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New events column #61

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New events column #61

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a209bcf
Deals with the new sequencing summary column
jsabban Jan 26, 2023
ab0da68
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jsabban Jan 26, 2023
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62 changes: 33 additions & 29 deletions MinIONQC.R
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@ suppressPackageStartupMessages(library(parallel))
suppressPackageStartupMessages(library(futile.logger))
suppressPackageStartupMessages(library(data.table))
suppressPackageStartupMessages(library(optparse))
suppressPackageStartupMessages(library(dplyr))



Expand Down Expand Up @@ -204,7 +205,8 @@ load_summary <- function(filepath, min.q){

suppressWarnings({
d = read_tsv(filepath, col_types = cols_only(channel = 'i',
num_events_template = 'i',
minknow_events = 'i',
num_events_template = 'i',
sequence_length_template = 'i',
mean_qscore_template = 'n',
sequence_length_2d = 'i',
Expand Down Expand Up @@ -239,17 +241,22 @@ load_summary <- function(filepath, min.q){
# it's a 1D2 or 2D run
d$sequence_length_template = as.numeric(as.character(d$sequence_length_2d))
d$mean_qscore_template = as.numeric(as.character(d$mean_qscore_2d))
d$num_events_template = NA
d$minknow_events = NA
d$start_time = as.numeric(as.character(d$start_time))

}else{
d$sequence_length_template = as.numeric(as.character(d$sequence_length_template))
d$mean_qscore_template = as.numeric(as.character(d$mean_qscore_template))
d$num_events_template = as.numeric(as.character(d$num_events_template))
if ( "minknow_events" %in% names(d) ) {
# Guppy v6.3.1 or newer
d$events_per_base = d$minknow_events/d$sequence_length_template
} else {
# older than Guppy v6.3.1
d$events_per_base = d$num_events_template/d$sequence_length_template
}
d$start_time = as.numeric(as.character(d$start_time))
}

d$events_per_base = d$num_events_template/d$sequence_length_template

flowcell = basename(dirname(filepath))

Expand Down Expand Up @@ -637,32 +644,29 @@ single.flowcell <- function(input.file, output.dir, q=7, base.dir = NA){
scale_colour_viridis(discrete = TRUE, begin = 0.25, end = 0.75, guide = guide_legend(title = "Reads"))
suppressMessages(ggsave(filename = file.path(output.dir, paste("reads_per_hour.", plot_format, sep="")), device=plot_format, width = p1m*960/75, height = p1m*480/75, plot = p9)) #

if(max(d$channel)<=512){
# minion
flog.info(paste(sep = "", flowcell, ": plotting read length vs. q score scatterplot"))
p10 = ggplot(subset(d, Q_cutoff=="All reads"), aes(x = sequence_length_template, y = mean_qscore_template, colour = events_per_base)) +
geom_point(alpha=0.05, size = 0.4) +
scale_x_log10(minor_breaks=log10_minor_break(), breaks = log10_major_break()) +
labs(colour='Events per base\n(log scale)\n') +
theme(text = element_text(size = 15)) +
xlab("Read length (bases)") +
ylab("Mean Q score of read")
}else{
# promethion
p10 = ggplot(subset(d, Q_cutoff=="All reads"), aes(x = sequence_length_template, y = mean_qscore_template, colour = events_per_base)) +
geom_bin2d() +
scale_x_log10(minor_breaks=log10_minor_break(), breaks = log10_major_break()) +
theme(text = element_text(size = 15)) +
scale_fill_viridis() +
xlab("Read length (bases)") +
ylab("Mean Q score of read")
}


if(max(d$events_per_base, na.rm=T)>0){
# a catch for 1D2 runs which don't have events per base
p10 = p10 + scale_colour_viridis(trans = "log", labels = scientific, option = 'inferno')
flog.info(paste(sep = "", flowcell, ": plotting read length vs. q score scatterplot"))
d_tmp <- d %>% filter(sequence_length_template != 0)
labs_label = 'Events per base\n'

# if log10 can be defined, do it
if ("events_per_base" %in% names(d_tmp) && min(d_tmp$events_per_base, na.rm=T)>0) {
d_tmp$events_per_base = log10(d_tmp$events_per_base)
labs_label = paste0(labs_label, '(log scale)\n')
}

if(max(d$channel)<=512){ bins_number = 2000 } else {bins_number = 5000 }

p10 = ggplot(subset(d_tmp, Q_cutoff=="All reads"), aes(x = sequence_length_template, y = mean_qscore_template, z = events_per_base)) +
stat_summary_2d(fun = "mean", bins = bins_number, show.legend=TRUE) +
scale_x_log10(minor_breaks=log10_minor_break(), breaks = log10_major_break()) +
theme(text = element_text(size = 15)) +
scale_fill_viridis() +
xlab("Read length (bases)") +
ylab("Mean Q score of read") +
labs(fill=labs_label)

rm(d_tmp)

# we keep it a bit wider, because the legend takes up a fair bit of the plot space
suppressMessages(ggsave(filename = file.path(output.dir, paste("length_vs_q.", plot_format, sep="")), device=plot_format, width = p2m*960/75, height = p1m*960/75, plot = p10)) #

Expand Down