Last updated: 2019-12-16

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Knit directory: Comparative_APA/analysis/

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Unstaged changes:
    Modified:   analysis/CorrbetweenInd.Rmd
    Modified:   analysis/OppositeMap.Rmd
    Modified:   analysis/PASnumperSpecies.Rmd
    Modified:   analysis/annotatePAS.Rmd
    Modified:   analysis/annotationInfo.Rmd
    Modified:   analysis/diffExpression.Rmd
    Modified:   analysis/investigatePantro5.Rmd
    Modified:   analysis/liftoverPAS.Rmd
    Modified:   analysis/multiMap.Rmd
    Modified:   analysis/verifyBAM.Rmd

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File Version Author Date Message
Rmd de41e07 brimittleman 2019-12-16 add gene comp 5v6 
library(VennDiagram)
Loading required package: grid
Loading required package: futile.logger
library(tidyverse)
── Attaching packages ─────────────────────────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.1.1       ✔ purrr   0.3.2  
✔ tibble  2.1.1       ✔ dplyr   0.8.0.1
✔ tidyr   0.8.3       ✔ stringr 1.3.1  
✔ readr   1.3.1       ✔ forcats 0.3.0  
── Conflicts ────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

Load in the DE genes from pantro5 and pantro6.

DEgenes=read.table("../data/DiffExpression/DE_genes.txt", header = F,col.names = c("Gene_stable_ID"),stringsAsFactors = F)
DEgenesPantro6=read.table("../data/DiffExpression/DE_genes_pantro6.txt", header = F,col.names = c("Gene_stable_ID"),stringsAsFactors = F)
overlap <- intersect(DEgenes$Gene_stable_ID, DEgenesPantro6$Gene_stable_ID) 
DE.unique <- setdiff(DEgenes$Gene_stable_ID, DEgenesPantro6$Gene_stable_ID) # n 1st NOT 2nd
DEgenesPantro6.unique <- setdiff(DEgenesPantro6$Gene_stable_ID, DEgenes$Gene_stable_ID)
full.list <- unique(c(DEgenes$Gene_stable_ID,DEgenesPantro6$Gene_stable_ID))

Plot:

grid.newpage()
venn.plot <- draw.pairwise.venn(area1 = length(DEgenes$Gene_stable_ID),
                           area2 = length(DEgenesPantro6$Gene_stable_ID),
                           cross.area = length(overlap),
                           c("Pantro5", "Pantro6"), scaled = TRUE,
                           fill = c("green", "blue"),
                           cex = 1.5,
                           cat.cex = 1.5,
                           cat.pos = c(320, 25),
                           cat.dist = .05) 


sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] forcats_0.3.0       stringr_1.3.1       dplyr_0.8.0.1      
 [4] purrr_0.3.2         readr_1.3.1         tidyr_0.8.3        
 [7] tibble_2.1.1        ggplot2_3.1.1       tidyverse_1.2.1    
[10] VennDiagram_1.6.20  futile.logger_1.4.3

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.5     haven_1.1.2          lattice_0.20-38     
 [4] colorspace_1.3-2     generics_0.0.2       htmltools_0.3.6     
 [7] yaml_2.2.0           rlang_0.4.0          later_0.7.5         
[10] pillar_1.3.1         withr_2.1.2          glue_1.3.0          
[13] lambda.r_1.2.3       modelr_0.1.2         readxl_1.1.0        
[16] plyr_1.8.4           munsell_0.5.0        gtable_0.2.0        
[19] workflowr_1.5.0      cellranger_1.1.0     rvest_0.3.2         
[22] evaluate_0.12        knitr_1.20           httpuv_1.4.5        
[25] broom_0.5.1          Rcpp_1.0.2           promises_1.0.1      
[28] backports_1.1.2      scales_1.0.0         formatR_1.5         
[31] jsonlite_1.6         fs_1.3.1             hms_0.4.2           
[34] digest_0.6.18        stringi_1.2.4        rprojroot_1.3-2     
[37] cli_1.1.0            tools_3.5.1          magrittr_1.5        
[40] lazyeval_0.2.1       futile.options_1.0.1 crayon_1.3.4        
[43] whisker_0.3-2        pkgconfig_2.0.2      xml2_1.2.0          
[46] lubridate_1.7.4      assertthat_0.2.0     rmarkdown_1.10      
[49] httr_1.3.1           rstudioapi_0.10      R6_2.3.0            
[52] nlme_3.1-137         git2r_0.26.1         compiler_3.5.1