Last updated: 2020-01-10

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Knit directory: Comparative_APA/analysis/

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Unstaged changes:
    Modified:   analysis/OppositeMap.Rmd
    Modified:   analysis/annotationInfo.Rmd
    Modified:   analysis/investigatePantro5.Rmd
    Modified:   analysis/multiMap.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 3aee984 brimittleman 2020-01-10 delta pau and sig
html 417783c brimittleman 2020-01-10 Build site.
Rmd 521dc81 brimittleman 2020-01-10 update dPAS > 0.2
html 4c87e96 brimittleman 2020-01-07 Build site.
Rmd 6e3027a brimittleman 2020-01-07 upset plots for comparisons

In this analysis I will use the UpSetR package to look at all of the differential gene regulation phenotype results in one plot. This should be easier to visualize than the venn diagrams.

library(UpSetR)
library(workflowr)
This is workflowr version 1.5.0
Run ?workflowr for help getting started
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()

Input the datasets:

#protein
Protein=read.table("../data/Khan_prot/HC_SigProtein.txt", header = T, stringsAsFactors = F)
#trans
Translation=read.table("../data/Wang_ribo/HC_SigTranslation.txt", header = T, stringsAsFactors = F)
#expression
nameID=read.table("../../genome_anotation_data/ensemble_to_genename.txt",sep="\t", header = T, stringsAsFactors = F)
DEgenes=read.table("../data/DiffExpression/DE_genes.txt", header = F,col.names = c("Gene_stable_ID"),stringsAsFactors = F) %>% inner_join(nameID, by="Gene_stable_ID") %>% dplyr::select(Gene.name)
#nuclear apa  
NucAPA=read.table("../data/DiffIso_Nuclear/SignifianceEitherGENES_Nuclear.txt",header = T,stringsAsFactors = F)
#totalAPA  
totAPA=read.table("../data/DiffIso_Total/SignifianceEitherGENES_Total.txt",header = T,stringsAsFactors = F)
DSgenes=read.table("../data/DiffSplice_liftedJunc/orderedGeneListFixed.txt",stringsAsFactors = F, col.names = "DS")

Create a named list object

# example of list input (list of named vectors)
listInput <- list(DE=DEgenes$Gene.name, DS=DSgenes$DS, DapaNuc=NucAPA$gene, DapaTot=totAPA$gene, DT=Translation$Gene, DP=Protein$gene.symbol)

Create plot:

upset(fromList(listInput), order.by = "freq", keep.order = T,empty.intersections = "on")

Version Author Date
417783c brimittleman 2020-01-10
4c87e96 brimittleman 2020-01-07

Do this without total APA:

listInput_nucOnly <- list(DE=DEgenes$Gene.name, DS=DSgenes$DS, DAPA=NucAPA$gene, DT=Translation$Gene, DP=Protein$gene.symbol)

upset(fromList(listInput_nucOnly), order.by = "freq", keep.order = T,empty.intersections = "on")

Version Author Date
417783c brimittleman 2020-01-10
4c87e96 brimittleman 2020-01-07

Add colors for certain queries:

#upset(movies, queries = list(list(query = intersects, params = list("Drama", 
#    "Comedy", "Action"), color = "orange", active = T), list(query = intersects, 
 #   params = list("Drama"), color = "red", active = F), list(query = intersects, 
 #   params = list("Action", "Drama"), active = T)))


upset(fromList(listInput_nucOnly), queries = list(list(query=intersects, params=list("DAPA", "DT", "DP"), color="red", active=T,query.name="APA,Ribo, Protein"),list(query=intersects, params=list("DE", "DT", "DP"), color="orange", active=T, query.name="Expression,Ribo, Protein"), list(query=intersects, params=list("DS", "DT", "DP"), color="green", active=T,query.name="Splicing ,Ribo, Protein"),list(query=intersects, params=list("DAPA", "DT"), color="blue", active=T, query.name="APA,Ribo") ,list(query=intersects, params=list("DAPA", "DP"), color="purple", active=T, query.name="APA, Protein")), order.by = "freq", query.legend = "bottom")

Version Author Date
417783c brimittleman 2020-01-10
4c87e96 brimittleman 2020-01-07

Can I do this by proportion???


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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] forcats_0.3.0   stringr_1.3.1   dplyr_0.8.0.1   purrr_0.3.2    
 [5] readr_1.3.1     tidyr_0.8.3     tibble_2.1.1    ggplot2_3.1.1  
 [9] tidyverse_1.2.1 workflowr_1.5.0 UpSetR_1.3.3   

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.5 haven_1.1.2      lattice_0.20-38  colorspace_1.3-2
 [5] generics_0.0.2   htmltools_0.3.6  yaml_2.2.0       rlang_0.4.0     
 [9] later_0.7.5      pillar_1.3.1     withr_2.1.2      glue_1.3.0      
[13] modelr_0.1.2     readxl_1.1.0     plyr_1.8.4       munsell_0.5.0   
[17] gtable_0.2.0     cellranger_1.1.0 rvest_0.3.2      evaluate_0.12   
[21] labeling_0.3     knitr_1.20       httpuv_1.4.5     broom_0.5.1     
[25] Rcpp_1.0.2       promises_1.0.1   scales_1.0.0     backports_1.1.2 
[29] jsonlite_1.6     fs_1.3.1         gridExtra_2.3    hms_0.4.2       
[33] digest_0.6.18    stringi_1.2.4    grid_3.5.1       rprojroot_1.3-2 
[37] cli_1.1.0        tools_3.5.1      magrittr_1.5     lazyeval_0.2.1  
[41] crayon_1.3.4     whisker_0.3-2    pkgconfig_2.0.2  xml2_1.2.0      
[45] lubridate_1.7.4  assertthat_0.2.0 rmarkdown_1.10   httr_1.3.1      
[49] rstudioapi_0.10  R6_2.3.0         nlme_3.1-137     git2r_0.26.1    
[53] compiler_3.5.1