tanu/LSHTM_analysis
1
0
Fork 0
Code Issues Pull requests Releases Wiki Activity

fix many plot functions to stop them using the "g=ggplot()" pattern,

Browse source 
which annoyingly throws away lots of useful data that RShiny needs for
clickable plots. Also split the "flame bar" for ligand distance out into
separate functions in generate_distance_colour_map.R. This can now be
easily incorporated into any "wide" graph showing all positions.
This commit is contained in:
Tanushree Tunstall 2022-08-03 18:56:14 +01:00
parent e498d46f8b
commit bdbc97c40a
8 changed files with 1323 additions and 725 deletions
Download patch file Download diff file Expand all files Collapse all files

82
scripts/functions/bp_subcolours.R
View file

@ -2,6 +2,7 @@
# 1b: Define function: coloured barplot by subgroup
# LINK: https://stackoverflow.com/questions/49818271/stacked-barplot-with-colour-gradients-for-each-bar
#########################################################
source("~/git/LSHTM_analysis/scripts/functions/generate_distance_colour_map.R")
ColourPalleteMulti = function(df, group, subgroup){
@ -35,6 +36,7 @@ ColourPalleteMulti = function(df, group, subgroup){
bp_stability_hmap <- function(plotdf = merged_df3
, xvar_colname = "position"
, yvar_colname = 'duet_scaled' #FIXME: temp, remove
#, bar_col_colname = "group"
, stability_colname = "duet_scaled"
, stability_outcome_colname = "duet_outcome"
@ -46,8 +48,27 @@ bp_stability_hmap <- function(plotdf = merged_df3
, my_pts = 20 # plot-title size
, my_xlab = "Position"
, my_ylab = "No. of nsSNPs"
# Custom 2: x-axis: geom tiles ~ lig distance
#, A_xvar_lig = T
, lig_dist_colname = LigDist_colname # from globals
, tpos0 = 0 # 0 is a magic number that does my sensible default
, tW0 = 1
, tH0 = 0.2
)
{
################################################
# Custom 2: x-axis geom tiles ~ lig distance
################################################
#=========================
# Build data with colours
# ~ ligand distance
#=========================
plotdf = generate_distance_colour_map(plotdf, yvar_colname = stability_colname, debug=TRUE)
# order the df by position and ensure it is a factor
plotdf = plotdf[order(plotdf[[xvar_colname]]), ]
@ -74,38 +95,45 @@ bp_stability_hmap <- function(plotdf = merged_df3
cat("\nNo. of sub colours generated:", length(subcols_bp_hmap))
#-------------------------------
# Generate the subcols barplot
#-------------------------------
cowplot::plot_grid(
ggplot(plotdf, aes_string(x = xvar_colname
# , ordered = T)
)) +
geom_bar(aes(fill = group)
, colour = "grey") +
#g = ggplot(plotdf, aes(x = factor(position, ordered = T)))
g = ggplot(plotdf, aes_string(x = xvar_colname
# , ordered = T)
))
scale_fill_manual( values = subcols_bp_hmap
, guide = "none") +
OutWidePlot = g + geom_bar(aes(fill = group)
, colour = "grey") +
scale_fill_manual( values = subcols_bp_hmap
, guide = "none") +
theme( axis.text.x = element_text(size = my_xaxls
, angle = 90
, hjust = 1
, vjust = 0.4)
, axis.text.y = element_text(size = my_yaxls
, angle = 0
theme( axis.text.x = element_text(size = my_xaxls
, angle = 90
, hjust = 1
, vjust = 0)
, axis.title.x = element_text(size = my_xaxts)
, axis.title.y = element_text(size = my_yaxts )
, plot.title = element_text(size = my_pts
, hjust = 0.5)) +
, vjust = 0.4)
, axis.text.y = element_text(size = my_yaxls
, angle = 0
, hjust = 1
, vjust = 0)
, axis.title.x = element_text(size = my_xaxts)
, axis.title.y = element_text(size = my_yaxts )
, plot.title = element_text(size = my_pts
, hjust = 0.5)) +
geom_tile(aes(, tpos0 # heat-mapped distance tiles along the bot
, width = tW0
, height = tH0)
, fill = plotdf$ligD_colours
, colour = plotdf$ligD_colours
, linetype = "blank") +
labs(title = p_title
, x = my_xlab
, y = my_ylab)
return(OutWidePlot)
labs(title = p_title
, x = my_xlab
, y = my_ylab),
generate_distance_legend(plotdf, yvar_colname = stability_colname),
ncol = 2,
#align = "hv",
rel_widths = c(9/10, 0.4/10)
)
}

575
scripts/functions/consurfP.R
View file

@ -87,7 +87,7 @@ wideP_consurf <- function(plotdf
, default_gt_clr = "white"
, debug=FALSE
){
){
if(missing(point_colours)){
temp_cols = colorRampPalette(c("seagreen", "sienna3"))(30)
@ -239,29 +239,11 @@ wideP_consurf <- function(plotdf
my_xlim = length(unique(plotdf[[xvar_colname]])); my_xlim
ymin = min(plotdf[[yvar_colname]]); ymin
ymax = max(plotdf[[yvar_colname]]); ymax
# DEBUG
# x_factor = as.factor(plotdf[[xvar_colname]])
# y_colour_factor = as.factor(plotdf[[yvar_colourN_colname]])
# cat('XXXX THIS:', str(x_factor))
#
# g = ggplot(plotdf, aes_string(x = x_factor)
# , y = yvar_colname
# , colour = y_colour_factor)
g = ggplot(plotdf, aes_string(x = sprintf("factor(%s)", xvar_colname)
, y = yvar_colname
, colour = sprintf("factor(%s)", yvar_colourN_colname)
))
# g = ggplot(plotdf, aes_string(x = "position")
# , y = "consurf_score"
# , colour = "consurf_colour_rev")
# g = ggplot(plotdf, aes_string(x = "position")
# , y = "consurf_score"
# , colour = "consurf_colour_rev")
# DEBUG
#g0=g
))
"if SPECIAL do SPECIAL THING, otherwise do NORMAL THING"
if (plot_type == "bar"){
@ -273,17 +255,15 @@ wideP_consurf <- function(plotdf
coord_cartesian(xlim = c(1, my_xlim)
, ylim = c(ymin, ymax)
, clip = "off") +
geom_point(size = p_size) +
scale_colour_manual(values = point_colours)
# , labels = leg_labels
# , name = leg_title1)
geom_point(size = p_size) +
scale_colour_manual(values = point_colours)
}
if (plot_error_bars){
g0 = g0 +
geom_errorbar(aes(ymin = eval(parse(text = lower_EB_colname))
, ymax = eval(parse(text = upper_EB_colname))
))
))
}else{
g0 = g0
@ -299,326 +279,303 @@ wideP_consurf <- function(plotdf
, vjust = 0.4
, face = "bold"
, colour = aa_pos_colours)
, axis.text.y = element_text(size = y_axts
, angle = 0
, hjust = 1
, vjust = 0)
, axis.title.x = element_text(size = x_axls)
, axis.title.y = element_text(size = y_axls )
, panel.background = element_rect(fill = panel_col_fill, color = panel_col)
, panel.grid.major = element_line(color = "black")
, panel.grid.minor = element_line(color = "black")
, plot.title = element_text(size = pts
, hjust = 0.5)
, plot.margin = margin(t = t_margin
, r = r_margin
, b = b_margin
, l = l_margin
, unit = unit_margin))+
guides(colour = guide_legend(title = "ConsurfXXXX")) +
, axis.text.y = element_text(size = y_axts
, angle = 0
, hjust = 1
, vjust = 0)
, axis.title.x = element_text(size = x_axls)
, axis.title.y = element_text(size = y_axls )
, panel.background = element_rect(fill = panel_col_fill, color = panel_col)
, panel.grid.major = element_line(color = "black")
, panel.grid.minor = element_line(color = "black")
, plot.title = element_text(size = pts
, hjust = 0.5)
, plot.margin = margin(t = t_margin
, r = r_margin
, b = b_margin
, l = l_margin
, unit = unit_margin))+
guides(colour = guide_legend(title = "ConsurfXXXX")) +
labs(title = ptitle
, x = xlab
, y = ylab)
labs(title = ptitle
, x = xlab
, y = ylab)
#------------------
#Extract legend1
#------------------
# yayy
g1_leg = ggplot(plotdf, aes_string(x = sprintf("factor(%s)"
, 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)))
#------------------
#Extract legend1
#------------------
# yayy
g1_leg = ggplot(plotdf, aes_string(x = sprintf("factor(%s)"
, 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)))
g1_leg = g1_leg + scale_fill_manual(values = consurf_palette2 , name = leg_title1)
g1_leg
g1_leg = g1_leg + scale_fill_manual(values = consurf_palette2 , name = leg_title1)
g1_leg
legend1 = get_legend(g1_leg)
legend1 = get_legend(g1_leg)
#####################################################
#============================================
# x-axis: geom_tiles ~ ligand distance
#============================================
#-------
# plot
#-------
if(A_xvar_lig){ # 0 is a magic number that does my sensible default
if (tpos0 == 0){
tpos0 = ymin-0.5
}
if (tpos1 == 0){
tpos1 = ymin-0.65
}
if (tpos2 == 0){
tpos2 = ymin-0.75
}
if (tpos3 == 0){
tpos3 = ymin-0.85
}
cat("\nColouring x-axis aa based on", lig_dist_colname
, "\nNo. of colours:", n_colours)
g2 = g1 + geom_tile(aes(, tpos0
, width = tW0
, height = tH0)
, fill = plotdf$ligD_colours
, colour = plotdf$ligD_colours
, linetype = "blank")
#cat("Nrows of plot df", length(plotdf$ligD_colours))
out = g2
#
# #------------------
# # Extract legend2
# #------------------
# labels = seq(lig_min, lig_max, len = 5); labels
# labelsD = round(labels, digits = 0); labelsD
#
# g2_leg = g1 +
# geom_tile(aes(fill = .data[[lig_dist_colname]])
# , colour = "white") +
# scale_fill_gradient2(midpoint = lig_mean
# , low = "green"
# , mid = "yellow"
# , high = "red"
# , breaks = labels
# #, n.breaks = 11
# #, minor_breaks = c(2, 4, 6, 8, 10)
# , limits = c(lig_min, lig_max)
# , labels = labelsD
# , name = leg_title2)
#
# legend2 = get_legend(g2_leg)
#
# }else{
# out = g1
# }
######################################################
#------------------
# Extract legend2
#------------------
labels = seq(lig_min, lig_max, len = 5); labels
labelsD = round(labels, digits = 0); labelsD
g2_leg = ggplot(plotdf, aes_string(x = sprintf("factor(%s)", xvar_colname)
, y = yvar_colname)
) +
geom_tile(aes(fill = .data[[lig_dist_colname]])
, colour = "white") +
scale_fill_gradient2(midpoint = lig_mean
, low = "green"
, mid = "yellow"
, high = "red"
, breaks = labels
#, n.breaks = 11
#, minor_breaks = c(2, 4, 6, 8, 10)
, limits = c(lig_min, lig_max)
, labels = labelsD
, name = leg_title2)
legend2 = get_legend(g2_leg)
}else{
out = g1
#####################################################
#============================================
# x-axis: geom_tiles ~ ligand distance
#============================================
#-------
# plot
#-------
if(A_xvar_lig){ # 0 is a magic number that does my sensible default
if (tpos0 == 0){
tpos0 = ymin-0.5
}
if (tpos1 == 0){
tpos1 = ymin-0.65
}
if (tpos2 == 0){
tpos2 = ymin-0.75
}
if (tpos3 == 0){
tpos3 = ymin-0.85
}
#####################################################
# #============================================
# # x-axis: geom_tiles ~ ligand distance
# #============================================
# if(A_xvar_lig){
# cat("\nColouring x-axis aa based on", lig_dist_colname
# , "\nNo. of colours:", n_colours)
cat("\nColouring x-axis aa based on", lig_dist_colname
, "\nNo. of colours:", n_colours)
g2 = g1 + geom_tile(aes(, tpos0
, width = tW0
, height = tH0)
, fill = plotdf$ligD_colours
, colour = plotdf$ligD_colours
, linetype = "blank")
#cat("Nrows of plot df", length(plotdf$ligD_colours))
out = g2
#
# g2 = g1 + geom_tile(aes(, tpos0
# , width = tW0
# , height = tH0)
# , fill = plotdf$ligD_colours
# , colour = plotdf$ligD_colours
# , linetype = "blank")
# #------------------
# # Extract legend2
# #------------------
# labels = seq(lig_min, lig_max, len = 5); labels
# labelsD = round(labels, digits = 0); labelsD
#
# #cat("Nrows of plot df", length(plotdf$ligD_colours))
# out = g2
# }else{
# g2_leg = g1 +
# geom_tile(aes(fill = .data[[lig_dist_colname]])
# , colour = "white") +
# scale_fill_gradient2(midpoint = lig_mean
# , low = "green"
# , mid = "yellow"
# , high = "red"
# , breaks = labels
# #, n.breaks = 11
# #, minor_breaks = c(2, 4, 6, 8, 10)
# , limits = c(lig_min, lig_max)
# , labels = labelsD
# , name = leg_title2)
#
# legend2 = get_legend(g2_leg)
#
# }else{
# out = g1
# }
#
############################################################################################
#==============================================
# x-axis: geom_tiles ~ active sites and others
#==============================================
if(A_xvar_aa){
#tpos = 0
#tW = 1
#tH = 0.2
######################################################
#------------------
# Extract legend2
#------------------
labels = seq(lig_min, lig_max, len = 5); labels
labelsD = round(labels, digits = 0); labelsD
g2_leg = ggplot(plotdf, aes_string(x = sprintf("factor(%s)", xvar_colname)
, y = yvar_colname)
) +
geom_tile(aes(fill = .data[[lig_dist_colname]])
, colour = "white") +
scale_fill_gradient2(midpoint = lig_mean
, low = "green"
, mid = "yellow"
, high = "red"
, breaks = labels
#, n.breaks = 11
#, minor_breaks = c(2, 4, 6, 8, 10)
, limits = c(lig_min, lig_max)
, labels = labelsD
, name = leg_title2)
#---------------------
# Add2plot: 3 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&3 sites")
cat("\nCreating column colours, column name:", aa_colour_colname3)
legend2 = get_legend(g2_leg)
cat("\nDoing Plot with 3 ligands")
}
out = out + geom_tile(aes(,tpos3
, width = tW
, height = tH )
, fill = plotdf[[aa_colour_colname3]]
, colour = plotdf[[aa_colour_colname3]]
, linetype = "solid") +
geom_tile(aes(, tpos2
, width = tW
, height = tH )
, fill = plotdf[[aa_colour_colname2]]
, colour = plotdf[[aa_colour_colname2]]
, linetype = "solid")+
}else{
out = g1
}
#==============================================
# x-axis: geom_tiles ~ active sites and others
#==============================================
if(A_xvar_aa){
#tpos = 0
#tW = 1
#tH = 0.2
geom_tile(aes(, tpos1
, width = tW
, height = tH)
, fill = plotdf[[aa_colour_colname1]]
, colour = plotdf[[aa_colour_colname1]]
, linetype = "solid")
if (debug){
cat("\nDone Plot with 3 ligands")
}
#---------------------
# Add2plot: 3 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&3 sites")
cat("\nCreating column colours, column name:", aa_colour_colname3)
cat("\nDoing Plot with 3 ligands")
}
#---------------------
# 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){
out = out + geom_tile(aes(,tpos3
, width = tW
, height = tH )
, fill = plotdf[[aa_colour_colname3]]
, colour = plotdf[[aa_colour_colname3]]
, linetype = "solid") +
geom_tile(aes(, tpos2
, width = tW
, height = tH )
, fill = plotdf[[aa_colour_colname2]]
, colour = plotdf[[aa_colour_colname2]]
, linetype = "solid")+
geom_tile(aes(, tpos1
, width = tW
, height = tH)
, fill = plotdf[[aa_colour_colname1]]
, colour = plotdf[[aa_colour_colname1]]
, linetype = "solid")
if (debug){
cat("\nDone Plot with 3 ligands")
}
}
#---------------------
# 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)
cat("\nDoing Plot with 2 ligands")
}
out = out +
geom_tile(aes(, tpos2
, width = tW
, height = tH)
, fill = plotdf[[aa_colour_colname2]]
, colour = plotdf[[aa_colour_colname2]]
, linetype = "solid")+
geom_tile(aes(, tpos1
, width = tW
, height = tH)
, fill = plotdf[[aa_colour_colname1]]
, colour = plotdf[[aa_colour_colname1]]
, linetype = "solid")
if (debug){
cat("\nDone Plot with 2 ligands")
}
}
out = out +
geom_tile(aes(, tpos2
, width = tW
, height = tH)
, fill = plotdf[[aa_colour_colname2]]
, colour = plotdf[[aa_colour_colname2]]
, linetype = "solid")+
geom_tile(aes(, tpos1
, width = tW
, height = tH)
, fill = plotdf[[aa_colour_colname1]]
, colour = plotdf[[aa_colour_colname1]]
, linetype = "solid")
if (debug){
cat("\nDone Plot with 2 ligands")
}
}
#---------------------
# Add2plot: 1 ligand
#---------------------
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){
#---------------------
# Add2plot: 1 ligand
#---------------------
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)
cat("\nDoing Plot with 1 ligands")
}
out = out +
geom_tile(aes(, tpos1
, width = tW
, height = tH)
, fill = plotdf[[aa_colour_colname1]]
, colour = plotdf[[aa_colour_colname1]]
, linetype = "solid")
cat("\nDone Plot with 1 ligand")
}
out = out +
geom_tile(aes(, tpos1
, width = tW
, height = tH)
, fill = plotdf[[aa_colour_colname1]]
, colour = plotdf[[aa_colour_colname1]]
, linetype = "solid")
#-----------------------------------
# Add2plot:NO ligands
# No Ligs: Just drug and active site
# DEFAULT: A_xvar_aa == 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("\nDone Plot with 1 ligand")
}
#-----------------------------------
# Add2plot:NO ligands
# No Ligs: Just drug and active site
# DEFAULT: A_xvar_aa == 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")
}
out = out + geom_tile(aes(, tpos3
, width = tW
, height = tH)
, fill = plotdf[[aa_colour_colname]]
, colour = plotdf[[aa_colour_colname]]
, linetype = "solid")
if (debug){
cat("\nDone Plot with: Active and Drug sites")
}
}
}else{
cat("\nNo annotation for additional ligands on xvar requested")
out = out + geom_tile(aes(, tpos3
, width = tW
, height = tH)
, fill = plotdf[[aa_colour_colname]]
, colour = plotdf[[aa_colour_colname]]
, linetype = "solid")
if (debug){
cat("\nDone Plot with: Active and Drug sites")
}
}
#==============================================
if (A_xvar_lig){
legs = cowplot::plot_grid(legend1
, legend2
, ncol = 1
, align = "hv"
, rel_heights = c(2/4,3/4))
}else{
cat("\nNo annotation for additional ligands on xvar requested")
}
#==============================================
if (A_xvar_lig){
legs = cowplot::plot_grid(legend1
, legend2
, ncol = 1
, align = "hv"
, rel_heights = c(2/4,3/4))
out2 = cowplot::plot_grid( out + theme(legend.position = "none")
, legs
, ncol = 2
, align = "hv"
, rel_widths = c(9/10, 0.4/10)
)
}else{
out2 = cowplot::plot_grid( out + theme(legend.position = "none")
, legend1
, ncol = 2
, align = "hv"
, rel_widths = c(9/10, 0.5/10)
)
}
#==============================================
out2 = cowplot::plot_grid( out + theme(legend.position = "none")
, legs
, ncol = 2
, align = "hv"
, rel_widths = c(9/10, 0.4/10)
)
}else{
out2 = cowplot::plot_grid( out + theme(legend.position = "none")
, legend1
, ncol = 2
, align = "hv"
, rel_widths = c(9/10, 0.5/10)
)
}
#==============================================
#==============================================
# if (A_xvar_lig){
# legs = grid.arrange(legend1
# , legend2
# , ncol = 1
# , heights = c(3/4,1))
#
# out2 = grid.arrange( out + theme(legend.position = "none")
# , legs
# , ncol = 2
# , widths = c(9/10, 0.5/10)
# )
# }else{
# out2 = grid.arrange( out + theme(legend.position = "none")
# , legend1
# , ncol = 2
# , widths = c(9/10, 0.5/10)
# )
# }
#==============================================
return(out2)
#return(out2)
#==============================================
# if (A_xvar_lig){
# legs = grid.arrange(legend1
# , legend2
# , ncol = 1
# , heights = c(3/4,1))
#
# out2 = grid.arrange( out + theme(legend.position = "none")
# , legs
# , ncol = 2
# , widths = c(9/10, 0.5/10)
# )
# }else{
# out2 = grid.arrange( out + theme(legend.position = "none")
# , legend1
# , ncol = 2
# , widths = c(9/10, 0.5/10)
# )
# }
#==============================================
return(out2)
#return(out2)
}

121
scripts/functions/generate_distance_colour_map.R Normal file
View file

@ -0,0 +1,121 @@
# takes a dataframe and returns the same dataframe with two extra columns for colours and position
generate_distance_colour_map = function(plotdf,
xvar_colname = "position",
yvar_colname = 'duet_scaled',
lig_dist_colname = "ligand_distance",
lig_dist_colours = c("green", "yellow", "orange", "red"),
#tpos0 = 0,
#tpos1 = 0,
#tpos2 = 0,
#tpos3 = 0,
debug = FALSE
)
{
#-------------------
# x and y axis
# range, scale, etc
#-------------------
my_xlim = length(unique(plotdf[[yvar_colname]])); my_xlim
ymin = min(plotdf[[yvar_colname]]); ymin
ymax = max(plotdf[[yvar_colname]]); ymax
#if (tpos0 == 0){
# tpos0 = ymin-0.5
#}
#if (tpos1 == 0){
# tpos1 = ymin-0.65
#}
#if (tpos2 == 0){
# tpos2 = ymin-0.75
#}
#if (tpos3 == 0){
# tpos3 = ymin-0.85
#}
if (debug) {
cat("\nAnnotating x-axis ~", lig_dist_colname, "requested...")
}
#-------------------------------------
# round column values: to colour by
#--------------------------------------
#plotdf = plotdf[order(plotdf[[lig_dist_colname]]),]
plotdf['lig_distR'] = round(plotdf[[lig_dist_colname]], digits = 0)
#head(plotdf['lig_distR'])
#-------------------------------------
# ligand distance range, min, max, etc
#--------------------------------------
lig_min = min(round(plotdf[[lig_dist_colname]]), na.rm = T); lig_min
lig_max = max(round(plotdf[[lig_dist_colname]]), na.rm = T); lig_max
lig_mean = round(mean(round(plotdf[[lig_dist_colname]]), na.rm = T)); lig_mean
#-------------------------------------
# Create mapping colour key
#--------------------------------------
# sorting removes NA, so that n_colours == length(ligD_valsR)
n_colours = length(sort(unique(round(plotdf[[lig_dist_colname]], digits = 0)))); n_colours
lig_cols = colorRampPalette(lig_dist_colours)(n_colours); lig_cols
ligD_valsR = sort(unique(round(plotdf[[lig_dist_colname]], digits = 0))); ligD_valsR
length(ligD_valsR)
if (debug) {
if (n_colours == length(ligD_valsR)) {
cat("\nStarting: mapping b/w"
, lig_dist_colname
, "and colours")
}else{
cat("\nCannot start mapping b/w", lig_dist_colname, "and colours..."
, "\nLength mismatch:"
, "No. of colours: ", n_colours
, "\nValues to map:", length(ligD_valsR))
}
}
ligDcolKey <- data.frame(ligD_colours = lig_cols
, lig_distR = ligD_valsR); ligDcolKey
names(ligDcolKey)
if (debug) {
cat("\nSuccessful: Mapping b/w", lig_dist_colname, "and colours")
}
#-------------------------------------
# merge colour key with plotdf
#--------------------------------------
plotdf = merge(plotdf, ligDcolKey, by = 'lig_distR')
plotdf_check = as.data.frame(cbind(position = plotdf[[xvar_colname]]
, ligD = plotdf[[lig_dist_colname]]
, ligDR = plotdf$lig_distR
, ligD_cols = plotdf$ligD_colours))
return(plotdf)
}
generate_distance_legend = function(plotdf,
yvar_colname,
xvar_colname = 'position',
lig_dist_colname = "ligand_distance",
legend_title = "Ligand\nDistance"
)
{
# build legend for ligand distance "heat bar"
lig_min = min(round(plotdf[[lig_dist_colname]]), na.rm = T); lig_min
lig_max = max(round(plotdf[[lig_dist_colname]]), na.rm = T); lig_max
lig_mean = round(mean(round(plotdf[[lig_dist_colname]]), na.rm = T)); lig_mean
labels = seq(lig_min, lig_max, len = 5); labels
labelsD = round(labels, digits = 0); labelsD
get_legend(ggplot(plotdf, aes_string(x = sprintf("factor(%s)", xvar_colname)
, y = yvar_colname)) +
geom_tile(aes(fill = .data[[lig_dist_colname]])
, colour = "white") +
scale_fill_gradient2(midpoint = lig_mean
, low = "green"
, mid = "yellow"
, high = "red"
, breaks = labels
, limits = c(lig_min, lig_max)
, labels = labelsD
, name = legend_title)
)
}

70
scripts/functions/lineage_dist.R
View file

@ -16,7 +16,7 @@ lineage_distP <- function(plotdf
, all_lineages = F
, use_lineages = c("L1", "L2", "L3", "L4")
, with_facet = F
, facet_wrap_var = ""
, facet_wrap_var = "" # FIXME: document what this is for
, fill_categ = "mutation_info_labels"
, fill_categ_cols = c("#E69F00", "#999999")
, my_ats = 15 # axis text size
@ -31,45 +31,43 @@ lineage_distP <- function(plotdf
{
if(!all_lineages){
plotdf = plotdf[plotdf[[y_axis]]%in%use_lineages,]
}
if(!all_lineages){
plotdf = plotdf[plotdf[[y_axis]]%in%use_lineages,]
}
LinDistP = ggplot(plotdf, aes_string(x = x_axis
, y = y_axis))+
ggplot(plotdf, aes_string(x = x_axis
, y = y_axis))+
geom_density_ridges(aes_string(fill = fill_categ)
, scale = 3
, size = 0.3
, alpha = 0.8) +
scale_x_continuous(expand = c(0.01, 0.01)) +
#coord_cartesian( xlim = c(-1, 1)) +
scale_fill_manual(values = fill_categ_cols) +
theme(axis.text.x = element_text(size = my_ats
, angle = 90
, hjust = 1
, vjust = 0.4)
, axis.text.y = element_text(size = my_ats)
, axis.title.x = element_text(size = my_ats)
, axis.title.y = element_blank()
, strip.text = element_text(size = my_strip_ts)
, legend.text = element_text(size = my_leg_ts)
, legend.title = element_text(size = my_leg_title)
, legend.position = c(0.8, 0.9)) +
labs(x = x_lab
, fill = leg_label)
geom_density_ridges(aes_string(fill = fill_categ)
, scale = 3
, size = 0.3
, alpha = 0.8) +
scale_x_continuous(expand = c(0.01, 0.01)) +
#coord_cartesian( xlim = c(-1, 1)) +
scale_fill_manual(values = fill_categ_cols) +
theme(axis.text.x = element_text(size = my_ats
, angle = 90
, hjust = 1
, vjust = 0.4)
, axis.text.y = element_text(size = my_ats)
, axis.title.x = element_text(size = my_ats)
, axis.title.y = element_blank()
, strip.text = element_text(size = my_strip_ts)
, legend.text = element_text(size = my_leg_ts)
, legend.title = element_text(size = my_leg_title)
, legend.position = c(0.8, 0.9)) +
labs(x = x_lab
, fill = leg_label) +
if (with_facet){
# FIXME: This didn't work BEFORE i fixed the ggplot() assignment thing!!!
if (with_facet){
# used reformulate or make as formula
#fwv = reformulate(facet_wrap_var)
fwv = as.formula(paste0("~", facet_wrap_var))
# used reformulate or make as formula
#fwv = reformulate(facet_wrap_var)
fwv = as.formula(paste0("~", facet_wrap_var))
LinDistP = LinDistP +
facet_wrap(fwv) +
theme(legend.position = leg_pos_wf
, legend.direction = leg_dir_wf)
}
return(LinDistP)
theme(legend.position = leg_pos_wf
, legend.direction = leg_dir_wf)
}
}

175
scripts/functions/logoP_or.R
View file

@ -1,5 +1,5 @@
# Input:
# Data:
# Data:
# plot_df: merged_df3 containing the OR column to use as y-axis or any other relevant column
# x_axis_colname = "position"
@ -7,19 +7,19 @@
# symbol_colname = "mutant_type"
# y_axis_log = F
# log_value = log10
# if used, y-axis label has "Log" appended to it
# if used, y-axis label has "Log" appended to it
# my_logo_col = c("chemistry", "hydrophobicity", "clustalx", "taylor")
# --> if clustalx and taylor, set variable to black bg + white font
# --> if chemistry and hydrophobicity, then grey bg + black font
# --> if clustalx and taylor, set variable to black bg + white font
# --> if chemistry and hydrophobicity, then grey bg + black font
# rm_empty_y = F
# option to remove empty positions i.e positions with no assocaited y-val
# option to remove empty positions i.e positions with no assocaited y-val
# y_axis_log = F
# option to use log scale
# FIXME Minor bug: if used with rm_empty_y, sometimes the labels are too small to render(!?)
# so positions appear empty despite having y-vals
# option to use log scale
# FIXME Minor bug: if used with rm_empty_y, sometimes the labels are too small to render(!?)
# so positions appear empty despite having y-vals
# ...other params
@ -39,48 +39,52 @@
# logo data: OR
#==================
LogoPlotCustomH <- function(plot_df
, x_axis_colname = "position"
, y_axis_colname = "or_mychisq"
, symbol_colname = "mutant_type"
, my_logo_col = "chemistry"
, rm_empty_y = F
, y_axis_log = F
, log_value = log10
, y_axis_increment = 5
, x_lab = "Position"
, y_lab = "Odds Ratio"
, x_ats = 12 # text size
, x_tangle = 90 # text angle
, y_ats = 22
, y_tangle = 0
, x_tts = 20 # title size
, y_tts = 23
, leg_pos = "none" # can be top, left, right and bottom or c(0.8, 0.9)
, leg_dir = "horizontal" #can be vertical or horizontal
, leg_ts = 15 # leg text size
, leg_tts = 16 # leg title size
)
, x_axis_colname = "position"
, y_axis_colname = "or_mychisq"
, symbol_colname = "mutant_type"
, my_logo_col = "chemistry"
, rm_empty_y = F
, y_axis_log = F
, log_value = log10
, y_axis_increment = 5
, x_lab = "Position"
, y_lab = "Odds Ratio"
, x_ats = 12 # text size
, x_tangle = 90 # text angle
, y_ats = 22
, y_tangle = 0
, x_tts = 20 # title size
, y_tts = 23
, leg_pos = "none" # can be top, left, right and bottom or c(0.8, 0.9)
, leg_dir = "horizontal" #can be vertical or horizontal
, leg_ts = 15 # leg text size
, leg_tts = 16 # leg title size
, tpos0 = 0 # 0 is a magic number that does my sensible default
, tW0 = 1
, tH0 = 0.3
)
{
#################################
# Data processing for logo plot
#################################
#################################
# Data processing for logo plot
#################################
plot_df = generate_distance_colour_map(plot_df, yvar_colname = y_axis_colname, debug=TRUE)
if (rm_empty_y){
plot_df = plot_df[!is.na(plot_df[y_axis_colname]),]
cat("\nRemoving empty positions...\n")
}else{
plot_df = plot_df
}
if (rm_empty_y){
plot_df = plot_df[!is.na(plot_df[y_axis_colname]),]
cat("\nRemoving empty positions...\n")
}else{
plot_df = plot_df
}
y_max = max(plot_df['or_mychisq'], na.rm = T)
cat("\nRemoving y scale incremenet:", y_axis_increment)
y_lim = round_any(y_max, y_axis_increment, f = ceiling)
y_max = max(plot_df['or_mychisq'], na.rm = T)
cat("\nRemoving y scale incremenet:", y_axis_increment)
y_lim = round_any(y_max, y_axis_increment, f = ceiling)
#-------------------
# logo data: LogOR
#-------------------
if (y_axis_log){
#-------------------
# logo data: LogOR
#-------------------
if (y_axis_log){
log_colname = paste0("log_", y_axis_colname)
plot_df[log_colname] = log_value(plot_df[y_axis_colname])
@ -95,7 +99,7 @@ LogoPlotCustomH <- function(plot_df
#y_lim = round_any(y_max, y_axis_increment, f = ceiling)
} else {
} else {
#-------------------
# logo data: OR
@ -142,56 +146,59 @@ LogoPlotCustomH <- function(plot_df
ytt_col = "black"
}
p0 = ggseqlogo(logo_dfP_wf
, method = "custom"
, col_scheme = my_logo_col
, seq_type = "aa") +
if (y_axis_log){
if (grepl("Log", y_lab)){
y_lab = y_lab
}else{
y_lab = paste("Log", y_lab)
}
}
ggseqlogo(logo_dfP_wf
, method = "custom"
, col_scheme = my_logo_col
, seq_type = "aa") +
#ylab("my custom height") +
theme(axis.text.x = element_text(size = x_ats
, angle = x_tangle
, hjust = 1
, vjust = 0.4
, colour = xfont_bgc)
, axis.text.y = element_text(size = y_ats
, angle = y_tangle
, hjust = 1
, vjust = 0
, colour = yfont_bgc)
, axis.title.x = element_text(size = x_tts
, angle = x_tangle
, hjust = 1
, vjust = 0.4
, colour = xfont_bgc)
, axis.text.y = element_text(size = y_ats
, angle = y_tangle
, hjust = 1
, vjust = 0
, colour = yfont_bgc)
, axis.title.x = element_text(size = x_tts
, colour = xtt_col)
, axis.title.y = element_text(size = y_tts
, axis.title.y = element_text(size = y_tts
, colour = ytt_col)
, legend.title = element_text(size = leg_tts
, legend.title = element_text(size = leg_tts
, colour = ytt_col)
, legend.text = element_text(size = leg_ts)
, legend.text = element_text(size = leg_ts)
, legend.position = leg_pos
, legend.direction = leg_dir
, plot.background = element_rect(fill = theme_bgc))+
, legend.position = leg_pos
, legend.direction = leg_dir
, plot.background = element_rect(fill = theme_bgc))+
scale_x_discrete(x_lab
#, breaks
, labels = position_or
, limits = factor(1:length(position_or)))
, limits = factor(1:length(position_or))) +
LogoPlot = p0 + scale_y_continuous(y_lab
scale_y_continuous(y_lab
, breaks = seq(0, (y_lim), by = y_axis_increment)
#, labels = seq(0, (y_lim), by = y_axis_increment)
, limits = c(0, y_lim))
if (y_axis_log){
if (grepl("Log", y_lab)){
y_lab = y_lab
}else{
y_lab = paste("Log", y_lab)
}
LogoPlot = p0 + ylab(y_lab)
}
return(LogoPlot)
, limits = c(0, y_lim)) +
ylab(y_lab) +
geom_tile(aes(plot_df$position, tpos0 # heat-mapped distance tiles along the bot
, width = tW0
, height = tH0)
, fill = plot_df$ligD_colours
, colour = plot_df$ligD_colours
, linetype = "blank")
#LogoPlot = p0 + ylab(y_lab)
#return(LogoPlot)
}

332
scripts/functions/logoP_snp.R
View file

@ -1,7 +1,7 @@
########################a###########################################################
# Input:
# Data
# plot_df: merged_df3 containing the OR column to use as y-axis or any other relevant column
# Data
# plot_df: merged_df3 containing the OR column to use as y-axis or any other relevant column
# x_axis_colname = "position"
# symbol_mut_colname = "mutant_type"
@ -15,7 +15,7 @@
# ...other params
# Returns: Logo plot from combined data containing all nsSNPs per position.
# Helps to see the overview of SNP diversity
# Helps to see the overview of SNP diversity
# TODO: SHINY
# select/drop down: omit_snp_count
@ -31,38 +31,47 @@
# NOTE: my_logo_col
LogoPlotSnps <- function(plot_df
, x_axis_colname = "position"
, symbol_mut_colname = "mutant_type"
, symbol_wt_colname = "mutant_type"
, omit_snp_count = c(0) # can be 1, 2, etc.
, my_logo_col = "chemistry"
, x_lab = "Position"
, y_lab = "Count"
, x_ats = 14 # text size
, x_tangle = 90 # text angle
, y_ats = 22
, y_tangle = 0
, x_tts = 20 # title size
, y_tts = 23
, leg_pos = "none" # can be top, left, right and bottom or c(0.8, 0.9)
, leg_dir = "horizontal" #can be vertical or horizontal
, leg_ts = 20 # leg text size
, leg_tts = 16 # leg title size
)
, x_axis_colname = "position"
, symbol_mut_colname = "mutant_type"
, symbol_wt_colname = "mutant_type"
, omit_snp_count = c(0) # can be 1, 2, etc.
, my_logo_col = "chemistry"
, x_lab = "Position"
, y_lab = "Count"
, x_ats = 14 # text size
, x_tangle = 90 # text angle
, y_ats = 22
, y_tangle = 0
, x_tts = 20 # title size
, y_tts = 23
, leg_pos = "none" # can be top, left, right and bottom or c(0.8, 0.9)
, leg_dir = "horizontal" #can be vertical or horizontal
, leg_ts = 20 # leg text size
, leg_tts = 16 # leg title size
, tpos0 = 0 # 0 is a magic number that does my sensible default
, tW0 = 1
, tH0 = 0.2
, debug=FALSE
)
{
# handle funky omit_snp_count. DOES NOT WORK YET
if (class(omit_snp_count) != "numeric"){
omit_snp_count <- as.numeric(unlist(str_extract_all(omit_snp_count, regex("[0-9]+"))))
}
############################################
# Data processing for logo plot for nsSNPS
############################################
setDT(plot_df)[, mut_pos_occurrence := .N, by = .(eval(parse(text=x_axis_colname)))]
############################################
# Data processing for logo plot for nsSNPS
############################################
# Generate "ligand distance" colour map
plot_df = generate_distance_colour_map(plot_df, debug=TRUE)
setDT(plot_df)[, mut_pos_occurrence := .N, by = .(eval(parse(text=x_axis_colname)))]
if (debug) {
table(plot_df[[x_axis_colname]])
table(plot_df$mut_pos_occurrence)
}
max_mut = max(table(plot_df[[x_axis_colname]]))
# Subset Data as specified by user
@ -73,13 +82,14 @@ LogoPlotSnps <- function(plot_df
my_data_snp = plot_df
u = unique(my_data_snp[[x_axis_colname]])
max_mult_mut = max(table(my_data_snp[[x_axis_colname]]))
cat("\nNo filtering requested:"
, "\nTotal no. of nsSNPs:", sum(table(plot_df$mut_pos_occurrence))
, "\nTotal no. of nsSNPs omitted:", sum(table(plot_df$mut_pos_occurrence)[omit_snp_count])
, "\nDim of data:", dim(my_data_snp)
, "\nNo. of positions:", length(u)
, "\nMax no. of muts at any position:", max_mult_mut)
if (debug) {
cat("\nNo filtering requested:"
, "\nTotal no. of nsSNPs:", sum(table(plot_df$mut_pos_occurrence))
, "\nTotal no. of nsSNPs omitted:", sum(table(plot_df$mut_pos_occurrence)[omit_snp_count])
, "\nDim of data:", dim(my_data_snp)
, "\nNo. of positions:", length(u)
, "\nMax no. of muts at any position:", max_mult_mut)
}
} else {
my_data_snp = subset(plot_df, !(mut_pos_occurrence%in%omit_snp_count) )
@ -88,19 +98,20 @@ LogoPlotSnps <- function(plot_df
got_rows = sum(table(my_data_snp$mut_pos_occurrence))
u = unique(my_data_snp[[x_axis_colname]])
max_mult_mut = max(table(my_data_snp[[x_axis_colname]]))
if (debug) {
if (got_rows == exp_nrows) {
cat("\nPass: Position with the stated nsSNP frequency filtered:", omit_snp_count
, "\nTotal no. of nsSNPs:", sum(table(plot_df$mut_pos_occurrence))
, "\nTotal no. of nsSNPs omitted:", sum(table(plot_df$mut_pos_occurrence)[omit_snp_count])
, "\nDim of subsetted data:", dim(my_data_snp)
, "\nNo. of positions:", length(u)
, "\nMax no. of muts at any position:", max_mult_mut)
} else {
if (got_rows == exp_nrows) {
cat("\nPass: Position with the stated nsSNP frequency filtered:", omit_snp_count
, "\nTotal no. of nsSNPs:", sum(table(plot_df$mut_pos_occurrence))
, "\nTotal no. of nsSNPs omitted:", sum(table(plot_df$mut_pos_occurrence)[omit_snp_count])
, "\nDim of subsetted data:", dim(my_data_snp)
, "\nNo. of positions:", length(u)
, "\nMax no. of muts at any position:", max_mult_mut)
} else {
cat("\nFAIL:Position with the stated nsSNP frequency COULD NOT be filtered..."
, "\nExpected:",exp_nrows
, "\nGot:", got_rows )
cat("\nFAIL:Position with the stated nsSNP frequency COULD NOT be filtered..."
, "\nExpected:",exp_nrows
, "\nGot:", got_rows )
}
}
}
@ -116,17 +127,21 @@ LogoPlotSnps <- function(plot_df
tab_mt = unclass(tab_mt)
if (is.matrix(tab_mt)){
cat("\nPASS: Mutant matrix successfully created..."
#, "\nRownames of mutant matrix:", rownames(tab_mt)
#, "\nColnames of mutant matrix:", colnames(tab_mt)
)
if (debug) {
cat("\nPASS: Mutant matrix successfully created..."
#, "\nRownames of mutant matrix:", rownames(tab_mt)
#, "\nColnames of mutant matrix:", colnames(tab_mt)
)
}
} else{
tab_mt = as.matrix(tab_mt, rownames = T)
if (is.matrix(tab_mt)){
cat("\nCreating mutant matrix..."
#, "\nRownames of mutant matrix:", rownames(tab_mt)
#, "\nColnames of mutant matrix:", colnames(tab_mt)
)
if (debug) {
cat("\nCreating mutant matrix..."
#, "\nRownames of mutant matrix:", rownames(tab_mt)
#, "\nColnames of mutant matrix:", colnames(tab_mt)
)
}
}
}
@ -146,16 +161,17 @@ LogoPlotSnps <- function(plot_df
wt
tab_wt = table(wt[[symbol_wt_colname]], wt[[x_axis_colname]]); tab_wt # should all be 1
if (debug) {
if ( identical(colnames(tab_mt), colnames(tab_wt) ) && identical(ncol(tab_mt), ncol(tab_wt)) ){
if ( identical(colnames(tab_mt), colnames(tab_wt) ) && identical(ncol(tab_mt), ncol(tab_wt)) ){
cat("\nPASS: Wild type matrix successfully created"
, "\nDim of wt matrix:", dim(tab_wt)
, "\nDim of mutant matrix:", dim(tab_mt)
, "\n"
#, "\nRownames of mutant matrix:", rownames(tab_wt)
#, "\nColnames of mutant matrix:", colnames(tab_wt)
)
cat("\nPASS: Wild type matrix successfully created"
, "\nDim of wt matrix:", dim(tab_wt)
, "\nDim of mutant matrix:", dim(tab_mt)
, "\n"
#, "\nRownames of mutant matrix:", rownames(tab_wt)
#, "\nColnames of mutant matrix:", colnames(tab_wt)
)
}
}
######################################
@ -188,128 +204,96 @@ LogoPlotSnps <- function(plot_df
#####################################
# Generating logo plots for nsSNPs
#####################################
cowplot::plot_grid(
#-------------------
# Mutant logo plot
#-------------------
ggseqlogo(tab_mt
, method = 'custom'
, col_scheme = my_logo_col
, seq_type = 'aa') +
#-------------------
# Mutant logo plot
#-------------------
p0 = ggseqlogo(tab_mt
, method = 'custom'
, col_scheme = my_logo_col
, seq_type = 'aa') +
theme(text=element_text(family="FreeSans"))+
theme(axis.text.x = element_blank()) +
theme_logo()+
theme(text=element_text(family="FreeSans"))+
theme(axis.text.x = element_blank()) +
theme_logo()+
scale_x_continuous(breaks = 1:ncol(tab_mt)
, expand = c(0.01,0)
, labels = colnames(tab_mt))+
scale_x_continuous(breaks = 1:ncol(tab_mt)
, expand = c(0.01,0)
, labels = colnames(tab_mt))+
scale_y_continuous(breaks = 0:(max_mult_mut-1)
, labels = c(1:max_mult_mut)
, limits = c(0, max_mult_mut)) +
#xlab(x_lab) +
ylab(y_lab)
scale_y_continuous(breaks = 0:(max_mult_mut-1)
, labels = c(1:max_mult_mut)
, limits = c(0, max_mult_mut)) +
# FIXME: currently broken, possibly due to ggseqlogo() not working in the
# way standard ggplot2() does
geom_tile(aes(plot_df$position, tpos0 # heat-mapped distance tiles along the bottom.
, width = tW0
, height = tH0)
, fill = plot_df$ligD_colours
, colour = plot_df$ligD_colours
, linetype = "blank") +
ylab(y_lab) +
theme(legend.position = leg_pos
, legend.direction = leg_dir
, legend.title = element_text(size = leg_tts
, colour = ytt_col)
, legend.text = element_text(size = leg_ts)
cat('\nDone: p0')
, axis.text.x = element_text(size = x_ats
, angle = x_tangle
, hjust = 1
, vjust = 0.4
, colour = xfont_bgc)
, axis.text.y = element_text(size = y_ats
, angle = y_tangle
, hjust = 1
, vjust = -1.0
, colour = yfont_bgc)
, axis.title.x = element_text(size = x_tts
, colour = xtt_col)
, axis.title.y = element_text(size = y_tts
, colour = ytt_col)
# further customisation
mut_logo_p = p0 + theme(legend.position = leg_pos
, legend.direction = leg_dir
#, legend.title = element_blank()
, legend.title = element_text(size = leg_tts
, colour = ytt_col)
, legend.text = element_text(size = leg_ts)
, plot.background = element_rect(fill = theme_bgc)
)
,ggseqlogo(tab_wt
, method = 'custom'
, col_scheme = my_logo_col
, seq_type = 'aa') +
, axis.text.x = element_text(size = x_ats
, angle = x_tangle
, hjust = 1
, vjust = 0.4
, colour = xfont_bgc)
#, axis.text.y = element_blank()
, axis.text.y = element_text(size = y_ats
, angle = y_tangle
, hjust = 1
, vjust = -1.0
, colour = yfont_bgc)
, axis.title.x = element_text(size = x_tts
, colour = xtt_col)
, axis.title.y = element_text(size = y_tts
, colour = ytt_col)
theme(text = element_text(family="FreeSans"))+
theme(axis.text.x = element_blank()
, axis.text.y = element_blank()) +
theme_logo()+
, plot.background = element_rect(fill = theme_bgc))
scale_x_continuous(breaks = 1:ncol(tab_wt)
, expand = c(0.01,0)
, labels = colnames(tab_wt))+
cat('\nDone: mut_logo_p')
#return(mut_logo_p)
LogoPlotL[['mut_logoP']] <- mut_logo_p
xlab(x_lab) +
theme(legend.position = "none"
, legend.direction = leg_dir
#, legend.title = element_blank()
, legend.title = element_text(size = y_tts
, colour = ytt_col)
, legend.text = element_text(size = leg_ts)
, axis.text.x = element_text(size = x_ats
, angle = x_tangle
, hjust = 1
, vjust = 0.4
, colour = xfont_bgc)
, axis.text.y = element_blank()
, axis.title.x = element_text(size = x_tts
, colour = xtt_col)
, axis.title.y = element_text(size = y_tts
, colour = ytt_col)
, plot.background = element_rect(fill = theme_bgc)
)
, nrow = 2
, align = "v"
, rel_heights = c(3/4, 1/4))
#------------------
# Wild logo plot
#------------------
p1 = ggseqlogo(tab_wt
, method = 'custom'
, col_scheme = my_logo_col
, seq_type = 'aa') +
theme(text = element_text(family="FreeSans"))+
theme(axis.text.x = element_blank()
, axis.text.y = element_blank()) +
theme_logo()+
scale_x_continuous(breaks = 1:ncol(tab_wt)
, expand = c(0.01,0)
, labels = colnames(tab_wt))+
xlab(x_lab)
cat('\nDone: p1')
# further customisation
wt_logo_p = p1 +
theme(legend.position = "none"
, legend.direction = leg_dir
#, legend.title = element_blank()
, legend.title = element_text(size = y_tts
, colour = ytt_col)
, legend.text = element_text(size = leg_ts)
, axis.text.x = element_text(size = x_ats
, angle = x_tangle
, hjust = 1
, vjust = 0.4
, colour = xfont_bgc)
, axis.text.y = element_blank()
, axis.title.x = element_text(size = x_tts
, colour = xtt_col)
, axis.title.y = element_text(size = y_tts
, colour = ytt_col)
, plot.background = element_rect(fill = theme_bgc))
cat('\nDone: wt_logo_p')
#return(wt_logo_p)
LogoPlotL[['wt_logoP']] <- wt_logo_p
#=========================================
# Output
# Combined plot: logo_mutliple_muts.svg
#=========================================
#suppressMessages( require(cowplot) )
#plot_grid(p1, p3, ncol = 1, align = 'v')
cat('\nDone: mut_logo_p + wt_logo_p')
# colour scheme: https://rdrr.io/cran/ggseqlogo/src/R/col_schemes.r
#cat("\nOutput plot:", LogoSNPs_comb, "\n")
#svg(LogoSNPs_combined, width = 32, height = 10)
LogoPlotL[['wt_logoP']] <- wt_logo_p
LogoSNPs_comb = cowplot::plot_grid(LogoPlotL[['mut_logoP']]
, LogoPlotL[['wt_logoP']]
, nrow = 2
, align = "v"
, rel_heights = c(3/4, 1/4))
return(LogoSNPs_comb)
}

9
scripts/functions/position_count_bp.R
View file

@ -105,9 +105,9 @@ site_snp_count_bp <- function (plotdf
# not sure if to use with sort or directly
my_x = sort(unique(snpsBYpos_df$snpsBYpos))
g = ggplot(snpsBYpos_df, aes(x = snpsBYpos))
OutPlot_pos_count = g + geom_bar(aes (alpha = 0.5)
, show.legend = FALSE) +
ggplot(snpsBYpos_df, aes(x = snpsBYpos)) +
geom_bar(aes (alpha = 0.5)
, show.legend = FALSE) +
scale_x_continuous(breaks = unique(snpsBYpos_df$snpsBYpos)) +
geom_label(stat = "count", aes(label = ..count..)
, color = "black"
@ -127,13 +127,10 @@ site_snp_count_bp <- function (plotdf
, plot.subtitle = element_text(size = subtitle_size
, hjust = 0.5
, colour = subtitle_colour)) +
labs(title = bp_plot_title
, subtitle = subtitle_text
, x = xaxis_title
, y = yaxis_title)
return(OutPlot_pos_count)
}
########################################################################

506
scripts/functions/wideP_consurf.R Normal file
View file

@ -0,0 +1,506 @@
#!/usr/bin/env Rscript
#########################################################
# TASK: function for wide plot
#with consurf score and error bars
#position numbers coloured by
# - ligand distance
# - active site residues
#########################################################
#==========================================================
# 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"
, 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 = "black"
, panel_col_fill = "black"
# 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"
# 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 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"
, aa_pos_lig1 = NULL
, aa_colour_lig1 = "blue"
, tpos1 = 0
, aa_pos_lig2 = NULL
, aa_colour_lig2 = "cyan"
, tpos2 = 0
, aa_pos_lig3 = NULL
, aa_colour_lig3 = "cornflowerblue"
, tpos3 = 0
, default_gt_clr = "white"
, debug=FALSE
){
if(missing(point_colours)){
temp_cols = colorRampPalette(c("seagreen", "sienna3"))(30)
point_colours = temp_cols
}else{
point_colours = point_colours
}
###############################
# custom 1: x-axis text colour
##############################
if (xtext_colour_aa){
positionF <- levels(as.factor(plot_df[[xvar_colname]]))
length(positionF)
aa_pos_colours = ifelse(positionF%in%xtext_colour_aa1, xtext_colours[1]
, ifelse(positionF%in%xtext_colour_aa2
, xtext_colours[2]
, xtext_colours[3]))
}else{
aa_pos_colours = default_xtc
}
################################################
# Custom 2: x-axis geom tiles ~ lig distance
################################################
#=========================
# Build data with colours
# ~ ligand distance
#=========================
if (A_xvar_lig){
cat("\nAnnotating x-axis ~", lig_dist_colname, "requested...")
#-------------------------------------
# round column values: to colour by
#--------------------------------------
#plot_df = plot_df[order(plot_df[[lig_dist_colname]]),]
plot_df['lig_distR'] = round(plot_df[[lig_dist_colname]], digits = 0)
head(plot_df['lig_distR'])
#-------------------------------------
# ligand distance range, min, max, etc
#--------------------------------------
lig_min = min(round(plot_df[[lig_dist_colname]]), na.rm = T); lig_min
lig_max = max(round(plot_df[[lig_dist_colname]]), na.rm = T); lig_max
lig_mean = round(mean(round(plot_df[[lig_dist_colname]]), na.rm = T)); lig_mean
#-------------------------------------
# Create mapping colour key
#--------------------------------------
# sorting removes NA, so that n_colours == length(ligD_valsR)
n_colours = length(sort(unique(round(plot_df[[lig_dist_colname]], digits = 0)))); n_colours
lig_cols = colorRampPalette(lig_dist_colours)(n_colours); lig_cols
ligD_valsR = sort(unique(round(plot_df[[lig_dist_colname]], digits = 0))); ligD_valsR
length(ligD_valsR)
if (n_colours == length(ligD_valsR)) {
cat("\nStarting: mapping b/w"
, lig_dist_colname
, "and colours")
}else{
cat("\nCannot start mapping b/w", lig_dist_colname, "and colours..."
, "\nLength mismatch:"
, "No. of colours: ", n_colours
, "\nValues to map:", length(ligD_valsR))
}
ligDcolKey <- data.frame(ligD_colours = lig_cols
, lig_distR = ligD_valsR); ligDcolKey
names(ligDcolKey)
cat("\nSuccessful: Mapping b/w", lig_dist_colname, "and colours")
#-------------------------------------
# merge colour key with 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
}
###############################################
# Custom 3: x-axis geom tiles ~ active sites
################################################
#==========================
# Build Data with colours
# ~ on active sites
#==========================
if(A_xvar_aa) {
cat("\nAnnotation for xvar requested. Building colours for annotation...")
aa_colour_colname = "bg_all"
aa_colour_colname1 = "col_bg1"
aa_colour_colname2 = "col_bg2"
aa_colour_colname3 = "col_bg3"
#--------------------------------------------------
# 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 ))
plot_df[[aa_colour_colname]]
cat("\nColumn created 'bg_all':", length(plot_df[[aa_colour_colname]]))
#------------------------------------------------
# column colour 1: Ligand 1 + drug binding sites
#------------------------------------------------
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]])
#------------------------------------------------
# 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]])
#------------------------------------------------
# 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]])
}
###################
# start plot
###################
#-------------------
# x and y axis
# range, scale, etc
#-------------------
my_xlim = length(unique(plot_df[[xvar_colname]])); my_xlim
ymin = min(plot_df[[yvar_colname]]); ymin
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)
))
"if SPECIAL do SPECIAL THING, otherwise do NORMAL THING"
if (plot_type == "bar"){
g0 = g +
geom_bar(stat = "identity")
}
else{
g0 = g +
coord_cartesian(xlim = c(1, my_xlim)
, ylim = c(ymin, ymax)
, clip = "off") +
geom_point(size = p_size) +
scale_colour_manual(values = point_colours)
}
if (plot_error_bars){
g0 = g0 +
geom_errorbar(aes(ymin = eval(parse(text = lower_EB_colname))
, ymax = eval(parse(text = upper_EB_colname))
))
}else{
g0 = g0
}
#---------------------
# add axis formatting
#---------------------
g1 = g0 + theme( axis.text.x = element_text(size = x_axts
, angle = 90
, hjust = 1
, vjust = 0.4
, face = "bold"
, colour = aa_pos_colours)
, axis.text.y = element_text(size = y_axts
, angle = 0
, hjust = 1
, vjust = 0)
, axis.title.x = element_text(size = x_axls)
, axis.title.y = element_text(size = y_axls )
, panel.background = element_rect(fill = panel_col_fill, color = panel_col)
, panel.grid.major = element_line(color = "black")
, panel.grid.minor = element_line(color = "black")
, plot.title = element_text(size = pts
, hjust = 0.5)
, plot.margin = margin(t = t_margin
, r = r_margin
, b = b_margin
, l = l_margin
, unit = unit_margin))+
guides(colour = guide_legend(title = "ConsurfXXXX")) +
labs(title = ptitle
, x = xlab
, y = ylab)
#------------------
#Extract legend1
#------------------
# yayy
g1_leg = ggplot(plot_df, aes_string(x = sprintf("factor(%s)"
, 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)))
g1_leg = g1_leg + scale_fill_manual(values = consurf_palette2 , name = leg_title1)
g1_leg
legend1 = get_legend(g1_leg)
#####################################################
#============================================
# x-axis: geom_tiles ~ ligand distance
#============================================
#-------
# plot
#-------
if(A_xvar_lig){ # 0 is a magic number that does my sensible default
if (tpos0 == 0){
tpos0 = ymin-0.5
}
if (tpos1 == 0){
tpos1 = ymin-0.65
}
if (tpos2 == 0){
tpos2 = ymin-0.75
}
if (tpos3 == 0){
tpos3 = ymin-0.85
}
cat("\nColouring x-axis aa based on", lig_dist_colname
, "\nNo. of colours:", n_colours)
g2 = g1 + geom_tile(aes(, 2
# g2 = g1 + geom_tile(aes(, tpos0
, width = tW0
, height = tH0)
, fill = plot_df$ligD_colours
, colour = plot_df$ligD_colours
, linetype = "blank")
#cat("Nrows of plot df", length(plot_df$ligD_colours))
out = g2
}else{
out = g1
}
#==============================================
# x-axis: geom_tiles ~ active sites and others
#==============================================
if(A_xvar_aa){
#tpos = 0
#tW = 1
#tH = 0.2
#---------------------
# Add2plot: 3 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&3 sites")
cat("\nCreating column colours, column name:", aa_colour_colname3)
cat("\nDoing Plot with 3 ligands")
}
out = out + geom_tile(aes(,tpos3
, width = tW
, height = tH )
, fill = plot_df[[aa_colour_colname3]]
, colour = plot_df[[aa_colour_colname3]]
, linetype = "solid") +
geom_tile(aes(, tpos2
, width = tW
, height = tH )
, fill = plot_df[[aa_colour_colname2]]
, colour = plot_df[[aa_colour_colname2]]
, linetype = "solid")+
geom_tile(aes(, tpos1
, width = tW
, height = tH)
, fill = plot_df[[aa_colour_colname1]]
, colour = plot_df[[aa_colour_colname1]]
, linetype = "solid")
if (debug){
cat("\nDone Plot with 3 ligands")
}
}
#---------------------
# 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)
cat("\nDoing Plot with 2 ligands")
}
out = out +
geom_tile(aes(, tpos2
, width = tW
, height = tH)
, fill = plot_df[[aa_colour_colname2]]
, colour = plot_df[[aa_colour_colname2]]
, linetype = "solid")+
geom_tile(aes(, tpos1
, width = tW
, height = tH)
, fill = plot_df[[aa_colour_colname1]]
, colour = plot_df[[aa_colour_colname1]]
, linetype = "solid")
if (debug){
cat("\nDone Plot with 2 ligands")
}
}
#---------------------
# Add2plot: 1 ligand
#---------------------
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)
cat("\nDoing Plot with 1 ligands")
}
out = out +
geom_tile(aes(, tpos1
, width = tW
, height = tH)
, fill = plot_df[[aa_colour_colname1]]
, colour = plot_df[[aa_colour_colname1]]
, linetype = "solid")
cat("\nDone Plot with 1 ligand")
}
#-----------------------------------
# Add2plot:NO ligands
# No Ligs: Just drug and active site
# DEFAULT: A_xvar_aa == 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")
}
out = out + geom_tile(aes(, tpos3
, width = tW
, height = tH)
, fill = plot_df[[aa_colour_colname]]
, colour = plot_df[[aa_colour_colname]]
, linetype = "solid")
if (debug){
cat("\nDone Plot with: Active and Drug sites")
}
}
}else{
cat("\nNo annotation for additional ligands on xvar requested")
}
if (A_xvar_lig){
legs = cowplot::plot_grid(legend1
, generate_distance_legend(plot_df, yvar_colname = yvar_colname)
, ncol = 1
, align = "hv"
, rel_heights = c(2/4,3/4))
out2 = cowplot::plot_grid( out + theme(legend.position = "none")
, legs
, ncol = 2
, align = "hv"
, rel_widths = c(9/10, 0.4/10)
)
}else{
out2 = cowplot::plot_grid( out + theme(legend.position = "none")
, legend1
, ncol = 2
, align = "hv"
, rel_widths = c(9/10, 0.5/10)
)
}
return(out2)
#return(out2)
}