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

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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
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193
scripts/functions/logoP_or.R
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@ -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
#################################
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)
#-------------------
# logo data: LogOR
#-------------------
if (y_axis_log){
#################################
# 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
}
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){
log_colname = paste0("log_", y_axis_colname)
plot_df[log_colname] = log_value(plot_df[y_axis_colname])
@ -95,8 +99,8 @@ LogoPlotCustomH <- function(plot_df
#y_lim = round_any(y_max, y_axis_increment, f = ceiling)
} else {
} else {
#-------------------
# logo data: OR
#-------------------
@ -105,7 +109,7 @@ LogoPlotCustomH <- function(plot_df
logo_dfP_wf = as.matrix(logo_df_plot %>% spread(x_axis_colname, y_axis_colname, fill = 0.0))
}
class(logo_dfP_wf)
rownames(logo_dfP_wf) = logo_dfP_wf[,1]
@ -116,7 +120,7 @@ LogoPlotCustomH <- function(plot_df
colnames(logo_dfP_wf)
position_or = as.numeric(colnames(logo_dfP_wf))
######################################
# Generating plots with given y_axis
#####################################
@ -130,7 +134,7 @@ LogoPlotCustomH <- function(plot_df
xtt_col = "white"
ytt_col = "white"
}
if (my_logo_col %in% c('chemistry', 'hydrophobicity')) {
cat('\nSelected colour scheme:', my_logo_col
, "\nUsing grey theme")
@ -141,57 +145,60 @@ LogoPlotCustomH <- function(plot_df
xtt_col = "black"
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)))
LogoPlot = p0 + scale_y_continuous(y_lab
, limits = factor(1:length(position_or))) +
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)
, 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)
}
return(LogoPlot)
}