Mercurial > repos > mingchen0919 > aurora_fastqc_site
view 03_per_tile_sequence_quality.Rmd @ 0:b7c115edd970 draft
planemo upload
author | mingchen0919 |
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date | Tue, 27 Feb 2018 10:37:12 -0500 |
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children | c64267b9f754 |
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--- output: html_document --- ```{r setup, include=FALSE, warning=FALSE, message=FALSE} knitr::opts_chunk$set( echo = as.logical(opt$X_e), error = TRUE, eval = TRUE ) ``` # Per tile sequence quality ```{r 'per tile sequence quality', fig.width=10} ## check if 'per tile sequence quality' module exits or not check_ptsq = grep('Per tile sequence quality', readLines(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'))) if (length(check_ptsq) > 0) { ## reads 1 ptsq_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Per tile sequence quality') ptsq_1$trim = 'before' ## reads 2 ptsq_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Per tile sequence quality') ptsq_2$trim = 'after' comb_ptsq = rbind(ptsq_1, ptsq_2) comb_ptsq$trim = factor(levels = c('before', 'after'), comb_ptsq$trim) comb_ptsq$Base = factor(levels = unique(comb_ptsq$Base), comb_ptsq$Base) # convert integers to charaters comb_ptsq$Tile = as.character(comb_ptsq$X.Tile) p = ggplot(data = comb_ptsq, aes(x = Base, y = Tile, fill = Mean)) + geom_raster() + facet_grid(. ~ trim) + xlab('Position in read (bp)') + ylab('') + theme(axis.text.x = element_text(angle=45)) ggplotly(p) } else { print('No "per tile sequence quality" data') } ```