39indQC

Last updated: 2018-09-24

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  Ignored files:
      Ignored:    .DS_Store
      Ignored:    .Rhistory
      Ignored:    .Rproj.user/
      Ignored:    output/.DS_Store
  
  Untracked files:
      Untracked:  analysis/ncbiRefSeq_sm.sort.mRNA.bed
      Untracked:  analysis/snake.config.notes.Rmd
      Untracked:  analysis/verifyBAM.Rmd
      Untracked:  data/18486.genecov.txt
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      Untracked:  data/comb_map_stats.csv
      Untracked:  data/comb_map_stats.xlsx
      Untracked:  data/comb_map_stats_39ind.csv
      Untracked:  data/combined_reads_mapped_three_prime_seq.csv
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  Unstaged changes:
      Modified:   analysis/28ind.peak.explore.Rmd
      Modified:   analysis/cleanupdtseq.internalpriming.Rmd
      Modified:   analysis/dif.iso.usage.leafcutter.Rmd
      Modified:   analysis/diff_iso_pipeline.Rmd
      Modified:   analysis/explore.filters.Rmd
      Modified:   analysis/overlap_qtls.Rmd
      Modified:   analysis/peakOverlap_oppstrand.Rmd
      Modified:   analysis/pheno.leaf.comb.Rmd
      Modified:   analysis/test.max2.Rmd
      Modified:   code/Snakefile
  
  

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I will use this to look at the map stats and peak stats for the full set of 39 ind.

library(tidyverse)

── Attaching packages ──────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──

✔ ggplot2 3.0.0     ✔ purrr   0.2.5
✔ tibble  1.4.2     ✔ dplyr   0.7.6
✔ tidyr   0.8.1     ✔ stringr 1.3.1
✔ readr   1.1.1     ✔ forcats 0.3.0

── Conflicts ─────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

library(workflowr)

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

library(reshape2)

Attaching package: 'reshape2'

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

    smiths

library(cowplot)

Attaching package: 'cowplot'

The following object is masked from 'package:ggplot2':

    ggsave

mapstats= read.csv("../data/comb_map_stats_39ind.csv", header = T, stringsAsFactors = F)
mapstats$line=as.factor(mapstats$line)
mapstats$fraction=as.factor(mapstats$fraction)
map_melt=melt(mapstats, id.vars=c("line", "fraction"), measure.vars = c("comb_reads", "comb_mapped", "comb_prop_mapped"))

prop_mapped= map_melt %>% filter(variable=="comb_prop_mapped")
mapped_reads= map_melt %>% filter(variable=="comb_mapped")


mapplot_prop=ggplot(prop_mapped, aes(y=value, x=line, fill=fraction)) + geom_bar(stat="identity",position="dodge") + labs( title="Proportion of reads mapped") + ylab("Proportion mapped")


mapplot_mapped=ggplot(mapped_reads, aes(y=value, x=line, fill=fraction)) + geom_bar(stat="identity",position="dodge") + labs( title="Number of Mapped reads") + ylab("Mapped")

plot_grid(mapplot_prop, mapplot_mapped)

Plot boxplots for total vs nuclear.

box_mapprop=ggplot(prop_mapped, aes(y=value, x=fraction, fill=fraction)) + geom_boxplot() + geom_jitter(position = position_jitter(.3)) + labs( title="Map Proportion") + ylab("Mapped Proportion")

box_map=ggplot(mapped_reads, aes(y=value, x=fraction, fill=fraction)) + geom_boxplot() + geom_jitter(position = position_jitter(.3)) + labs( title="Number of Mapped reads") + ylab("Mapped")


plot_grid(box_map, box_mapprop)

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] bindrcpp_0.2.2  cowplot_0.9.3   reshape2_1.4.3  workflowr_1.1.1
 [5] forcats_0.3.0   stringr_1.3.1   dplyr_0.7.6     purrr_0.2.5    
 [9] readr_1.1.1     tidyr_0.8.1     tibble_1.4.2    ggplot2_3.0.0  
[13] tidyverse_1.2.1

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.4  haven_1.1.2       lattice_0.20-35  
 [4] colorspace_1.3-2  htmltools_0.3.6   yaml_2.2.0       
 [7] rlang_0.2.2       R.oo_1.22.0       pillar_1.3.0     
[10] glue_1.3.0        withr_2.1.2       R.utils_2.7.0    
[13] modelr_0.1.2      readxl_1.1.0      bindr_0.1.1      
[16] plyr_1.8.4        munsell_0.5.0     gtable_0.2.0     
[19] cellranger_1.1.0  rvest_0.3.2       R.methodsS3_1.7.1
[22] evaluate_0.11     labeling_0.3      knitr_1.20       
[25] broom_0.5.0       Rcpp_0.12.18      scales_1.0.0     
[28] backports_1.1.2   jsonlite_1.5      hms_0.4.2        
[31] digest_0.6.16     stringi_1.2.4     grid_3.5.1       
[34] rprojroot_1.3-2   cli_1.0.0         tools_3.5.1      
[37] magrittr_1.5      lazyeval_0.2.1    crayon_1.3.4     
[40] whisker_0.3-2     pkgconfig_2.0.2   xml2_1.2.0       
[43] lubridate_1.7.4   assertthat_0.2.0  rmarkdown_1.10   
[46] httr_1.3.1        rstudioapi_0.7    R6_2.2.2         
[49] nlme_3.1-137      git2r_0.23.0      compiler_3.5.1   

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