Combined Lane QC

Last updated: 2018-07-30

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I want to use this analysis to run simple QC on the first 32 libraries now that we have 2 lanes per library.

First, I will look at the new map stats to see how many more reads/mapped reads the socond lane provided.

library(tidyr)
library(reshape2)

Attaching package: 'reshape2'

The following object is masked from 'package:tidyr':

    smiths

library(ggplot2)
library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

library(workflowr)

This is workflowr version 1.1.1
Run ?workflowr for help getting started

comb_map=read.csv("../data/combined_reads_mapped_three_prime_seq.csv", header = T, stringsAsFactors = T)
comb_map$line=as.factor(comb_map$line)

mapped_melt=melt(comb_map, id.vars=c("line", "fraction"), measure.vars = c( "lane1_mapped", "comb_mapped"))
mapped_melt$line=as.factor(mapped_melt$line)

ggplot(mapped_melt, aes(y=value, x=line, by=fraction,fill=fraction)) + geom_bar(stat="identity", position = "dodge") + facet_grid(.~ variable)+ labs(y="Reads Mapped") 

Next I want to look at the x more mapped reads we got by line and fraction

ggplot(comb_map, aes(x=line,y=combed_xrmappedmore, fill=fraction)) + geom_bar(stat="identity", position = "dodge") + labs(title="X more mapped reads in adding second lane", y="X more mapped reads")

sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] workflowr_1.1.1 dplyr_0.7.6     ggplot2_3.0.0   reshape2_1.4.3 
[5] tidyr_0.8.1    

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.18      pillar_1.3.0      compiler_3.5.1   
 [4] git2r_0.23.0      plyr_1.8.4        bindr_0.1.1      
 [7] R.methodsS3_1.7.1 R.utils_2.6.0     tools_3.5.1      
[10] digest_0.6.15     evaluate_0.11     tibble_1.4.2     
[13] gtable_0.2.0      pkgconfig_2.0.1   rlang_0.2.1      
[16] rstudioapi_0.7    yaml_2.1.19       bindrcpp_0.2.2   
[19] withr_2.1.2       stringr_1.3.1     knitr_1.20       
[22] tidyselect_0.2.4  rprojroot_1.3-2   grid_3.5.1       
[25] glue_1.3.0        R6_2.2.2          rmarkdown_1.10   
[28] purrr_0.2.5       magrittr_1.5      whisker_0.3-2    
[31] backports_1.1.2   scales_0.5.0      htmltools_0.3.6  
[34] assertthat_0.2.0  colorspace_1.3-2  labeling_0.3     
[37] stringi_1.2.4     lazyeval_0.2.1    munsell_0.5.0    
[40] crayon_1.3.4      R.oo_1.22.0      

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