consurf tile fixes
This commit is contained in:
parent
0234a8f77b
commit
28510471f0
2 changed files with 169 additions and 163 deletions
|
|
@ -459,3 +459,4 @@ LogoPlotMSA <- function(unified_msa
|
|||
return(LogoED_comb)
|
||||
|
||||
}
|
||||
#LogoPlotMSA(unified_msa)
|
||||
|
|
|
|||
|
|
@ -12,81 +12,79 @@
|
|||
# wideP():
|
||||
# input args
|
||||
#==========================================================
|
||||
wideP_consurf <- function(plot_df
|
||||
, xvar_colname = "position"
|
||||
, yvar_colname = "consurf_score"
|
||||
, yvar_colourN_colname = "consurf_colour_rev" # num from 0-1
|
||||
, plot_error_bars = T
|
||||
, upper_EB_colname = "consurf_ci_upper"
|
||||
, lower_EB_colname = "consurf_ci_lower"
|
||||
wideP_consurf2 <- function(plot_df
|
||||
, xvar_colname = "position"
|
||||
, yvar_colname = "consurf_score"
|
||||
, yvar_colourN_colname = "consurf_colour_rev" # num from 0-1
|
||||
, plot_error_bars = T
|
||||
, upper_EB_colname = "consurf_ci_upper"
|
||||
, lower_EB_colname = "consurf_ci_lower"
|
||||
|
||||
, plot_type = "point" # default is point
|
||||
, point_colours
|
||||
, p_size = 2
|
||||
, leg_title1 = ""
|
||||
, leg_labels = c("0": "Insufficient Data"
|
||||
, "1": "Variable"
|
||||
, "2", "3", "4", "5", "6", "7", "8"
|
||||
, "9": "Conserved")
|
||||
, panel_col = "white"
|
||||
, panel_col_fill = "white"
|
||||
, plot_type = "point" # default is point
|
||||
, point_colours
|
||||
, p_size = 2
|
||||
, leg_title1 = ""
|
||||
, leg_labels = c("0": "Insufficient Data"
|
||||
, "1": "Variable"
|
||||
, "2", "3", "4", "5", "6", "7", "8"
|
||||
, "9": "Conserved")
|
||||
, panel_col = "white"
|
||||
, panel_col_fill = "white"
|
||||
|
||||
# axes title and label sizes
|
||||
, x_axls = 12 # x-axis label size
|
||||
, y_axls = 15 # y-axis label size
|
||||
, x_axts = 12 # x-axis text size
|
||||
, y_axts = 12 # y-axis text size
|
||||
, default_xtc = "black" # x-axis text colour
|
||||
, ptitle = ""
|
||||
, xlab = ""
|
||||
, ylab = ""
|
||||
, pts = 20
|
||||
# axes title and label sizes
|
||||
, x_axls = 12 # x-axis label size
|
||||
, y_axls = 15 # y-axis label size
|
||||
, x_axts = 12 # x-axis text size
|
||||
, y_axts = 12 # y-axis text size
|
||||
, default_xtc = "black" # x-axis text colour
|
||||
, ptitle = ""
|
||||
, xlab = ""
|
||||
, ylab = ""
|
||||
, pts = 20
|
||||
|
||||
# plot margins
|
||||
, t_margin = 0.5
|
||||
, r_margin = 0.5
|
||||
, b_margin = 1
|
||||
, l_margin = 1
|
||||
, unit_margin = "cm"
|
||||
# plot margins
|
||||
, t_margin = 0.5
|
||||
, r_margin = 0.5
|
||||
, b_margin = 1
|
||||
, l_margin = 1
|
||||
, unit_margin = "cm"
|
||||
|
||||
# Custom 1: x-axis: text colour
|
||||
, xtext_colour_aa = F
|
||||
, xtext_colour_aa1 = active_aa_pos
|
||||
, xtext_colour_aa2 = aa_pos_drug
|
||||
, xtext_colours = c("purple", "brown", "black")
|
||||
# Custom 1: x-axis: text colour
|
||||
, xtext_colour_aa = F
|
||||
, xtext_colour_aa1 = active_aa_pos
|
||||
, xtext_colour_aa2 = aa_pos_drug
|
||||
, xtext_colours = c("purple", "brown", "black")
|
||||
|
||||
# Custom 2: x-axis: geom tiles ~ lig distance
|
||||
, A_xvar_lig = T
|
||||
, leg_title2 = "Ligand Distance"
|
||||
, lig_dist_colname = LigDist_colname # from globals
|
||||
, lig_dist_colours = c("green", "yellow", "orange", "red")
|
||||
, tpos0 = 0 # 0 is a magic number that does my sensible default
|
||||
, tW0 = 1
|
||||
, tH0 = 0.3
|
||||
# Custom 2: x-axis: geom tiles ~ lig distance
|
||||
, annotate_ligand_distance = T
|
||||
, leg_title2 = "Ligand Distance"
|
||||
, lig_dist_colname = LigDist_colname # from globals
|
||||
, lig_dist_colours = c("green", "yellow", "orange", "red")
|
||||
, tpos0 = 0 # 0 is a magic number that does my sensible default
|
||||
, tW0 = 1
|
||||
, tH0 = 0.3
|
||||
|
||||
# Custom 3: x-axis: geom tiles ~ active sites and ligand
|
||||
, A_xvar_aa = F
|
||||
, aa_pos_drug = NULL
|
||||
, drug_aa_colour = "purple"
|
||||
, tW = 1
|
||||
, tH = 0.2
|
||||
, active_aa_pos = NULL
|
||||
, active_aa_colour = "brown"
|
||||
# Custom 3: x-axis: geom tiles ~ active sites and ligand
|
||||
, annotate_active_sites = F
|
||||
, aa_pos_drug = aa_pos_drug
|
||||
, drug_aa_colour = "purple"
|
||||
, active_aa_pos = NULL
|
||||
, active_aa_colour = "brown"
|
||||
|
||||
, aa_pos_lig1 = NULL
|
||||
, aa_colour_lig1 = "blue"
|
||||
, tpos1 = 0
|
||||
, aa_pos_lig1 = NULL
|
||||
, aa_colour_lig1 = "blue"
|
||||
, tpos1 = 0
|
||||
|
||||
, aa_pos_lig2 = NULL
|
||||
, aa_colour_lig2 = "cyan"
|
||||
, tpos2 = 0
|
||||
, aa_pos_lig2 = NULL
|
||||
, aa_colour_lig2 = "cyan"
|
||||
, tpos2 = 0
|
||||
|
||||
, aa_pos_lig3 = NULL
|
||||
, aa_colour_lig3 = "cornflowerblue"
|
||||
, tpos3 = 0
|
||||
, aa_pos_lig3 = NULL
|
||||
, aa_colour_lig3 = "cornflowerblue"
|
||||
, tpos3 = 0
|
||||
|
||||
, default_gt_clr = "white"
|
||||
, debug=FALSE
|
||||
, default_gt_clr = "white"
|
||||
, debug=FALSE
|
||||
){
|
||||
|
||||
if(missing(point_colours)){
|
||||
|
|
@ -119,7 +117,7 @@ wideP_consurf <- function(plot_df
|
|||
# Build data with colours
|
||||
# ~ ligand distance
|
||||
#=========================
|
||||
if (A_xvar_lig){
|
||||
if (annotate_ligand_distance){
|
||||
cat("\nAnnotating x-axis ~", lig_dist_colname, "requested...")
|
||||
|
||||
#-------------------------------------
|
||||
|
|
@ -159,7 +157,7 @@ wideP_consurf <- function(plot_df
|
|||
|
||||
ligDcolKey <- data.frame(ligD_colours = lig_cols
|
||||
, lig_distR = ligD_valsR); ligDcolKey
|
||||
names(ligDcolKey)
|
||||
#names(ligDcolKey)
|
||||
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_check = as.data.frame(cbind(position = plot_df[[xvar_colname]]
|
||||
, ligD = plot_df[[lig_dist_colname]]
|
||||
, ligDR = plot_df$lig_distR
|
||||
, ligD_cols = plot_df$ligD_colours))
|
||||
} else{
|
||||
plot_df = plot_df
|
||||
, ligD = plot_df[[lig_dist_colname]]
|
||||
, ligDR = plot_df$lig_distR
|
||||
, ligD_cols = plot_df$ligD_colours))
|
||||
}
|
||||
|
||||
###############################################
|
||||
|
|
@ -184,7 +180,7 @@ wideP_consurf <- function(plot_df
|
|||
# ~ on active sites
|
||||
#==========================
|
||||
|
||||
if(A_xvar_aa) {
|
||||
if(annotate_active_sites) {
|
||||
cat("\nAnnotation for xvar requested. Building colours for annotation...")
|
||||
|
||||
aa_colour_colname = "bg_all"
|
||||
|
|
@ -196,9 +192,9 @@ wideP_consurf <- function(plot_df
|
|||
# column colour 0: Active site + drug binding sites
|
||||
#--------------------------------------------------
|
||||
plot_df[[aa_colour_colname]] = ifelse(plot_df[[xvar_colname]]%in%aa_pos_drug
|
||||
, drug_aa_colour
|
||||
, ifelse(plot_df[[xvar_colname]]%in%active_aa_pos
|
||||
, active_aa_colour, default_gt_clr ))
|
||||
, drug_aa_colour
|
||||
, ifelse(plot_df[[xvar_colname]]%in%active_aa_pos
|
||||
, active_aa_colour, default_gt_clr ))
|
||||
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")
|
||||
plot_df[[aa_colour_colname1]] = plot_df[[aa_colour_colname]]
|
||||
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
|
||||
#------------------------------------------------
|
||||
plot_df[[aa_colour_colname2]] = plot_df[[aa_colour_colname1]]
|
||||
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
|
||||
#------------------------------------------------
|
||||
plot_df[[aa_colour_colname3]] = plot_df[[aa_colour_colname2]]
|
||||
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
|
||||
|
||||
g = ggplot(plot_df, aes_string(x = sprintf("factor(%s)", xvar_colname)
|
||||
, y = yvar_colname
|
||||
, colour = sprintf("factor(%s)", yvar_colourN_colname)
|
||||
, y = yvar_colname
|
||||
, colour = sprintf("factor(%s)", yvar_colourN_colname)
|
||||
))
|
||||
|
||||
#"if SPECIAL do SPECIAL THING, otherwise do NORMAL THING"
|
||||
if (plot_type == "bar"){
|
||||
cat('\ndoing bar plot')
|
||||
g0 = g +
|
||||
geom_bar(stat = "identity")
|
||||
}
|
||||
|
|
@ -256,6 +253,7 @@ wideP_consurf <- function(plot_df
|
|||
}
|
||||
|
||||
if (plot_error_bars){
|
||||
cat('\nplotting error bars')
|
||||
g0 = g0 +
|
||||
geom_errorbar(aes(ymin = eval(parse(text = lower_EB_colname))
|
||||
, ymax = eval(parse(text = upper_EB_colname))
|
||||
|
|
@ -291,7 +289,7 @@ wideP_consurf <- function(plot_df
|
|||
, b = b_margin
|
||||
, l = l_margin
|
||||
, unit = unit_margin))+
|
||||
guides(colour = guide_legend(title = "ConsurfXXXX")) +
|
||||
#guides(colour = guide_legend(title = "ConsurfXXXX")) +
|
||||
|
||||
labs(title = ptitle
|
||||
, x = xlab
|
||||
|
|
@ -302,7 +300,7 @@ wideP_consurf <- function(plot_df
|
|||
#------------------
|
||||
# yayy
|
||||
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(aes_string(fill = sprintf("factor(%s)"
|
||||
, yvar_colourN_colname)))
|
||||
|
|
@ -320,7 +318,7 @@ wideP_consurf <- function(plot_df
|
|||
#-------
|
||||
# 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){
|
||||
tpos0 = ymin-0.5
|
||||
}
|
||||
|
|
@ -339,8 +337,6 @@ wideP_consurf <- function(plot_df
|
|||
, "\nNo. of colours:", n_colours)
|
||||
|
||||
g2 = g1 + geom_tile(aes(, tpos0
|
||||
# g2 = g1 + geom_tile(aes(, tpos0
|
||||
|
||||
, width = tW0
|
||||
, height = tH0)
|
||||
, fill = plot_df$ligD_colours
|
||||
|
|
@ -349,14 +345,19 @@ wideP_consurf <- function(plot_df
|
|||
|
||||
#cat("Nrows of plot df", length(plot_df$ligD_colours))
|
||||
out = g2
|
||||
|
||||
cat('\nOut is g2')
|
||||
}else{
|
||||
cat('\nOut is g1')
|
||||
out = g1
|
||||
}
|
||||
#==============================================
|
||||
# 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
|
||||
#tW = 1
|
||||
#tH = 0.2
|
||||
|
|
@ -366,67 +367,70 @@ wideP_consurf <- function(plot_df
|
|||
#---------------------
|
||||
if (all(!is.null(active_aa_pos) &&
|
||||
!is.null(aa_pos_drug) &&
|
||||
!is.null(aa_pos_lig1) && !is.null(aa_pos_lig2) && !is.null(aa_pos_lig3))) {
|
||||
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)
|
||||
!is.null(aa_pos_lig1) &&
|
||||
!is.null(aa_pos_lig2) &&
|
||||
!is.null(aa_pos_lig3))) {
|
||||
#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")
|
||||
}
|
||||
#out = out + geom_tile(aes(,tpos3
|
||||
out = out + geom_tile(aes(,2
|
||||
, width = tW
|
||||
, height = tH )
|
||||
cat("\nDoing Plot with 3 ligands")
|
||||
#}
|
||||
out = out + geom_tile(aes(,tpos3
|
||||
, width = tW0
|
||||
, height = tH0 )
|
||||
, fill = plot_df[[aa_colour_colname3]]
|
||||
, colour = plot_df[[aa_colour_colname3]]
|
||||
, linetype = "solid") +
|
||||
geom_tile(aes(, tpos2
|
||||
, width = tW
|
||||
, height = tH )
|
||||
, width = tW0
|
||||
, height = tH0 )
|
||||
, fill = plot_df[[aa_colour_colname2]]
|
||||
, colour = plot_df[[aa_colour_colname2]]
|
||||
, linetype = "solid")+
|
||||
|
||||
geom_tile(aes(, tpos1
|
||||
, width = tW
|
||||
, height = tH)
|
||||
, width = tW0
|
||||
, height = tH0)
|
||||
, fill = plot_df[[aa_colour_colname1]]
|
||||
, colour = plot_df[[aa_colour_colname1]]
|
||||
, linetype = "solid")
|
||||
if (debug){
|
||||
cat("\nDone Plot with 3 ligands")
|
||||
}
|
||||
}
|
||||
#if (debug){
|
||||
cat("\nDone Plot with 3 ligands")
|
||||
#}
|
||||
} else {cat("\n3 Lig Plot condition FAIL")}
|
||||
#---------------------
|
||||
# Add2plot: 2 ligands
|
||||
#---------------------
|
||||
|
||||
if (all(!is.null(active_aa_pos) &&
|
||||
!is.null(aa_pos_drug) &&
|
||||
!is.null(aa_pos_lig1) && !is.null(aa_pos_lig2) && is.null(aa_pos_lig3))) {
|
||||
if (debug){
|
||||
cat("\n\nAnnotating xvar with active, drug binding, and Lig 1&2 sites")
|
||||
cat("\nCreating column colours, column name:", aa_colour_colname2)
|
||||
!is.null(aa_pos_lig1) &&
|
||||
!is.null(aa_pos_lig2) &&
|
||||
is.null(aa_pos_lig3))) {
|
||||
#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 +
|
||||
geom_tile(aes(, tpos2
|
||||
, width = tW
|
||||
, height = tH)
|
||||
, width = tW0
|
||||
, height = tH0)
|
||||
, fill = plot_df[[aa_colour_colname2]]
|
||||
, colour = plot_df[[aa_colour_colname2]]
|
||||
, linetype = "solid")+
|
||||
geom_tile(aes(, tpos1
|
||||
, width = tW
|
||||
, height = tH)
|
||||
, width = tW0
|
||||
, height = tH0)
|
||||
, fill = plot_df[[aa_colour_colname1]]
|
||||
, colour = plot_df[[aa_colour_colname1]]
|
||||
, linetype = "solid")
|
||||
if (debug){
|
||||
cat("\nDone Plot with 2 ligands")
|
||||
}
|
||||
}
|
||||
#if (debug){
|
||||
cat("\nDone Plot with 2 ligands")
|
||||
#}
|
||||
} else {cat("\n2 Lig Plot condition FAIL")}
|
||||
|
||||
#---------------------
|
||||
# Add2plot: 1 ligand
|
||||
|
|
@ -434,53 +438,54 @@ wideP_consurf <- function(plot_df
|
|||
if (all(!is.null(active_aa_pos) &&
|
||||
!is.null(aa_pos_drug) &&
|
||||
!is.null(aa_pos_lig1) && is.null(aa_pos_lig2) && is.null(aa_pos_lig3))) {
|
||||
if (debug){
|
||||
cat("\n\nAnnotating xvar with active, drug binding, and Lig 1 sites")
|
||||
cat("\nCreating column colours, column name:", aa_colour_colname1)
|
||||
#if (debug){
|
||||
cat("\n\nAnnotating xvar with active, drug binding, and Lig 1 sites")
|
||||
cat("\nCreating column colours, column name:", aa_colour_colname1)
|
||||
|
||||
cat("\nDoing Plot with 1 ligands")
|
||||
}
|
||||
cat("\nDoing Plot with 1 ligands")
|
||||
#}
|
||||
out = out +
|
||||
geom_tile(aes(, tpos1
|
||||
, width = tW
|
||||
, height = tH)
|
||||
, width = tW0
|
||||
, height = tH0)
|
||||
, fill = plot_df[[aa_colour_colname1]]
|
||||
, colour = plot_df[[aa_colour_colname1]]
|
||||
, linetype = "solid")
|
||||
|
||||
cat("\nDone Plot with 1 ligand")
|
||||
|
||||
}
|
||||
} else {cat("\n3 Lig Plot condition FAIL")}
|
||||
|
||||
#-----------------------------------
|
||||
# Add2plot:NO ligands
|
||||
# No Ligs: Just drug and active site
|
||||
# DEFAULT: A_xvar_aa == TRUE
|
||||
# DEFAULT: annotate_active_sites == TRUE
|
||||
#----------------------------------
|
||||
if (all(!is.null(active_aa_pos) &&
|
||||
!is.null(aa_pos_drug) &&
|
||||
is.null(aa_pos_lig1) &&
|
||||
is.null(aa_pos_lig2) &&
|
||||
is.null(aa_pos_lig3))) {
|
||||
if (debug){
|
||||
cat("\n\nAnnotating xvar with active and drug binding sites")
|
||||
cat("\nCreating column colours, column name:", aa_colour_colname)
|
||||
cat("\nDoing Plot with 0 ligands: active and drug site only")
|
||||
}
|
||||
#if (debug){
|
||||
cat("\n\nAnnotating xvar with active and drug binding sites")
|
||||
cat("\nCreating column colours, column name:", aa_colour_colname)
|
||||
cat("\nDoing Plot with 0 ligands: active and drug site only")
|
||||
#}
|
||||
out = out + geom_tile(aes(, tpos3
|
||||
, width = tW
|
||||
, height = tH)
|
||||
, width = tW0
|
||||
, height = tH0)
|
||||
, fill = plot_df[[aa_colour_colname]]
|
||||
, colour = plot_df[[aa_colour_colname]]
|
||||
, linetype = "solid")
|
||||
if (debug){
|
||||
cat("\nDone Plot with: Active and Drug sites")
|
||||
}
|
||||
#if (debug){
|
||||
cat("\nDone Plot with: Active and Drug sites")
|
||||
}
|
||||
}else{
|
||||
#}
|
||||
} else {
|
||||
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
|
||||
, generate_distance_legend(plot_df, yvar_colname = yvar_colname)
|
||||
, ncol = 1
|
||||
|
|
@ -505,12 +510,12 @@ wideP_consurf <- function(plot_df
|
|||
#return(out2)
|
||||
|
||||
}
|
||||
|
||||
|
||||
# wideP_consurf(
|
||||
#
|
||||
# wideP_consurf2(
|
||||
# merged_df3,
|
||||
# A_xvar_aa = T,
|
||||
# annotate_active_sites = TRUE,
|
||||
# active_aa_pos = active_aa_pos,
|
||||
# aa_pos_drug = aa_pos_drug,
|
||||
# aa_pos_lig1 = aa_pos_lig1,
|
||||
# aa_pos_lig2 = aa_pos_lig2,
|
||||
# aa_pos_lig3 = aa_pos_lig3,
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue