196 lines
6.5 KiB
R
196 lines
6.5 KiB
R
# Input:
|
|
# Data:
|
|
# plot_df: merged_df3 containing the OR column to use as y-axis or any other relevant column
|
|
|
|
# x_axis_colname = "position"
|
|
# y_axis_colname = "or_mychisq"
|
|
# symbol_colname = "mutant_type"
|
|
# y_axis_log = F
|
|
# log_value = log10
|
|
# 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
|
|
|
|
# rm_empty_y = F
|
|
# 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
|
|
|
|
# ...other params
|
|
|
|
# Returns: Logo plot from combined data containing specific y-value such as OR, etc by position.
|
|
|
|
# TODO: SHINY
|
|
# select/drop down option to remove empty positions
|
|
# select/drop down option for colour
|
|
# select/drop down option for log scale
|
|
# include WT
|
|
|
|
# Make it hover over position and then get the corresponding data table!
|
|
########################a###########################################################
|
|
|
|
|
|
#==================
|
|
# 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
|
|
)
|
|
|
|
{
|
|
#################################
|
|
# 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){
|
|
|
|
log_colname = paste0("log_", y_axis_colname)
|
|
plot_df[log_colname] = log_value(plot_df[y_axis_colname])
|
|
logo_df = plot_df[, c(x_axis_colname, symbol_colname, log_colname)]
|
|
logo_df_plot = logo_df[, c(x_axis_colname, symbol_colname, log_colname)]
|
|
logo_dfP_wf = as.matrix(logo_df_plot %>% spread(x_axis_colname, log_colname, fill = 0.0))
|
|
|
|
#!!! For consideration: to add y_axis 'breaks' and 'limits' !!!
|
|
#y_max = max(plot_df[[log_colname]], na.rm = T)
|
|
#y_axis_increment =
|
|
#cat("\nRemoving y scale incremenet:", y_axis_increment)
|
|
|
|
#y_lim = round_any(y_max, y_axis_increment, f = ceiling)
|
|
|
|
} else {
|
|
|
|
#-------------------
|
|
# logo data: OR
|
|
#-------------------
|
|
logo_df = plot_df[, c(x_axis_colname, symbol_colname, y_axis_colname)]
|
|
logo_df_plot = logo_df[, c(x_axis_colname, symbol_colname, y_axis_colname)]
|
|
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]
|
|
dim(logo_dfP_wf)
|
|
|
|
logo_dfP_wf = logo_dfP_wf[,-1]
|
|
str(logo_dfP_wf)
|
|
|
|
colnames(logo_dfP_wf)
|
|
position_or = as.numeric(colnames(logo_dfP_wf))
|
|
|
|
######################################
|
|
# Generating plots with given y_axis
|
|
#####################################
|
|
if (my_logo_col %in% c('clustalx','taylor')) {
|
|
cat("\nSelected colour scheme:", my_logo_col
|
|
, "\nUsing black theme\n")
|
|
|
|
theme_bgc = "black"
|
|
xfont_bgc = "white"
|
|
yfont_bgc = "white"
|
|
xtt_col = "white"
|
|
ytt_col = "white"
|
|
}
|
|
|
|
if (my_logo_col %in% c('chemistry', 'hydrophobicity')) {
|
|
cat('\nSelected colour scheme:', my_logo_col
|
|
, "\nUsing grey theme")
|
|
|
|
theme_bgc = "grey"
|
|
xfont_bgc = "black"
|
|
yfont_bgc = "black"
|
|
xtt_col = "black"
|
|
ytt_col = "black"
|
|
}
|
|
|
|
p0 = 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
|
|
, colour = xtt_col)
|
|
, axis.title.y = element_text(size = y_tts
|
|
, colour = ytt_col)
|
|
, legend.title = element_text(size = leg_tts
|
|
, colour = ytt_col)
|
|
, legend.text = element_text(size = leg_ts)
|
|
|
|
, 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
|
|
, 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)
|
|
|
|
}
|