Mercurial > repos > mingchen0919 > rmarkdown_fastqc_site
view 5_per_base_sequence_content.Rmd @ 0:d732d4526c6d draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
author | mingchen0919 |
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date | Tue, 08 Aug 2017 10:14:46 -0400 |
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--- title: "Per Base Sequence Content" output: html_document --- ```{r setup, include=FALSE, warning=FALSE, message=FALSE} knitr::opts_chunk$set(echo = ECHO) ``` ## Per Base Sequence Content ```{r} PBSC_df = data.frame() PBSC_file_paths = read.csv('PBSC_file_paths.txt', header = TRUE, stringsAsFactors = FALSE) for(i in 1:nrow(PBSC_file_paths)) { # file_path = paste0('REPORT_OUTPUT_DIR/', PBSC_file_paths[i,2]) file_path = PBSC_file_paths[i,2] pbsc_df = read.csv(file_path, sep='\t', header=TRUE, stringsAsFactors = FALSE) %>% mutate(Base1=as.numeric(str_split_fixed(X.Base, '-', 2)[,1]), Base2=as.numeric(str_split_fixed(X.Base, '-', 2)[,2])) %>% (function (df) { df1 = select(df, -Base2) df2 = select(df, -Base1) %>% filter(Base2 != '') colnames(df1) = c(colnames(df1)[1:5], 'Base') colnames(df2) = c(colnames(df2)[1:5], 'Base') res = rbind(df1, df2) %>% arrange(Base) return(res) }) pbsc_df$sample_id = rep(PBSC_file_paths[i,1], nrow(pbsc_df)) PBSC_df = rbind(PBSC_df, pbsc_df) } ``` ```{r out.width="100%"} PBSC_df_2 = select(PBSC_df, -X.Base) %>% melt(id = c('Base', 'sample_id'), value.name = 'base_percentage') p = ggplot(data = PBSC_df_2, aes(x = Base, y = base_percentage, group = variable, color = variable)) + geom_line() + facet_wrap(~ sample_id) ggplotly(p) ```