| Previous changeset 11:507eec497730 (2017-11-07) Next changeset 13:6faa68239cd7 (2017-11-09) |
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Commit message:
add boxplot for per base sequence quality |
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modified:
02_per_base_sequence_quality.Rmd |
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| diff -r 507eec497730 -r 68ea2ebbf866 02_per_base_sequence_quality.Rmd --- a/02_per_base_sequence_quality.Rmd Tue Nov 07 16:52:24 2017 -0500 +++ b/02_per_base_sequence_quality.Rmd Thu Nov 09 09:23:43 2017 -0500 |
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| @@ -21,27 +21,32 @@ ## reads 1 pbsq_1 = extract_data_module('REPORT_DIR/reads_1_fastqc_data.txt', 'Per base sequence quality') pbsq_1$id = 1:length(pbsq_1$X.Base) - -melt_pbsq_1 = filter(melt(pbsq_1, id=c('X.Base', 'id')), variable == 'Mean') -melt_pbsq_1$trim = 'before' - +pbsq_1$trim = 'before' ## reads 2 pbsq_2 = extract_data_module('REPORT_DIR/reads_2_fastqc_data.txt', 'Per base sequence quality') pbsq_2$id = 1:length(pbsq_2$X.Base) +pbsq_2$trim = 'after' -melt_pbsq_2 = filter(melt(pbsq_2, id=c('X.Base', 'id')), variable == 'Mean') -melt_pbsq_2$trim = 'after' - -comb_pbsq = rbind(melt_pbsq_1, melt_pbsq_2) +comb_pbsq = rbind(pbsq_1, pbsq_2) comb_pbsq$trim = factor(levels = c('before', 'after'), comb_pbsq$trim) p = ggplot(data = comb_pbsq) + - geom_line(mapping = aes(x = id, y = value, group = variable, color = variable)) + - scale_x_continuous(breaks = pbsq_2$id, labels = pbsq_2$X.Base) + - facet_grid(. ~ trim) + - ylim(0, max(comb_pbsq$value) + 5) + + geom_boxplot(mapping = aes(x = id, + lower = Lower.Quartile, + upper = Upper.Quartile, + middle = Median, + ymin = X10th.Percentile, + ymax = X90th.Percentile, + fill = "yellow"), + stat = 'identity') + + geom_line(mapping = aes(x = id, y = Mean, color = "red")) + + scale_x_continuous(breaks = pbsq_2$id, labels = pbsq_2$X.Base) + + scale_fill_identity() + + scale_color_identity() + + ylim(0, max(comb_pbsq$Upper.Quartile) + 5) + + facet_grid(. ~ trim) + theme(axis.text.x = element_text(angle=45)) -ggplotly(p) +p ``` \ No newline at end of file |