Mercurial > repos > jdv > nanopore_qc
diff nanopore_qc.R @ 4:4b7d1bcf210c draft
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit dfa6f9934da27ffddc4da6c16d97d4057662ef65
author | jdv |
---|---|
date | Mon, 12 Mar 2018 15:04:45 -0400 |
parents | 192df6f6a41e |
children | 0cf41189f086 |
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--- a/nanopore_qc.R Mon Dec 04 15:23:55 2017 -0500 +++ b/nanopore_qc.R Mon Mar 12 15:04:45 2018 -0400 @@ -143,6 +143,9 @@ d$num_events_template = as.numeric(as.character(d$num_events_template)) d$start_time = as.numeric(as.character(d$start_time)) } + + # ignore 0-length reads + d <- d[d$sequence_length_template > 0,] d$events_per_base = d$num_events_template/d$sequence_length_template @@ -334,6 +337,7 @@ # make plots flog.info(paste(sep = "", flowcell, ": plotting length histogram")) len.lims <- quantile(d$sequence_length_template,c(0.01,0.99)) + len.lims[1] <- max(1,len.lims[1]) p1 = ggplot(d, aes(x = sequence_length_template)) + geom_histogram(bins = 200, fill="steelblue") +