Last updated: 2018-07-30
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Rmd | 422a428 | Briana Mittleman | 2018-07-30 | add peak cove pipeline and combined lane qc |
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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