pos,
  aa_pos_lig1=aa_pos_lig1,
  aa_pos_lig2=aa_pos_lig2,
  aa_pos_lig3=aa_pos_lig3,
  drug_colour = tile_map$tile_colour[1],
  lig1_colour = tile_map$tile_colour[2],
  lig2_colour = tile_map$tile_colour[3],
  lig3_colour = tile_map$tile_colour[4]
)

logo_or_centre = LogoPlotCustomH(
  small_df3, y_axis_increment=10, 
  rm_empty_y=FALSE,
  aa_pos_drug=aa_pos_drug,
  active_aa_pos=active_aa_pos,
  aa_pos_lig1=aa_pos_lig1,
  aa_pos_lig2=aa_pos_lig2,
  aa_pos_lig3=aa_pos_lig3,
  drug_colour = tile_map$tile_colour[1],
  lig1_colour = tile_map$tile_colour[2],
  lig2_colour = tile_map$tile_colour[3],
  lig3_colour = tile_map$tile_colour[4]
)

stability_centre = stab()

# HIGH
small_df3 = merged_df3[merged_df3['position'] > centre,]
mutable_df3  = cbind(small_df3)
print(paste0("Plotting HIGH Rows: ", nrow(small_df3)))


logo_p_snps_high = LogoPlotSnps(
  mutable_df3, 
  y_lab="SAV Diversity" ,
  aa_pos_drug=aa_pos_drug,
  active_aa_pos=active_aa_pos,
  aa_pos_lig1=aa_pos_lig1,
  aa_pos_lig2=aa_pos_lig2,
  aa_pos_lig3=aa_pos_lig3,
  drug_colour = tile_map$tile_colour[1],
  lig1_colour = tile_map$tile_colour[2],
  lig2_colour = tile_map$tile_colour[3],
  lig3_colour = tile_map$tile_colour[4]
)+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3)

logo_or_high = LogoPlotCustomH(
  small_df3, 
  y_axis_increment=10, 
  y_lab="", 
  aa_pos_drug=aa_pos_drug,
  active_aa_pos=active_aa_pos,
  aa_pos_lig1=aa_pos_lig1,
  aa_pos_lig2=aa_pos_lig2,
  aa_pos_lig3=aa_pos_lig3,
  rm_empty_y=FALSE,
  drug_colour = tile_map$tile_colour[1],
  lig1_colour = tile_map$tile_colour[2],
  lig2_colour = tile_map$tile_colour[3],
  lig3_colour = tile_map$tile_colour[4]
)+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3)


stability_high   = stab()+ annotate(geom="text", label="Wild-Type Position",x=0.5,y=0.025, size=3)
#### "sorted" stability plots ####

# do stability plots for later assembly
stability_high_reorder   = bp_stability_hmap(
  snpcount_high_df,
  reorder_position = T,
  p_title = NULL,
  my_ylab = NULL,
  yvar_colname = 'avg_stability_scaled',
  stability_colname = "avg_stability_scaled",
  stability_outcome_colname = "avg_stability_outcome",
  my_xaxls = 6, # x-axis label size
  my_yaxls = 8, # y-axis label size
  aa_pos_drug=aa_pos_drug,
  active_aa_pos=active_aa_pos,
  aa_pos_lig1=aa_pos_lig1,
  aa_pos_lig2=aa_pos_lig2,
  aa_pos_lig3=aa_pos_lig3,
  drug_colour = tile_map$tile_colour[1],
  lig1_colour = tile_map$tile_colour[2],
  lig2_colour = tile_map$tile_colour[3],
  lig3_colour = tile_map$tile_colour[4],
  x_label="Wild-Type Position"
  
)
stability_centre_reorder = bp_stability_hmap(
  snpcount_low_high_df,
  reorder_position = T,
  p_title = NULL,
  yvar_colname = 'avg_stability_scaled',
  stability_colname = "avg_stability_scaled",
  stability_outcome_colname = "avg_stability_outcome",
  my_ylab = "",
  y_max_override = max(snpcount_high_df$pos_count),
  my_xaxls = 6, # x-axis label size
  my_yaxls = 8, # y-axis label size
  aa_pos_drug=aa_pos_drug,
  active_aa_pos=active_aa_pos,
  aa_pos_lig1=aa_pos_lig1,
  aa_pos_lig2=aa_pos_lig2,
  aa_pos_lig3=aa_pos_lig3,
  drug_colour = tile_map$tile_colour[1],
  lig1_colour = tile_map$tile_colour[2],
  lig2_colour = tile_map$tile_colour[3],
  lig3_colour = tile_map$tile_colour[4]
)

stability_low_reorder    = bp_stability_hmap(
  snpcount_low_low_df,
  reorder_position = T,
  p_title = NULL,
  yvar_colname = 'avg_stability_scaled',
  stability_colname = "avg_stability_scaled",
  stability_outcome_colname = "avg_stability_outcome",
  my_ylab = NULL,
  y_max_override = max(snpcount_high_df$pos_count),
  my_xaxls = 6, # x-axis label size
  my_yaxls = 8, # y-axis label size
  aa_pos_drug=aa_pos_drug,
  active_aa_pos=active_aa_pos,
  aa_pos_lig1=aa_pos_lig1,
  aa_pos_lig2=aa_pos_lig2,
  aa_pos_lig3=aa_pos_lig3,
  drug_colour = tile_map$tile_colour[1],
  lig1_colour = tile_map$tile_colour[2],
  lig2_colour = tile_map$tile_colour[3],
  lig3_colour = tile_map$tile_colour[4]
  
)

jpeg(paste0(outdir,"alr_average_stability-sorted.jpeg"), height = 6, width=11.5, unit="in",res=300)
cowplot::plot_grid(
  cowplot::plot_grid(heat_bar_legend, tile_legend, snp_tile_legend, nrow=1),
  cowplot::plot_grid(stability_high_reorder, stability_centre_reorder, stability_low_reorder,ncol=1),
  ncol=1,
  rel_heights = c(1,12)
)
dev.off()

jpeg(paste0(outdir,"alr_average_stability-unsorted.jpeg"), height = 6, width=11.5, unit="in",res=300)
cowplot::plot_grid(
  cowplot::plot_grid(heat_bar_legend, tile_legend, snp_tile_legend, nrow=1),
  cowplot::plot_grid(stability_high, stability_centre, stability_low,ncol=1),
  ncol=1,
  rel_heights = c(1,12)
)
dev.off()

jpeg(paste0(outdir,"alr_snp.jpeg"), height = 6, width=11.5, unit="in",res=300)
cowplot::plot_grid(
  cowplot::plot_grid(heat_bar_legend, tile_legend, logoplot_chemistry_legend, nrow=1),
  cowplot::plot_grid(logo_p_snps_low, logo_p_snps_centre, logo_p_snps_high, ncol=1, align='hv'),
  ncol=1,
  rel_heights = c(1,12)
)
dev.off()

jpeg(paste0(outdir,"alr_or.jpeg"), height = 6, width=11.5, unit="in",res=300)
cowplot::plot_grid(
  cowplot::plot_grid(heat_bar_legend, tile_legend, logoplot_chemistry_legend, nrow=1),
  cowplot::plot_grid(logo_or_low, logo_or_centre, logo_or_high, ncol=1, align='hv'),
  ncol=1,
  rel_heights = c(1,12)
)
dev.off()