Last updated: 2020-04-27
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Knit directory: Comparative_APA/analysis/
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Rmd | b653f27 | brimittleman | 2020-04-27 | add simpson |
html | 448aa08 | brimittleman | 2020-04-24 | Build site. |
Rmd | 93d00f3 | brimittleman | 2020-04-24 | add info content |
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()
library(workflowr)
This is workflowr version 1.6.0
Run ?workflowr for help getting started
library(ggpubr)
Loading required package: magrittr
Attaching package: 'magrittr'
The following object is masked from 'package:purrr':
set_names
The following object is masked from 'package:tidyr':
extract
nPAS=read.table("../data/PAS_doubleFilter/PAS_5perc_either_HumanCoord_BothUsage_meta_doubleFilter.txt", header = T, stringsAsFactors = F) %>% group_by(gene) %>% summarise(nperGene=n())
nameID=read.table("../../genome_anotation_data/ensemble_to_genename.txt",sep="\t", header = T, stringsAsFactors = F)
DE= read.table("../data/DiffExpression/DEtested_allres.txt",header=F, stringsAsFactors = F,col.names = c('Gene_stable_ID', 'logFC' ,'AveExpr', 't', 'P.Value', 'adj.P.Val', 'B')) %>% inner_join(nameID, by="Gene_stable_ID") %>% dplyr::select(-Gene_stable_ID, -Source_of_gene_name) %>% rename("gene"=Gene.name) %>% mutate(DE=ifelse(adj.P.Val<=.05, "Yes","No")) %>% inner_join(nPAS, by="gene")
ggplot(DE, aes(x= DE, y=nperGene )) + geom_boxplot() + stat_compare_means()+ labs(y="Number of PAS",title="DE status by number of PAS: Remove genes with 1 PAS")
Version | Author | Date |
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448aa08 | brimittleman | 2020-04-24 |
Remove 1:
DE_no1 = DE %>% filter(nperGene>1)
ggplot(DE_no1, aes(x= DE, y=nperGene )) + geom_boxplot() + stat_compare_means() + labs(y="Number of PAS",title="DE status by number of PAS: Remove genes with 1 PAS")
Version | Author | Date |
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448aa08 | brimittleman | 2020-04-24 |
So number of PAS and de is not informative for DE but is for dominance structure….
What about when I look at it by dominance:
HumanRes=read.table("../data/DomDefGreaterX/Human_AllGenes_DiffTop.txt", col.names = c("Human_PAS", "gene","Human_DiffDom"),stringsAsFactors = F)
ChimpRes=read.table("../data/DomDefGreaterX/Chimp_AllGenes_DiffTop.txt", col.names = c("Chimp_PAS", "gene","Chimp_DiffDom"),stringsAsFactors = F)
BothRes=HumanRes %>% inner_join(ChimpRes,by="gene")
BothRes_40=BothRes %>% filter(Chimp_DiffDom >=0.4 | Human_DiffDom>=0.4) %>% mutate(Set= ifelse(Human_PAS==Chimp_PAS,"Same", "Different"),cut=40)
BothRes_40_each= BothRes_40 %>% mutate(Dom=ifelse(Human_DiffDom>=.4, ifelse(Chimp_DiffDom >=.4, "Both", "Human"), "Chimp"))
BothRes_40_eachsm= BothRes_40_each %>% select(gene, Set, Dom)
BothRes_40_each_DE= DE %>% full_join(BothRes_40_eachsm,by="gene") %>% mutate(Set= replace_na(Set, "None"),Dom= replace_na(Dom, "None")) %>% filter(nperGene>1)
ggplot(BothRes_40_each_DE,aes(x=Dom, by=DE, y=nperGene, fill=DE)) + geom_boxplot(notch = T) + stat_compare_means() + labs(y="Number of PAS", title="DE and number of PAS by domianance structure")
notch went outside hinges. Try setting notch=FALSE.
ggplot(BothRes_40_each_DE,aes(x=Set, by=DE, y=nperGene, fill=DE)) + geom_boxplot(notch = T) + stat_compare_means() + labs(y="Number of PAS", title="DE and number of PAS by domianance structure")+ scale_fill_brewer(palette="Set1")
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] ggpubr_0.2 magrittr_1.5 workflowr_1.6.0 forcats_0.3.0
[5] stringr_1.3.1 dplyr_0.8.0.1 purrr_0.3.2 readr_1.3.1
[9] tidyr_0.8.3 tibble_2.1.1 ggplot2_3.1.1 tidyverse_1.2.1
loaded via a namespace (and not attached):
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[4] colorspace_1.3-2 generics_0.0.2 htmltools_0.3.6
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[28] scales_1.0.0 backports_1.1.2 jsonlite_1.6
[31] fs_1.3.1 hms_0.4.2 digest_0.6.18
[34] stringi_1.2.4 grid_3.5.1 rprojroot_1.3-2
[37] cli_1.1.0 tools_3.5.1 lazyeval_0.2.1
[40] crayon_1.3.4 whisker_0.3-2 pkgconfig_2.0.2
[43] xml2_1.2.0 lubridate_1.7.4 assertthat_0.2.0
[46] rmarkdown_1.10 httr_1.3.1 rstudioapi_0.10
[49] R6_2.3.0 nlme_3.1-137 git2r_0.26.1
[52] compiler_3.5.1