Last updated: 2020-05-31
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Knit directory: Comparative_APA/analysis/
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library(workflowr)
This is workflowr version 1.6.0
Run ?workflowr for help getting started
library(tidyverse)
── Attaching packages ───────────────────────────────────────────────── tidyverse 1.2.1 ──
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── Conflicts ──────────────────────────────────────────────────── tidyverse_conflicts() ──
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Attaching package: 'ggpubr'
The following object is masked from 'package:cowplot':
get_legend
library(RColorBrewer)
I will ask if there if dominance and DE are related. First I can ask if genes with dominant PAS are enriched in the DE genes.
PAS=read.table("../data/PAS_doubleFilter/PAS_5perc_either_HumanCoord_BothUsage_meta_doubleFilter.txt", header = T, stringsAsFactors = F)
MetaCol=colnames(PAS)
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")) %>% select(gene,DE)
DE_yes= DE %>% filter(DE=="Yes")
Domiance
#9
HumanDom9=read.table("../data/DomDefGreaterX/Human_.9_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Human9") %>% mutate(DE=ifelse(gene %in% DE_yes$gene,"Yes","No"))
ChimpDom9=read.table("../data/DomDefGreaterX/Chimp_.9_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Chimp9") %>% mutate(DE=ifelse(gene %in% DE_yes$gene,"Yes","No"))
#8
HumanDom8=read.table("../data/DomDefGreaterX/Human_.8_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Human8")%>% mutate(DE=ifelse(gene %in% DE_yes$gene,"Yes","No"))
ChimpDom8=read.table("../data/DomDefGreaterX/Chimp_.8_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Chimp8") %>% mutate(DE=ifelse(gene %in% DE_yes$gene,"Yes","No"))
#7
HumanDom7=read.table("../data/DomDefGreaterX/Human_.7_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Human7")%>% mutate(DE=ifelse(gene %in% DE_yes$gene,"Yes","No"))
ChimpDom7=read.table("../data/DomDefGreaterX/Chimp_.7_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Chimp7")%>% mutate(DE=ifelse(gene %in% DE_yes$gene,"Yes","No"))
#6
HumanDom6=read.table("../data/DomDefGreaterX/Human_.6_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Human6") %>% mutate(DE=ifelse(gene %in% DE_yes$gene,"Yes","No"))
ChimpDom6=read.table("../data/DomDefGreaterX/Chimp_.6_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Chimp6") %>% mutate(DE=ifelse(gene %in% DE_yes$gene,"Yes","No"))
#5
HumanDom5=read.table("../data/DomDefGreaterX/Human_.5_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Human5") %>% mutate(DE=ifelse(gene %in% DE_yes$gene,"Yes","No"))
ChimpDom5=read.table("../data/DomDefGreaterX/Chimp_.5_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Chimp5")%>% mutate(DE=ifelse(gene %in% DE_yes$gene,"Yes","No"))
#4
HumanDom4=read.table("../data/DomDefGreaterX/Human_.4_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Human4")%>% mutate(DE=ifelse(gene %in% DE_yes$gene,"Yes","No"))
ChimpDom4=read.table("../data/DomDefGreaterX/Chimp_.4_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Chimp4")%>% mutate(DE=ifelse(gene %in% DE_yes$gene,"Yes","No"))
#3
HumanDom3=read.table("../data/DomDefGreaterX/Human_.3_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Human3") %>% mutate(DE=ifelse(gene %in% DE_yes$gene,"Yes","No"))
ChimpDom3=read.table("../data/DomDefGreaterX/Chimp_.3_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Chimp3")%>% mutate(DE=ifelse(gene %in% DE_yes$gene,"Yes","No"))
#2
HumanDom2=read.table("../data/DomDefGreaterX/Human_.2_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Human2")%>% mutate(DE=ifelse(gene %in% DE_yes$gene,"Yes","No"))
ChimpDom2=read.table("../data/DomDefGreaterX/Chimp_.2_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Chimp2")%>% mutate(DE=ifelse(gene %in% DE_yes$gene,"Yes","No"))
#1
HumanDom1=read.table("../data/DomDefGreaterX/Human_.1_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Human1")%>% mutate(DE=ifelse(gene %in% DE_yes$gene,"Yes","No"))
ChimpDom1=read.table("../data/DomDefGreaterX/Chimp_.1_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Chimp1") %>% mutate(DE=ifelse(gene %in% DE_yes$gene,"Yes","No"))
#all
HumanDomAll= HumanDom1 %>% bind_rows(HumanDom2) %>% bind_rows(HumanDom3) %>% bind_rows(HumanDom4) %>% bind_rows(HumanDom5) %>% bind_rows(HumanDom6) %>% bind_rows(HumanDom7) %>% bind_rows(HumanDom8) %>% bind_rows(HumanDom9)
ChimpDomAll= ChimpDom1 %>% bind_rows(ChimpDom2) %>% bind_rows(ChimpDom3) %>% bind_rows(ChimpDom4) %>% bind_rows(ChimpDom5) %>% bind_rows(ChimpDom6) %>% bind_rows(ChimpDom7) %>% bind_rows(ChimpDom8) %>% bind_rows(ChimpDom9)
ChimpSet=c('Chimp1','Chimp2', 'Chimp3', 'Chimp4', 'Chimp5', 'Chimp6', 'Chimp7', 'Chimp8','Chimp9')
EnrichChimp=c()
PvalueChimp=c()
for (i in ChimpSet){
x=nrow(ChimpDomAll %>% filter(set==i, DE=="Yes"))
m=nrow(DE_yes)
n=nrow(DE) - nrow(DE_yes)
k=nrow(ChimpDomAll %>% filter(set==i))
N=nrow(DE)
PvalueChimp=c(PvalueChimp, phyper(x,m,n,k,lower.tail=F))
enrich=(x/k)/(m/N)
EnrichChimp=c(EnrichChimp, enrich)
}
PvalueChimp
[1] 1.0000000 1.0000000 1.0000000 0.9999842 0.9999501 0.9971507 0.9994521
[8] 0.9839957 0.5079290
EnrichChimp
[1] 0.8849697 0.8877147 0.8880516 0.9057939 0.8959653 0.9108136 0.8719019
[8] 0.8855119 0.9896978
HumanSet=c('Human1','Human2', 'Human3', 'Human4', 'Human5', 'Human6', 'Human7', 'Human8','Human9')
EnrichHuman=c()
PvalueHuman=c()
for (i in HumanSet){
x=nrow(HumanDomAll %>% filter(set==i, DE=="Yes"))
m=nrow(DE_yes)
n=nrow(DE) - nrow(DE_yes)
k=nrow(HumanDomAll %>% filter(set==i))
N=nrow(DE)
PvalueHuman=c(PvalueHuman, phyper(x,m,n,k,lower.tail=F))
enrich=(x/k)/(m/N)
EnrichHuman=c(EnrichHuman, enrich)
}
PvalueHuman
[1] 1.0000000 1.0000000 0.9999997 0.9999064 0.9992779 0.9991470 0.9853263
[8] 0.6526253 0.6747532
EnrichHuman
[1] 0.8885286 0.8749491 0.8850791 0.8975969 0.8974753 0.8785672 0.8903590
[8] 0.9674743 0.9054783
No enrichment for these. The real question is if genes with different dominant PAS are DE. This requires chosing how to call different dominant.
Are genes with different dominant at the cutoff .4 cutoff enriched for DE:
FourRes=read.table("../data/DomStructure_4/InclusiveDominantPASat4.txt", header = T,stringsAsFactors = F)
FourRes_diff= FourRes %>% filter(Set=="Different")
FourRes_same= FourRes %>% filter(Set=="Same")
x=length(intersect(FourRes_diff$gene,DE_yes$gene))
m=nrow(DE_yes)
n=nrow(DE) - nrow(DE_yes)
k=nrow(FourRes %>% filter(Set=="Different"))
N=nrow(DE)
phyper(x,m,n,k,lower.tail=F)
[1] 0.09585894
(x/k)/(m/N)
[1] 1.117149
x=length(intersect(FourRes_same$gene,DE_yes$gene))
m=nrow(DE_yes)
n=nrow(DE) - nrow(DE_yes)
k=nrow(FourRes %>% filter(Set=="Same"))
N=nrow(DE)
phyper(x,m,n,k,lower.tail=F)
[1] 0.9999999
(x/k)/(m/N)
[1] 0.883703
This is conditioned on the gene having a dominant PAS.
do this based on a set tested both
All4= FourRes %>% select(gene,Set) %>% inner_join(DE, by="gene")
x=nrow(All4 %>% filter(Set=="Different", DE=="Yes"))
m=nrow(All4 %>% filter( DE=="Yes"))
n=nrow(All4 %>% filter( DE=="No"))
k=nrow(All4 %>% filter(Set=="Different"))
N=nrow(All4)
phyper(x,m,n,k,lower.tail=F)
[1] 0.0009822532
(x/k)/(m/N)
[1] 1.305745
I am not sure what the set should be.
x=nrow(All4 %>% filter(Set=="Same", DE=="Yes"))
m=nrow(All4 %>% filter(DE=="Yes"))
n=nrow(All4 %>% filter(DE=="No"))
k=nrow(All4 %>% filter(Set=="Same"))
N=nrow(All4)
phyper(x,m,n,k,lower.tail=F)
[1] 0.9982958
(x/k)/(m/N)
[1] 0.9792784
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_10=BothRes %>% filter(Chimp_DiffDom >=0.1 | Human_DiffDom>=0.1) %>% mutate(Set= ifelse(Human_PAS==Chimp_PAS,"Same", "Different"),cut=10)
BothRes_20=BothRes %>% filter(Chimp_DiffDom >=0.2 | Human_DiffDom>=0.2) %>% mutate(Set= ifelse(Human_PAS==Chimp_PAS,"Same", "Different"),cut=20)
BothRes_30=BothRes %>% filter(Chimp_DiffDom >=0.3 | Human_DiffDom>=0.3) %>% mutate(Set= ifelse(Human_PAS==Chimp_PAS,"Same", "Different"),cut=30)
BothRes_40=BothRes %>% filter(Chimp_DiffDom >=0.4 | Human_DiffDom>=0.4) %>% mutate(Set= ifelse(Human_PAS==Chimp_PAS,"Same", "Different"),cut=40)
BothRes_50=BothRes %>% filter(Chimp_DiffDom >=0.5 | Human_DiffDom>=0.5) %>% mutate(Set= ifelse(Human_PAS==Chimp_PAS,"Same", "Different"),cut=50)
BothRes_60=BothRes %>% filter(Chimp_DiffDom >=0.6 | Human_DiffDom>=0.6) %>% mutate(Set= ifelse(Human_PAS==Chimp_PAS,"Same", "Different"),cut=60)
BothRes_70=BothRes %>% filter(Chimp_DiffDom >=0.7 | Human_DiffDom>=0.7) %>% mutate(Set= ifelse(Human_PAS==Chimp_PAS,"Same", "Different"),cut=70)
BothRes_80=BothRes %>% filter(Chimp_DiffDom >=0.8 | Human_DiffDom>=0.8) %>% mutate(Set= ifelse(Human_PAS==Chimp_PAS,"Same", "Different"),cut=80)
BothRes_90=BothRes %>% filter(Chimp_DiffDom >=0.9 | Human_DiffDom>=0.9) %>% mutate(Set= ifelse(Human_PAS==Chimp_PAS,"Same", "Different"),cut=90)
BothResAll=BothRes_10 %>% bind_rows(BothRes_20) %>% bind_rows(BothRes_30) %>% bind_rows(BothRes_40) %>% bind_rows(BothRes_50) %>% bind_rows(BothRes_60) %>% bind_rows(BothRes_70) %>% bind_rows(BothRes_80) %>% bind_rows(BothRes_90)
Pval=c()
Enrich=c()
set=c(10,20,30,40,50,60,70,80,90)
expected=c()
actual=c()
All4= BothResAll %>% select(gene,cut,Set) %>% inner_join(DE, by="gene")
for (i in set){
x=nrow(All4 %>% filter(cut==i, Set=="Different", DE=="Yes"))
actual=c(actual, x)
m=nrow(All4 %>% filter(cut==i, DE=="Yes"))
n=nrow(All4 %>% filter(cut==i, DE=="No"))
k=nrow(All4 %>% filter(cut==i, Set=="Different"))
N=nrow(All4 %>% filter(cut==i))
val=phyper(x-1,m,n,k,lower.tail=F)
Pval= c(Pval, val)
en=(x/k)/(m/N)
Enrich=c(Enrich, en)
#ex=which(grepl(max(dhyper(1:x, m, n, k)), dhyper(1:x, m, n, k)))
ex=k*(m/N)
expected=c(expected,ex)
}
ResDF=as.data.frame(cbind(set,Pval,Enrich, actual, expected))
ResDF$set=as.factor(ResDF$set)
ResDF$Pval=as.numeric(as.character(ResDF$Pval))
ResDF$Enrich=as.numeric(as.character(ResDF$Enrich))
diffP=ggplot(ResDF,aes(x=set, y=-log10(Pval),fill=set)) + geom_bar(stat="identity") +labs(title="Enrichment pvalues for DE and different dominant",x="Dominance Cutoff")+ scale_fill_brewer(palette = "RdYlBu") + theme(legend.position = "none")+ geom_hline(yintercept = 1.30103)
diffE=ggplot(ResDF,aes(x=set, y=Enrich,fill=set)) + geom_bar(stat="identity") + geom_hline(yintercept = 1)+labs(title="Enrichment for DE and different dominant",x="Dominance Cutoff")+ scale_fill_brewer(palette = "RdYlBu") + theme(legend.position = "none")
PvalSame=c()
EnrichSame=c()
expectedSame=c()
actualSame=c()
for (i in set){
x=nrow(All4 %>% filter(cut==i, Set=="Same", DE=="Yes"))
actualSame=c(actualSame, x)
m=nrow(All4 %>% filter(cut==i, DE=="Yes"))
n=nrow(All4 %>% filter(cut==i, DE=="No"))
k=nrow(All4 %>% filter(cut==i, Set=="Same"))
N=nrow(All4 %>% filter(cut==i))
val=phyper(x-1,m,n,k,lower.tail=F)
PvalSame= c(PvalSame, val)
en=(x/k)/(m/N)
EnrichSame=c(EnrichSame, en)
#ex=which(grepl(max(dhyper(1:x, m, n, k)), dhyper(1:x, m, n, k)))
ex=k*(m/N)
expectedSame=c(expectedSame,ex)
}
ResDFSame=as.data.frame(cbind(set,PvalSame,EnrichSame, actualSame,expectedSame))
ResDFSame$set=as.factor(ResDFSame$set)
ResDFSame$PvalSame=as.numeric(as.character(ResDFSame$PvalSame))
ResDFSame$EnrichSame=as.numeric(as.character(ResDFSame$EnrichSame))
Samep=ggplot(ResDFSame,aes(x=set, y=-log10(PvalSame),fill=set)) + geom_bar(stat="identity") +labs(title="Enrichment pvalues for DE and same dominant",x="Dominance Cutoff")+ scale_fill_brewer(palette = "RdYlBu") + theme(legend.position = "none")+ geom_hline(yintercept = 1.30103)
SameE=ggplot(ResDFSame,aes(x=set, y=EnrichSame,fill=set)) + geom_bar(stat="identity") + geom_hline(yintercept = 1)+labs(title="Enrichment for DE and same dominant",x="Dominance Cutoff")+ scale_fill_brewer(palette = "RdYlBu") + theme(legend.position = "none")
ResDF
set Pval Enrich actual expected
1 10 0.025369960 1.070079 430 401.839506
2 20 0.003500182 1.146763 221 192.716425
3 30 0.002404823 1.227587 116 94.494294
4 40 0.001704216 1.305745 76 58.204341
5 50 0.004173416 1.346146 51 37.885924
6 60 0.002304926 1.461459 36 24.632911
7 70 0.023483381 1.491590 18 12.067662
8 80 0.228627744 1.247994 11 8.814145
9 90 0.384878104 1.191860 6 5.034146
ResDFSame
set PvalSame EnrichSame actualSame expectedSame
1 10 0.9785161 0.9816444 1506 1534.16049
2 20 0.9973903 0.9779256 1253 1281.28357
3 30 0.9984228 0.9794500 1025 1046.50571
4 40 0.9990177 0.9792784 841 858.79566
5 50 0.9977739 0.9808864 673 686.11408
6 60 0.9990053 0.9786078 520 531.36709
7 70 0.9905316 0.9838326 361 366.93234
8 80 0.8790630 0.9902498 222 224.18586
9 90 0.8120858 0.9880709 80 80.96585
Look at propotion of DE genes
PropDE=as.data.frame(cbind(set, OverlapDE=actual, DE=rep(nrow(DE_yes),9))) %>% mutate(Prop=OverlapDE/DE)
PropDE$set=as.factor(PropDE$set)
ggplot(PropDE, aes(x=set,y=Prop,fill=set)) + geom_bar(stat="identity")+ labs(title="Proportion of DE genes with different dominant PAS", y="Proportion of DE genes",x="Dominance Cuttoff")+ scale_fill_brewer(palette = "RdYlBu") + theme(legend.position = "none")+geom_text(aes(label=OverlapDE), position=position_dodge(width=0.9), vjust=1.5)
plot grid:
plot_grid(diffE, SameE, diffP, Samep)
plot_grid( diffP, Samep)
ggdotchart(ResDF,y="Enrich",x= "set", color="set",add = "segments", rotate = TRUE, dot.size = 10, label = round(ResDF$Enrich,2), font.label = list(color = "black", size = 10, vjust = 0.5),ggtheme = theme_pubr(),sort="d", legend="none", palette="RdYlBu", title="Enrichment for DE and dAPA Different Dominant") + geom_hline(yintercept = 1)
ggdotchart(ResDFSame,y="EnrichSame",x= "set", color="set",add = "segments", rotate = TRUE, dot.size = 10, label = round(ResDFSame$EnrichSame,2), font.label = list(color = "black", size = 10, vjust = 0.5),ggtheme = theme_pubr(),sort="d", legend="none", palette="RdYlBu", title="Enrichment for DE and dAPA Same Dominant") + geom_hline(yintercept = 1)
Plot together:
ResDFfix=ResDF %>% mutate(type="Different")
ResDFSamefix=ResDFSame %>% mutate(type="Same")
colnames(ResDFSamefix)=colnames(ResDFfix)
ResDFfix_both=ResDFfix %>% bind_rows(ResDFSamefix)
DEdomPlot=ggplot(ResDFfix_both,aes(x=set,group=type,col=set,y=Enrich))+ geom_bar(stat="identity",col="grey",alpha=.3,width=.01)+geom_point(size=10) + coord_flip()+ geom_hline(yintercept = 1) +scale_color_brewer(palette="RdYlBu")+geom_text(col="black",aes(label = round(Enrich,2)))+ facet_grid(~type)+labs(x="Dominance Cutoff", y="Enrichment",title="Enrichment for DE by Dominance") + theme(legend.position = "none")
DEdomPlot
Add info about DE to All4.
diffIsoGenes= read.table("../data/DiffIso_Nuclear_DF/SignifianceEitherGENES_Nuclear.txt",stringsAsFactors = F, header = T)
All4DiffIso= All4 %>% mutate(dAPA=ifelse(gene %in% diffIsoGenes$gene, "Yes", "No"))
PvalSameapa=c()
pvalBothSideapa=c()
EnrichSameAPA=c()
ExpectedSameAPA=c()
actualSameapa=c()
#same dapa
for (i in set){
x=nrow(All4DiffIso %>% filter(cut==i, Set=="Same", DE=="Yes", dAPA=="Yes"))
actualSameapa=c(actualSameapa, x)
m=nrow(All4DiffIso %>% filter(cut==i, DE=="Yes", dAPA=="Yes"))
n=nrow(All4DiffIso %>% filter(cut==i, DE=="No", dAPA=="Yes"))
k=nrow(All4DiffIso %>% filter(cut==i, Set=="Same", dAPA=="Yes"))
N=nrow(All4DiffIso %>% filter(cut==i,dAPA=="Yes"))
val=phyper(x-1,m,n,k,lower.tail=F)
val2=phyper(x,m,n,k,lower.tail=T)
pvalBothSideapa=c(pvalBothSideapa, val2)
PvalSameapa= c(PvalSameapa, val)
en=(x/k)/(m/N)
EnrichSameAPA=c(EnrichSameAPA, en)
#ex=which(grepl(max(dhyper(1:x, m, n, k)), dhyper(1:x, m, n, k)))
ex=k*(m/N)
ExpectedSameAPA=c(ExpectedSameAPA,ex)
}
actualSameapa
[1] 231 207 172 136 103 80 46 26 7
ExpectedSameAPA
[1] 234.67700 217.20264 187.27941 146.76411 110.98324 84.50000 48.48485
[8] 25.65333 6.50000
EnrichSameAPA
[1] 0.9843316 0.9530271 0.9184138 0.9266571 0.9280681 0.9467456 0.9487500
[8] 1.0135135 1.0769231
PvalSameapa
[1] 0.6908226 0.9271034 0.9951886 0.9867290 0.9779845 0.9302170 0.8874905
[8] 0.5307203 0.5000000
pvalBothSideapa
[1] 0.352383333 0.093628644 0.007647351 0.021604183 0.037785694 0.118754602
[7] 0.209980308 0.663841564 0.793175394
set
[1] 10 20 30 40 50 60 70 80 90
PvalSameNo=c()
EnrichSameNo=c()
ExpectedSameNo=c()
actualSameNo=c()
pvalBothSideno=c()
#no dapa
for (i in set){
x=nrow(All4DiffIso %>% filter(cut==i, Set=="Same", DE=="Yes", dAPA=="No"))
actualSameNo=c(actualSameNo, x)
m=nrow(All4DiffIso %>% filter(cut==i, DE=="Yes", dAPA=="No"))
n=nrow(All4DiffIso %>% filter(cut==i, DE=="No", dAPA=="No"))
k=nrow(All4DiffIso %>% filter(cut==i, Set=="Same", dAPA=="No"))
N=nrow(All4DiffIso %>% filter(cut==i,dAPA=="No"))
val=phyper(x-1,m,n,k,lower.tail=F)
val2=phyper(x,m,n,k,lower.tail=T)
pvalBothSideno=c(pvalBothSideno, val2)
PvalSameNo= c(PvalSameNo, val)
en=(x/k)/(m/N)
EnrichSameNo=c(EnrichSameNo, en)
#ex=which(grepl(max(dhyper(1:x, m, n, k)), dhyper(1:x, m, n, k)))
ex=k*(m/N)
ExpectedSameNo=c(ExpectedSameNo,ex)
}
actualSameNo
[1] 1275 1046 853 705 570 440 315 196 73
ExpectedSameNo
[1] 1282.2282 1048.5219 849.3733 704.5488 570.0000 440.0000 315.0000
[8] 196.0000 73.0000
EnrichSameNo
[1] 0.9943628 0.9975948 1.0042699 1.0006404 1.0000000 1.0000000 1.0000000
[8] 1.0000000 1.0000000
PvalSameNo
[1] 0.78224457 0.71829130 0.08718982 0.54027531 1.00000000 1.00000000
[7] 1.00000000 1.00000000 1.00000000
pvalBothSideno
[1] 0.2483884 0.3483472 0.9662289 0.8354296 1.0000000 1.0000000 1.0000000
[8] 1.0000000 1.0000000
pval bothsided:
pvalBothSideno
[1] 0.2483884 0.3483472 0.9662289 0.8354296 1.0000000 1.0000000 1.0000000
[8] 1.0000000 1.0000000
PvalSameNo
[1] 0.78224457 0.71829130 0.08718982 0.54027531 1.00000000 1.00000000
[7] 1.00000000 1.00000000 1.00000000
pvalBothSideapa
[1] 0.352383333 0.093628644 0.007647351 0.021604183 0.037785694 0.118754602
[7] 0.209980308 0.663841564 0.793175394
ResDFSameAPA=as.data.frame(cbind(set,pval=PvalSameapa,pvalOpp=pvalBothSideapa,enrich=EnrichSameAPA, actual=actualSameapa,expected=ExpectedSameAPA)) %>% mutate(dAPA="Yes")
ResDFSameNo=as.data.frame(cbind(set,pval=PvalSameNo,pvalOpp=pvalBothSideno,enrich=EnrichSameNo, actual=actualSameNo,expected=ExpectedSameNo))%>% mutate(dAPA="No")
ResDFSameApaBoth= ResDFSameAPA %>% bind_rows(ResDFSameNo)
ResDFSameApaBoth$set=as.factor(ResDFSameApaBoth$set)
ggplot(ResDFSameApaBoth,aes(x=set, by=dAPA, fill=set,alpha=dAPA, y=enrich)) + geom_bar(stat="identity", position="dodge") +scale_fill_brewer(palette="RdYlBu")+ scale_alpha_discrete(range = c(0.6, 1)) + geom_hline(yintercept = 1) + labs( title="Enrichment for DE by in genes with Same Dominant",x="Dominance Cutoff", y="Enrichement")
Warning: Using alpha for a discrete variable is not advised.
Try ggplot dot plot.
ResDFSameApaBoth_len= ResDFSameApaBoth %>% mutate(linelength=ifelse(dAPA=="Yes", enrich, 0))
ggplot(ResDFSameApaBoth_len,aes(x=set,col=set,shape=dAPA, y=enrich,label = round(enrich,3)))+ geom_bar(stat="identity",color="grey",aes(y=linelength),width=.01)+geom_point(size=10) + coord_flip() + geom_hline(yintercept = 1) +scale_color_brewer(palette="RdYlBu")+ labs( title="Enrichment for DE by in genes with Same Dominant",x="Dominance Cutoff", y="Enrichement")+geom_text(color = "black", size = 3) + theme(legend.position = "bottom")
enrichmentp=ggplot(ResDFSameApaBoth,aes(x=set, by=dAPA, fill=set, y=-log10(pval))) + geom_bar(stat="identity", position="dodge") +scale_fill_brewer(palette="RdYlBu") + labs( title="enrichment p-value ",x="Dominance Cutoff", y="-log10(P-value)") + facet_grid(~dAPA) + theme(legend.position = "none")+ geom_hline(yintercept = 1.30103)
oppenrichp=ggplot(ResDFSameApaBoth,aes(x=set, by=dAPA, fill=set, y=-log10(pvalOpp))) + geom_bar(stat="identity", position="dodge") +scale_fill_brewer(palette="RdYlBu") + labs( title="depletion p-value ",x="Dominance Cutoff", y="-log10(P-value)") + facet_grid(~dAPA) + theme(legend.position = "none")+ geom_hline(yintercept = 1.30103)
plot_grid(enrichmentp,oppenrichp, nrow=2)
Version | Author | Date |
---|---|---|
69e8fd5 | brimittleman | 2020-04-28 |
Plot pvalue with enriichemtn
pvals=plot_grid( diffP, Samep)
plot_grid(DEdomPlot,pvals, nrow = 2)
pdf("../output/dediffdom.pdf", height=8, width=11)
plot_grid(DEdomPlot,pvals, nrow = 2)
dev.off()
png
2
Write out dataframes for main figures:
write.table(ResDFfix_both,"../output/FigureDF/SameDiffDomEnrichinDE.txt", col.names = T, row.names = F, quote = F)
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] RColorBrewer_1.1-2 ggpubr_0.2 magrittr_1.5
[4] cowplot_0.9.4 forcats_0.3.0 stringr_1.3.1
[7] dplyr_0.8.0.1 purrr_0.3.2 readr_1.3.1
[10] tidyr_0.8.3 tibble_2.1.1 ggplot2_3.1.1
[13] tidyverse_1.2.1 workflowr_1.6.0
loaded via a namespace (and not attached):
[1] tidyselect_0.2.5 reshape2_1.4.3 haven_1.1.2 lattice_0.20-38
[5] colorspace_1.3-2 generics_0.0.2 htmltools_0.3.6 yaml_2.2.0
[9] rlang_0.4.0 later_0.7.5 pillar_1.3.1 glue_1.3.0
[13] withr_2.1.2 modelr_0.1.2 readxl_1.1.0 plyr_1.8.4
[17] munsell_0.5.0 gtable_0.2.0 cellranger_1.1.0 rvest_0.3.2
[21] evaluate_0.12 labeling_0.3 knitr_1.20 httpuv_1.4.5
[25] broom_0.5.1 Rcpp_1.0.4.6 promises_1.0.1 scales_1.0.0
[29] backports_1.1.2 jsonlite_1.6 fs_1.3.1 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 lazyeval_0.2.1 crayon_1.3.4
[41] whisker_0.3-2 pkgconfig_2.0.2 xml2_1.2.0 lubridate_1.7.4
[45] assertthat_0.2.0 rmarkdown_1.10 httr_1.3.1 rstudioapi_0.10
[49] R6_2.3.0 nlme_3.1-137 git2r_0.26.1 compiler_3.5.1