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consurf tile fixes

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This commit is contained in:
Tanushree Tunstall 2022-08-08 15:37:17 +01:00
parent 0234a8f77b
commit 28510471f0
2 changed files with 169 additions and 163 deletions
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1
scripts/functions/logoP_msa.R
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@ -459,3 +459,4 @@ LogoPlotMSA <- function(unified_msa
return(LogoED_comb) return(LogoED_comb)
} }
#LogoPlotMSA(unified_msa)

295
scripts/functions/wideP_consurf.R
View file

@ -12,81 +12,79 @@
# wideP(): # wideP():
# input args # input args
#========================================================== #==========================================================
wideP_consurf <- function(plot_df wideP_consurf2 <- function(plot_df
, xvar_colname = "position" , xvar_colname = "position"
, yvar_colname = "consurf_score" , yvar_colname = "consurf_score"
, yvar_colourN_colname = "consurf_colour_rev" # num from 0-1 , yvar_colourN_colname = "consurf_colour_rev" # num from 0-1
, plot_error_bars = T , plot_error_bars = T
, upper_EB_colname = "consurf_ci_upper" , upper_EB_colname = "consurf_ci_upper"
, lower_EB_colname = "consurf_ci_lower" , lower_EB_colname = "consurf_ci_lower"
, plot_type = "point" # default is point , plot_type = "point" # default is point
, point_colours , point_colours
, p_size = 2 , p_size = 2
, leg_title1 = "" , leg_title1 = ""
, leg_labels = c("0": "Insufficient Data" , leg_labels = c("0": "Insufficient Data"
, "1": "Variable" , "1": "Variable"
, "2", "3", "4", "5", "6", "7", "8" , "2", "3", "4", "5", "6", "7", "8"
, "9": "Conserved") , "9": "Conserved")
, panel_col = "white" , panel_col = "white"
, panel_col_fill = "white" , panel_col_fill = "white"
# axes title and label sizes # axes title and label sizes
, x_axls = 12 # x-axis label size , x_axls = 12 # x-axis label size
, y_axls = 15 # y-axis label size , y_axls = 15 # y-axis label size
, x_axts = 12 # x-axis text size , x_axts = 12 # x-axis text size
, y_axts = 12 # y-axis text size , y_axts = 12 # y-axis text size
, default_xtc = "black" # x-axis text colour , default_xtc = "black" # x-axis text colour
, ptitle = "" , ptitle = ""
, xlab = "" , xlab = ""
, ylab = "" , ylab = ""
, pts = 20 , pts = 20
# plot margins # plot margins
, t_margin = 0.5 , t_margin = 0.5
, r_margin = 0.5 , r_margin = 0.5
, b_margin = 1 , b_margin = 1
, l_margin = 1 , l_margin = 1
, unit_margin = "cm" , unit_margin = "cm"
# Custom 1: x-axis: text colour # Custom 1: x-axis: text colour
, xtext_colour_aa = F , xtext_colour_aa = F
, xtext_colour_aa1 = active_aa_pos , xtext_colour_aa1 = active_aa_pos
, xtext_colour_aa2 = aa_pos_drug , xtext_colour_aa2 = aa_pos_drug
, xtext_colours = c("purple", "brown", "black") , xtext_colours = c("purple", "brown", "black")
# Custom 2: x-axis: geom tiles ~ lig distance # Custom 2: x-axis: geom tiles ~ lig distance
, A_xvar_lig = T , annotate_ligand_distance = T
, leg_title2 = "Ligand Distance" , leg_title2 = "Ligand Distance"
, lig_dist_colname = LigDist_colname # from globals , lig_dist_colname = LigDist_colname # from globals
, lig_dist_colours = c("green", "yellow", "orange", "red") , lig_dist_colours = c("green", "yellow", "orange", "red")
, tpos0 = 0 # 0 is a magic number that does my sensible default , tpos0 = 0 # 0 is a magic number that does my sensible default
, tW0 = 1 , tW0 = 1
, tH0 = 0.3 , tH0 = 0.3
# Custom 3: x-axis: geom tiles ~ active sites and ligand # Custom 3: x-axis: geom tiles ~ active sites and ligand
, A_xvar_aa = F , annotate_active_sites = F
, aa_pos_drug = NULL , aa_pos_drug = aa_pos_drug
, drug_aa_colour = "purple" , drug_aa_colour = "purple"
, tW = 1 , active_aa_pos = NULL
, tH = 0.2 , active_aa_colour = "brown"
, active_aa_pos = NULL
, active_aa_colour = "brown"
, aa_pos_lig1 = NULL , aa_pos_lig1 = NULL
, aa_colour_lig1 = "blue" , aa_colour_lig1 = "blue"
, tpos1 = 0 , tpos1 = 0
, aa_pos_lig2 = NULL , aa_pos_lig2 = NULL
, aa_colour_lig2 = "cyan" , aa_colour_lig2 = "cyan"
, tpos2 = 0 , tpos2 = 0
, aa_pos_lig3 = NULL , aa_pos_lig3 = NULL
, aa_colour_lig3 = "cornflowerblue" , aa_colour_lig3 = "cornflowerblue"
, tpos3 = 0 , tpos3 = 0
, default_gt_clr = "white" , default_gt_clr = "white"
, debug=FALSE , debug=FALSE
){ ){
if(missing(point_colours)){ if(missing(point_colours)){
@ -119,7 +117,7 @@ wideP_consurf <- function(plot_df
# Build data with colours # Build data with colours
# ~ ligand distance # ~ ligand distance
#========================= #=========================
if (A_xvar_lig){ if (annotate_ligand_distance){
cat("\nAnnotating x-axis ~", lig_dist_colname, "requested...") cat("\nAnnotating x-axis ~", lig_dist_colname, "requested...")
#------------------------------------- #-------------------------------------
@ -159,7 +157,7 @@ wideP_consurf <- function(plot_df
ligDcolKey <- data.frame(ligD_colours = lig_cols ligDcolKey <- data.frame(ligD_colours = lig_cols
, lig_distR = ligD_valsR); ligDcolKey , lig_distR = ligD_valsR); ligDcolKey
names(ligDcolKey) #names(ligDcolKey)
cat("\nSuccessful: Mapping b/w", lig_dist_colname, "and colours") cat("\nSuccessful: Mapping b/w", lig_dist_colname, "and colours")
#------------------------------------- #-------------------------------------
@ -168,11 +166,9 @@ wideP_consurf <- function(plot_df
plot_df = merge(plot_df, ligDcolKey, by = 'lig_distR') plot_df = merge(plot_df, ligDcolKey, by = 'lig_distR')
plot_df_check = as.data.frame(cbind(position = plot_df[[xvar_colname]] plot_df_check = as.data.frame(cbind(position = plot_df[[xvar_colname]]
, ligD = plot_df[[lig_dist_colname]] , ligD = plot_df[[lig_dist_colname]]
, ligDR = plot_df$lig_distR , ligDR = plot_df$lig_distR
, ligD_cols = plot_df$ligD_colours)) , ligD_cols = plot_df$ligD_colours))
} else{
plot_df = plot_df
} }
############################################### ###############################################
@ -184,7 +180,7 @@ wideP_consurf <- function(plot_df
# ~ on active sites # ~ on active sites
#========================== #==========================
if(A_xvar_aa) { if(annotate_active_sites) {
cat("\nAnnotation for xvar requested. Building colours for annotation...") cat("\nAnnotation for xvar requested. Building colours for annotation...")
aa_colour_colname = "bg_all" aa_colour_colname = "bg_all"
@ -196,9 +192,9 @@ wideP_consurf <- function(plot_df
# column colour 0: Active site + drug binding sites # column colour 0: Active site + drug binding sites
#-------------------------------------------------- #--------------------------------------------------
plot_df[[aa_colour_colname]] = ifelse(plot_df[[xvar_colname]]%in%aa_pos_drug plot_df[[aa_colour_colname]] = ifelse(plot_df[[xvar_colname]]%in%aa_pos_drug
, drug_aa_colour , drug_aa_colour
, ifelse(plot_df[[xvar_colname]]%in%active_aa_pos , ifelse(plot_df[[xvar_colname]]%in%active_aa_pos
, active_aa_colour, default_gt_clr )) , active_aa_colour, default_gt_clr ))
plot_df[[aa_colour_colname]] plot_df[[aa_colour_colname]]
cat("\nColumn created 'bg_all':", length(plot_df[[aa_colour_colname]])) cat("\nColumn created 'bg_all':", length(plot_df[[aa_colour_colname]]))
@ -208,20 +204,20 @@ wideP_consurf <- function(plot_df
cat("\nAssigning colours to drug binding and ligand-1 binding residues") cat("\nAssigning colours to drug binding and ligand-1 binding residues")
plot_df[[aa_colour_colname1]] = plot_df[[aa_colour_colname]] plot_df[[aa_colour_colname1]] = plot_df[[aa_colour_colname]]
plot_df[[aa_colour_colname1]] = ifelse(plot_df[[xvar_colname]]%in%aa_pos_lig1 plot_df[[aa_colour_colname1]] = ifelse(plot_df[[xvar_colname]]%in%aa_pos_lig1
, aa_colour_lig1, plot_df[[aa_colour_colname]]) , aa_colour_lig1, plot_df[[aa_colour_colname]])
#------------------------------------------------ #------------------------------------------------
# column colour 2: Ligand 2 # column colour 2: Ligand 2
#------------------------------------------------ #------------------------------------------------
plot_df[[aa_colour_colname2]] = plot_df[[aa_colour_colname1]] plot_df[[aa_colour_colname2]] = plot_df[[aa_colour_colname1]]
plot_df[[aa_colour_colname2]] = ifelse(plot_df[[xvar_colname]]%in%aa_pos_lig2 plot_df[[aa_colour_colname2]] = ifelse(plot_df[[xvar_colname]]%in%aa_pos_lig2
, aa_colour_lig2, plot_df[[aa_colour_colname1]]) , aa_colour_lig2, plot_df[[aa_colour_colname1]])
#------------------------------------------------ #------------------------------------------------
# column colour 3: Ligand 3 # column colour 3: Ligand 3
#------------------------------------------------ #------------------------------------------------
plot_df[[aa_colour_colname3]] = plot_df[[aa_colour_colname2]] plot_df[[aa_colour_colname3]] = plot_df[[aa_colour_colname2]]
plot_df[[aa_colour_colname3]] = ifelse(plot_df[[xvar_colname]]%in%aa_pos_lig3 plot_df[[aa_colour_colname3]] = ifelse(plot_df[[xvar_colname]]%in%aa_pos_lig3
, aa_colour_lig3, plot_df[[aa_colour_colname2]]) , aa_colour_lig3, plot_df[[aa_colour_colname2]])
} }
################### ###################
@ -237,12 +233,13 @@ wideP_consurf <- function(plot_df
ymax = max(plot_df[[yvar_colname]]); ymax ymax = max(plot_df[[yvar_colname]]); ymax
g = ggplot(plot_df, aes_string(x = sprintf("factor(%s)", xvar_colname) g = ggplot(plot_df, aes_string(x = sprintf("factor(%s)", xvar_colname)
, y = yvar_colname , y = yvar_colname
, colour = sprintf("factor(%s)", yvar_colourN_colname) , colour = sprintf("factor(%s)", yvar_colourN_colname)
)) ))
#"if SPECIAL do SPECIAL THING, otherwise do NORMAL THING" #"if SPECIAL do SPECIAL THING, otherwise do NORMAL THING"
if (plot_type == "bar"){ if (plot_type == "bar"){
cat('\ndoing bar plot')
g0 = g + g0 = g +
geom_bar(stat = "identity") geom_bar(stat = "identity")
} }
@ -256,6 +253,7 @@ wideP_consurf <- function(plot_df
} }
if (plot_error_bars){ if (plot_error_bars){
cat('\nplotting error bars')
g0 = g0 + g0 = g0 +
geom_errorbar(aes(ymin = eval(parse(text = lower_EB_colname)) geom_errorbar(aes(ymin = eval(parse(text = lower_EB_colname))
, ymax = eval(parse(text = upper_EB_colname)) , ymax = eval(parse(text = upper_EB_colname))
@ -291,7 +289,7 @@ wideP_consurf <- function(plot_df
, b = b_margin , b = b_margin
, l = l_margin , l = l_margin
, unit = unit_margin))+ , unit = unit_margin))+
guides(colour = guide_legend(title = "ConsurfXXXX")) + #guides(colour = guide_legend(title = "ConsurfXXXX")) +
labs(title = ptitle labs(title = ptitle
, x = xlab , x = xlab
@ -302,7 +300,7 @@ wideP_consurf <- function(plot_df
#------------------ #------------------
# yayy # yayy
g1_leg = ggplot(plot_df, aes_string(x = sprintf("factor(%s)" g1_leg = ggplot(plot_df, aes_string(x = sprintf("factor(%s)"
, xvar_colname) )) , xvar_colname) ))
g1_leg = g1_leg + geom_bar(); g1_leg g1_leg = g1_leg + geom_bar(); g1_leg
g1_leg = g1_leg + geom_bar(aes_string(fill = sprintf("factor(%s)" g1_leg = g1_leg + geom_bar(aes_string(fill = sprintf("factor(%s)"
, yvar_colourN_colname))) , yvar_colourN_colname)))
@ -320,7 +318,7 @@ wideP_consurf <- function(plot_df
#------- #-------
# plot # plot
#------- #-------
if(A_xvar_lig){ # 0 is a magic number that does my sensible default if(annotate_ligand_distance){ # 0 is a magic number that does my sensible default
if (tpos0 == 0){ if (tpos0 == 0){
tpos0 = ymin-0.5 tpos0 = ymin-0.5
} }
@ -339,8 +337,6 @@ wideP_consurf <- function(plot_df
, "\nNo. of colours:", n_colours) , "\nNo. of colours:", n_colours)
g2 = g1 + geom_tile(aes(, tpos0 g2 = g1 + geom_tile(aes(, tpos0
# g2 = g1 + geom_tile(aes(, tpos0
, width = tW0 , width = tW0
, height = tH0) , height = tH0)
, fill = plot_df$ligD_colours , fill = plot_df$ligD_colours
@ -349,14 +345,19 @@ wideP_consurf <- function(plot_df
#cat("Nrows of plot df", length(plot_df$ligD_colours)) #cat("Nrows of plot df", length(plot_df$ligD_colours))
out = g2 out = g2
cat('\nOut is g2')
}else{ }else{
cat('\nOut is g1')
out = g1 out = g1
} }
#============================================== #==============================================
# x-axis: geom_tiles ~ active sites and others # x-axis: geom_tiles ~ active sites and others
#============================================== #==============================================
if(A_xvar_aa){ if(annotate_active_sites){
cat('\nDrug Positions: ',aa_pos_drug)
cat ('\nLig 1 Positions:', aa_pos_lig1)
cat ('\nLig 2 Positions:', aa_pos_lig2)
cat ('\nLig 2 Positions:', aa_pos_lig3)
#tpos = 0 #tpos = 0
#tW = 1 #tW = 1
#tH = 0.2 #tH = 0.2
@ -366,67 +367,70 @@ wideP_consurf <- function(plot_df
#--------------------- #---------------------
if (all(!is.null(active_aa_pos) && if (all(!is.null(active_aa_pos) &&
!is.null(aa_pos_drug) && !is.null(aa_pos_drug) &&
!is.null(aa_pos_lig1) && !is.null(aa_pos_lig2) && !is.null(aa_pos_lig3))) { !is.null(aa_pos_lig1) &&
if (debug){ !is.null(aa_pos_lig2) &&
cat("\n\nAnnotating xvar with active, drug binding, and Lig 1&2&3 sites") !is.null(aa_pos_lig3))) {
cat("\nCreating column colours, column name:", aa_colour_colname3) #if (debug){
cat("\n\nAnnotating xvar with active, drug binding, and Lig 1 & 2 & 3 sites")
#cat("\nCreating column colours, column name:", aa_colour_colname3)
cat("\nDoing Plot with 3 ligands") cat("\nDoing Plot with 3 ligands")
} #}
#out = out + geom_tile(aes(,tpos3 out = out + geom_tile(aes(,tpos3
out = out + geom_tile(aes(,2 , width = tW0
, width = tW , height = tH0 )
, height = tH )
, fill = plot_df[[aa_colour_colname3]] , fill = plot_df[[aa_colour_colname3]]
, colour = plot_df[[aa_colour_colname3]] , colour = plot_df[[aa_colour_colname3]]
, linetype = "solid") + , linetype = "solid") +
geom_tile(aes(, tpos2 geom_tile(aes(, tpos2
, width = tW , width = tW0
, height = tH ) , height = tH0 )
, fill = plot_df[[aa_colour_colname2]] , fill = plot_df[[aa_colour_colname2]]
, colour = plot_df[[aa_colour_colname2]] , colour = plot_df[[aa_colour_colname2]]
, linetype = "solid")+ , linetype = "solid")+
geom_tile(aes(, tpos1 geom_tile(aes(, tpos1
, width = tW , width = tW0
, height = tH) , height = tH0)
, fill = plot_df[[aa_colour_colname1]] , fill = plot_df[[aa_colour_colname1]]
, colour = plot_df[[aa_colour_colname1]] , colour = plot_df[[aa_colour_colname1]]
, linetype = "solid") , linetype = "solid")
if (debug){ #if (debug){
cat("\nDone Plot with 3 ligands") cat("\nDone Plot with 3 ligands")
} #}
} } else {cat("\n3 Lig Plot condition FAIL")}
#--------------------- #---------------------
# Add2plot: 2 ligands # Add2plot: 2 ligands
#--------------------- #---------------------
if (all(!is.null(active_aa_pos) && if (all(!is.null(active_aa_pos) &&
!is.null(aa_pos_drug) && !is.null(aa_pos_drug) &&
!is.null(aa_pos_lig1) && !is.null(aa_pos_lig2) && is.null(aa_pos_lig3))) { !is.null(aa_pos_lig1) &&
if (debug){ !is.null(aa_pos_lig2) &&
cat("\n\nAnnotating xvar with active, drug binding, and Lig 1&2 sites") is.null(aa_pos_lig3))) {
cat("\nCreating column colours, column name:", aa_colour_colname2) #if (debug){
cat("\n\nAnnotating xvar with active, drug binding, and Lig 1&2 sites")
cat("\nCreating column colours, column name:", aa_colour_colname2)
cat("\nDoing Plot with 2 ligands") cat("\nDoing Plot with 2 ligands")
} #}
out = out + out = out +
geom_tile(aes(, tpos2 geom_tile(aes(, tpos2
, width = tW , width = tW0
, height = tH) , height = tH0)
, fill = plot_df[[aa_colour_colname2]] , fill = plot_df[[aa_colour_colname2]]
, colour = plot_df[[aa_colour_colname2]] , colour = plot_df[[aa_colour_colname2]]
, linetype = "solid")+ , linetype = "solid")+
geom_tile(aes(, tpos1 geom_tile(aes(, tpos1
, width = tW , width = tW0
, height = tH) , height = tH0)
, fill = plot_df[[aa_colour_colname1]] , fill = plot_df[[aa_colour_colname1]]
, colour = plot_df[[aa_colour_colname1]] , colour = plot_df[[aa_colour_colname1]]
, linetype = "solid") , linetype = "solid")
if (debug){ #if (debug){
cat("\nDone Plot with 2 ligands") cat("\nDone Plot with 2 ligands")
} #}
} } else {cat("\n2 Lig Plot condition FAIL")}
#--------------------- #---------------------
# Add2plot: 1 ligand # Add2plot: 1 ligand
@ -434,53 +438,54 @@ wideP_consurf <- function(plot_df
if (all(!is.null(active_aa_pos) && if (all(!is.null(active_aa_pos) &&
!is.null(aa_pos_drug) && !is.null(aa_pos_drug) &&
!is.null(aa_pos_lig1) && is.null(aa_pos_lig2) && is.null(aa_pos_lig3))) { !is.null(aa_pos_lig1) && is.null(aa_pos_lig2) && is.null(aa_pos_lig3))) {
if (debug){ #if (debug){
cat("\n\nAnnotating xvar with active, drug binding, and Lig 1 sites") cat("\n\nAnnotating xvar with active, drug binding, and Lig 1 sites")
cat("\nCreating column colours, column name:", aa_colour_colname1) cat("\nCreating column colours, column name:", aa_colour_colname1)
cat("\nDoing Plot with 1 ligands") cat("\nDoing Plot with 1 ligands")
} #}
out = out + out = out +
geom_tile(aes(, tpos1 geom_tile(aes(, tpos1
, width = tW , width = tW0
, height = tH) , height = tH0)
, fill = plot_df[[aa_colour_colname1]] , fill = plot_df[[aa_colour_colname1]]
, colour = plot_df[[aa_colour_colname1]] , colour = plot_df[[aa_colour_colname1]]
, linetype = "solid") , linetype = "solid")
cat("\nDone Plot with 1 ligand") cat("\nDone Plot with 1 ligand")
} } else {cat("\n3 Lig Plot condition FAIL")}
#----------------------------------- #-----------------------------------
# Add2plot:NO ligands # Add2plot:NO ligands
# No Ligs: Just drug and active site # No Ligs: Just drug and active site
# DEFAULT: A_xvar_aa == TRUE # DEFAULT: annotate_active_sites == TRUE
#---------------------------------- #----------------------------------
if (all(!is.null(active_aa_pos) && if (all(!is.null(active_aa_pos) &&
!is.null(aa_pos_drug) && !is.null(aa_pos_drug) &&
is.null(aa_pos_lig1) && is.null(aa_pos_lig1) &&
is.null(aa_pos_lig2) && is.null(aa_pos_lig2) &&
is.null(aa_pos_lig3))) { is.null(aa_pos_lig3))) {
if (debug){ #if (debug){
cat("\n\nAnnotating xvar with active and drug binding sites") cat("\n\nAnnotating xvar with active and drug binding sites")
cat("\nCreating column colours, column name:", aa_colour_colname) cat("\nCreating column colours, column name:", aa_colour_colname)
cat("\nDoing Plot with 0 ligands: active and drug site only") cat("\nDoing Plot with 0 ligands: active and drug site only")
} #}
out = out + geom_tile(aes(, tpos3 out = out + geom_tile(aes(, tpos3
, width = tW , width = tW0
, height = tH) , height = tH0)
, fill = plot_df[[aa_colour_colname]] , fill = plot_df[[aa_colour_colname]]
, colour = plot_df[[aa_colour_colname]] , colour = plot_df[[aa_colour_colname]]
, linetype = "solid") , linetype = "solid")
if (debug){ #if (debug){
cat("\nDone Plot with: Active and Drug sites") cat("\nDone Plot with: Active and Drug sites")
}
} }
}else{ #}
} else {
cat("\nNo annotation for additional ligands on xvar requested") cat("\nNo annotation for additional ligands on xvar requested")
} }
if (A_xvar_lig){ if (annotate_ligand_distance){
cat('\nOutput: Plot + distance heat-bar + other stuff')
legs = cowplot::plot_grid(legend1 legs = cowplot::plot_grid(legend1
, generate_distance_legend(plot_df, yvar_colname = yvar_colname) , generate_distance_legend(plot_df, yvar_colname = yvar_colname)
, ncol = 1 , ncol = 1
@ -505,12 +510,12 @@ wideP_consurf <- function(plot_df
#return(out2) #return(out2)
} }
#
# wideP_consurf2(
# wideP_consurf(
# merged_df3, # merged_df3,
# A_xvar_aa = T, # annotate_active_sites = TRUE,
# active_aa_pos = active_aa_pos, # active_aa_pos = active_aa_pos,
# aa_pos_drug = aa_pos_drug,
# aa_pos_lig1 = aa_pos_lig1, # aa_pos_lig1 = aa_pos_lig1,
# aa_pos_lig2 = aa_pos_lig2, # aa_pos_lig2 = aa_pos_lig2,
# aa_pos_lig3 = aa_pos_lig3, # aa_pos_lig3 = aa_pos_lig3,