New Dominance Definition

90% difference

PASnum= MetaPAS %>% select(PAS, gene, Chimp, Human) %>% gather(Species, usage, -PAS, -gene) %>% filter(usage >0) %>% group_by(gene,Species) %>% summarise(nPAS=n())
PASnumHuman=PASnum %>% filter(Species=="Human") %>% select(-Species)
PASnumChimp=PASnum %>% filter(Species=="Chimp") %>% select(-Species)



HumanDom9=read.table("../data/DomDefGreaterX/Human_.9_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Human9") %>% inner_join(PASnumHuman, by="gene")
nrow(HumanDom9)

[1] 65

ChimpDom9=read.table("../data/DomDefGreaterX/Chimp_.9_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Chimp9") %>% inner_join(PASnumChimp, by="gene")
nrow(ChimpDom9)

[1] 173

Explore these:

BothDom9=HumanDom9 %>% bind_rows(ChimpDom9)
genloc9=ggplot(BothDom9, aes(x=loc, fill=set)) + geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.9",y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
genloc9

Past versions of unnamed-chunk-6-1.png

BothDom9_prop= BothDom9 %>% group_by(set, loc) %>% summarise(nLoc=n()) %>% ungroup() %>% group_by(set) %>% mutate(nSet=sum(nLoc), prop=nLoc/nSet)

proploc9=ggplot(BothDom9_prop, aes(x=loc,by=set, fill=set,y=prop)) + geom_bar(stat="identity",position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.9",y="Proportion",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")

There are way more in chimp at this cutoff.

Look at how many genes have the same and different dominant at .9 difference:

HumanDom9_sm=HumanDom9 %>% select(PAS, gene, loc) %>% rename(HumanPAS=PAS, HumanLoc=loc)
ChimpDom9_sm=ChimpDom9 %>% select(PAS, gene, loc)%>% rename(ChimpPAS=PAS, ChimpLoc=loc)

both9sm=ChimpDom9_sm %>% inner_join(HumanDom9_sm, by="gene")
nrow(both9sm)

[1] 0

Look at the number of PAS in these genes:

None of the same genes are represented here.

ggplot(BothDom9, aes(x=nPAS, fill=set)) + geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="Number of PAS per gene with .9 difference",y="genes")

Past versions of unnamed-chunk-9-1.png

grid.newpage()
venn.plot9 <- draw.pairwise.venn(area1 = length(HumanDom9_sm$gene),
                           area2 = length(ChimpDom9_sm$gene),
                           cross.area = nrow(both9sm),
                           c("Human", "Chimp"), scaled = TRUE,
                           fill = c("orange", "green"),
                           cex = 1.5,
                           cat.cex = 1.5,
                           cat.pos = c(320, 25),
                           cat.dist = .05) 

Past versions of unnamed-chunk-10-1.png

Look at the location of the PAS not in gene.

HumanDom9_smLab= HumanDom9 %>% mutate(Set="Human")
ChimpDom9_smLab= ChimpDom9 %>% mutate(Set="Chimp")
BothDom9_smLab=HumanDom9_smLab %>% bind_rows(ChimpDom9_smLab)
diffgenes9=ggplot(BothDom9_smLab,aes(x=loc, fill=Set))+ geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2")+  labs(title="Non Matched: 0.9", y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
diffgenes9

Past versions of unnamed-chunk-11-1.png

BothDom9_smLab_prop=BothDom9_smLab%>% group_by(set, loc) %>% summarise(nLoc=n()) %>% ungroup() %>% group_by(set) %>% mutate(nSet=sum(nLoc), prop=nLoc/nSet)
propDiff9=ggplot(BothDom9_smLab_prop, aes(x=loc,by=set, fill=set,y=prop)) + geom_bar(stat="identity",position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.9: Different Genes",y="Proportion",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")

80% difference

HumanDom8=read.table("../data/DomDefGreaterX/Human_.8_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Human8") %>% inner_join(PASnumHuman, by="gene")
nrow(HumanDom8)

[1] 318

ChimpDom8=read.table("../data/DomDefGreaterX/Chimp_.8_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Chimp8") %>% inner_join(PASnumChimp, by="gene")
nrow(ChimpDom8)

[1] 571

BothDom8=HumanDom8 %>% bind_rows(ChimpDom8)
genloc8=ggplot(BothDom8, aes(x=loc, fill=set)) + geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.8",y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
genloc8

Past versions of unnamed-chunk-13-1.png

HumanDom8_sm=HumanDom8 %>% select(PAS, gene, loc) %>% rename(HumanPAS=PAS, HumanLoc=loc)
ChimpDom8_sm=ChimpDom8 %>% select(PAS, gene, loc)%>% rename(ChimpPAS=PAS, ChimpLoc=loc)

both8sm=ChimpDom8_sm %>% inner_join(HumanDom8_sm, by="gene")
nrow(both8sm)

[1] 192

There are 192 genes that are the same.

grid.newpage()
venn.plot8 <- draw.pairwise.venn(area1 = length(HumanDom8_sm$gene),
                           area2 = length(ChimpDom8_sm$gene),
                           cross.area = nrow(both8sm),
                           c("Human", "Chimp"), scaled = TRUE,
                           fill = c("orange", "green"),
                           cex = 1.5,
                           cat.cex = 1.5,
                           cat.pos = c(320, 25),
                           cat.dist = .05) 

Past versions of unnamed-chunk-15-1.png

For these I can look to see if the PAS are the same or different:

both8sm_same= both8sm %>% filter(ChimpPAS==HumanPAS)
nrow(both8sm_same)

[1] 189

both8sm_diff= both8sm %>% filter(ChimpPAS!=HumanPAS)
nrow(both8sm_diff)

[1] 3

location for same:

same8=ggplot(both8sm_same,aes(x=ChimpLoc,fill=ChimpLoc)) +geom_bar(stat = "count") +scale_fill_brewer(palette = "Dark2")+ labs(title="Matched Gene Matched PAS .8", y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
same8

Past versions of unnamed-chunk-17-1.png

Only 3 are in different PAS

both8sm_diff

     ChimpPAS    gene ChimpLoc    HumanPAS HumanLoc
1  human21024   CKS1B     utr3  human21027      end
2 chimp163919  IFNGR2     utr3 human215583   intron
3 human324647 NSUN5P1     utr5 human324646     utr5

ggplot(BothDom8, aes(x=nPAS, fill=set)) + geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="Number of PAS per gene with .8 difference",y="genes")

Past versions of unnamed-chunk-19-1.png

HumanDom8_smLab= HumanDom8 %>% anti_join(ChimpDom8,by = "gene") %>% mutate(Set="Human")
ChimpDom8_smLab=  ChimpDom8 %>% anti_join(HumanDom8,by = "gene") %>% mutate(Set="Chimp")
BothDom8_smLab=HumanDom8_smLab %>% bind_rows(ChimpDom8_smLab)
diffgenes8=ggplot(BothDom8_smLab,aes(x=loc, fill=Set))+ geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") +  labs(title="Non Matched: 0.8", y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
diffgenes8

BothDom8_prop= BothDom8 %>% group_by(set, loc) %>% summarise(nLoc=n()) %>% ungroup() %>% group_by(set) %>% mutate(nSet=sum(nLoc), prop=nLoc/nSet)

proploc8=ggplot(BothDom8_prop, aes(x=loc,by=set, fill=set,y=prop)) + geom_bar(stat="identity",position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.8",y="Proportion",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")

BothDom8_smLab_prop=BothDom8_smLab%>% group_by(set, loc) %>% summarise(nLoc=n()) %>% ungroup() %>% group_by(set) %>% mutate(nSet=sum(nLoc), prop=nLoc/nSet)
propDiff8=ggplot(BothDom8_smLab_prop, aes(x=loc,by=set, fill=set,y=prop)) + geom_bar(stat="identity",position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.8: Different Genes",y="Proportion",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")

70% difference

HumanDom7=read.table("../data/DomDefGreaterX/Human_.7_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Human7") %>% inner_join(PASnumHuman, by="gene")
nrow(HumanDom7)

[1] 637

ChimpDom7=read.table("../data/DomDefGreaterX/Chimp_.7_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Chimp7") %>% inner_join(PASnumChimp, by="gene")
nrow(ChimpDom7)

[1] 988

BothDom7=HumanDom7 %>% bind_rows(ChimpDom7)
genloc7=ggplot(BothDom7, aes(x=loc, fill=set)) + geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.7",y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
genloc7

Past versions of unnamed-chunk-23-1.png

HumanDom7_sm=HumanDom7 %>% select(PAS, gene, loc) %>% rename(HumanPAS=PAS, HumanLoc=loc)
ChimpDom7_sm=ChimpDom7 %>% select(PAS, gene, loc)%>% rename(ChimpPAS=PAS, ChimpLoc=loc)

both7sm=ChimpDom7_sm %>% inner_join(HumanDom7_sm, by="gene")
nrow(both7sm)

[1] 473

grid.newpage()
venn.plot7 <- draw.pairwise.venn(area1 = length(HumanDom7_sm$gene),
                           area2 = length(ChimpDom7_sm$gene),
                           cross.area = nrow(both7sm),
                           c("Human", "Chimp"), scaled = TRUE,
                           fill = c("orange", "green"),
                           cex = 1.5,
                           cat.cex = 1.5,
                           cat.pos = c(320, 25),
                           cat.dist = .05) 

Past versions of unnamed-chunk-25-1.png

both7sm_same= both7sm %>% filter(ChimpPAS==HumanPAS)
nrow(both7sm_same)

[1] 467

both7sm_diff= both7sm %>% filter(ChimpPAS!=HumanPAS)
nrow(both7sm_diff)

[1] 6

location for same:

same7=ggplot(both7sm_same,aes(x=ChimpLoc,fill=ChimpLoc)) +geom_bar(stat = "count") +scale_fill_brewer(palette = "Dark2")+ labs(title="Matched Gene Matched PAS .7", y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
same7

Past versions of unnamed-chunk-27-1.png

both7sm_diff

     ChimpPAS    gene ChimpLoc    HumanPAS HumanLoc
1  human21024   CKS1B     utr3  human21027      end
2 chimp137870    TMC8     utr3 human151981     utr3
3 human162402  MFSD12     utr3 human162401     utr3
4 chimp182091   MAT2A     utr3 human184286      cds
5 chimp163919  IFNGR2     utr3 human215583   intron
6 human324647 NSUN5P1     utr5 human324646     utr5

ggplot(BothDom7, aes(x=nPAS, fill=set)) + geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="Number of PAS per gene with .7 difference",y="genes")

Past versions of unnamed-chunk-29-1.png

HumanDom7_smLab= HumanDom7 %>% anti_join(ChimpDom7,by = "gene") %>% mutate(Set="Human")
ChimpDom7_smLab=  ChimpDom7 %>% anti_join(HumanDom7,by = "gene") %>% mutate(Set="Chimp")
BothDom7_smLab=HumanDom7_smLab %>% bind_rows(ChimpDom7_smLab)
diffgenes7=ggplot(BothDom7_smLab,aes(x=loc, fill=Set))+ geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="Location of dominant PAS in genes \nnot matched between species: 0.7", y="genes")+  labs(title="Non Matched: 0.7", y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
diffgenes7

Past versions of unnamed-chunk-30-1.png

BothDom7_prop= BothDom7 %>% group_by(set, loc) %>% summarise(nLoc=n()) %>% ungroup() %>% group_by(set) %>% mutate(nSet=sum(nLoc), prop=nLoc/nSet)

proploc7=ggplot(BothDom7_prop, aes(x=loc,by=set, fill=set,y=prop)) + geom_bar(stat="identity",position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.7",y="Proportion",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")

BothDom7_smLab_prop=BothDom7_smLab%>% group_by(set, loc) %>% summarise(nLoc=n()) %>% ungroup() %>% group_by(set) %>% mutate(nSet=sum(nLoc), prop=nLoc/nSet)
propDiff7=ggplot(BothDom7_smLab_prop, aes(x=loc,by=set, fill=set,y=prop)) + geom_bar(stat="identity",position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.7: Different Genes",y="Proportion",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")

60% difference

HumanDom6=read.table("../data/DomDefGreaterX/Human_.6_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Human6") %>% inner_join(PASnumHuman, by="gene")
nrow(HumanDom6)

[1] 1014

ChimpDom6=read.table("../data/DomDefGreaterX/Chimp_.6_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Chimp6") %>% inner_join(PASnumChimp, by="gene")
nrow(ChimpDom6)

[1] 1404

BothDom6=HumanDom6 %>% bind_rows(ChimpDom6)
genloc6=ggplot(BothDom6, aes(x=loc, fill=set)) + geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.6",y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
genloc6

Past versions of unnamed-chunk-33-1.png

HumanDom6_sm=HumanDom6 %>% select(PAS, gene, loc) %>% rename(HumanPAS=PAS, HumanLoc=loc)
ChimpDom6_sm=ChimpDom6 %>% select(PAS, gene, loc)%>% rename(ChimpPAS=PAS, ChimpLoc=loc)

both6sm=ChimpDom6_sm %>% inner_join(HumanDom6_sm, by="gene")
nrow(both6sm)

[1] 803

grid.newpage()
venn.plot6 <- draw.pairwise.venn(area1 = length(HumanDom6_sm$gene),
                           area2 = length(ChimpDom6_sm$gene),
                           cross.area = nrow(both6sm),
                           c("Human", "Chimp"), scaled = TRUE,
                           fill = c("orange", "green"),
                           cex = 1.5,
                           cat.cex = 1.5,
                           cat.pos = c(320, 25),
                           cat.dist = .05) 

Past versions of unnamed-chunk-35-1.png

both6sm_same= both6sm %>% filter(ChimpPAS==HumanPAS)
nrow(both6sm_same)

[1] 796

both6sm_diff= both6sm %>% filter(ChimpPAS!=HumanPAS)
nrow(both6sm_diff)

[1] 7

location for same:

same6=ggplot(both6sm_same,aes(x=ChimpLoc,fill=ChimpLoc)) +geom_bar(stat = "count") +scale_fill_brewer(palette = "Dark2")+ labs(title="Matched Gene Matched PAS .6", y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
same6

Past versions of unnamed-chunk-37-1.png

both6sm_diff

     ChimpPAS    gene ChimpLoc    HumanPAS HumanLoc
1  human21024   CKS1B     utr3  human21027      end
2  human60067    FTH1     utr3  human60068      cds
3 chimp137870    TMC8     utr3 human151981     utr3
4 human162402  MFSD12     utr3 human162401     utr3
5 chimp182091   MAT2A     utr3 human184286      cds
6 chimp163919  IFNGR2     utr3 human215583   intron
7 human324647 NSUN5P1     utr5 human324646     utr5

ggplot(BothDom6, aes(x=nPAS, fill=set)) + geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="Number of PAS per gene with .6 difference",y="genes")

Past versions of unnamed-chunk-39-1.png

HumanDom6_smLab= HumanDom6 %>% anti_join(ChimpDom6,by = "gene") %>% mutate(Set="Human")
ChimpDom6_smLab=  ChimpDom6 %>% anti_join(HumanDom6,by = "gene") %>% mutate(Set="Chimp")
BothDom6_smLab=HumanDom6_smLab %>% bind_rows(ChimpDom6_smLab)
diffgenes6=ggplot(BothDom6_smLab,aes(x=loc, fill=Set))+ geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") +  labs(title="Non Matched: 0.6", y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
diffgenes6

Past versions of unnamed-chunk-40-1.png

BothDom6_prop= BothDom6 %>% group_by(set, loc) %>% summarise(nLoc=n()) %>% ungroup() %>% group_by(set) %>% mutate(nSet=sum(nLoc), prop=nLoc/nSet)

proploc6=ggplot(BothDom6_prop, aes(x=loc,by=set, fill=set,y=prop)) + geom_bar(stat="identity",position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.6",y="Proportion",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")

BothDom6_smLab_prop=BothDom6_smLab%>% group_by(set, loc) %>% summarise(nLoc=n()) %>% ungroup() %>% group_by(set) %>% mutate(nSet=sum(nLoc), prop=nLoc/nSet)
propDiff6=ggplot(BothDom6_smLab_prop, aes(x=loc,by=set, fill=set,y=prop)) + geom_bar(stat="identity",position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.6: Different Genes",y="Proportion",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")

50% difference

HumanDom5=read.table("../data/DomDefGreaterX/Human_.5_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Human5") %>% inner_join(PASnumHuman, by="gene")
nrow(HumanDom5)

[1] 1404

ChimpDom5=read.table("../data/DomDefGreaterX/Chimp_.5_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Chimp5") %>% inner_join(PASnumChimp, by="gene")
nrow(ChimpDom5)

[1] 1908

BothDom5=HumanDom5 %>% bind_rows(ChimpDom5)
genloc5=ggplot(BothDom5, aes(x=loc, fill=set)) + geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.5",y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
genloc5

Past versions of unnamed-chunk-43-1.png

HumanDom5_sm=HumanDom5 %>% select(PAS, gene, loc) %>% rename(HumanPAS=PAS, HumanLoc=loc)
ChimpDom5_sm=ChimpDom5 %>% select(PAS, gene, loc)%>% rename(ChimpPAS=PAS, ChimpLoc=loc)

both5sm=ChimpDom5_sm %>% inner_join(HumanDom5_sm, by="gene")
nrow(both5sm)

[1] 1160

grid.newpage()
venn.plot5 <- draw.pairwise.venn(area1 = length(HumanDom5_sm$gene),
                           area2 = length(ChimpDom5_sm$gene),
                           cross.area = nrow(both5sm),
                           c("Human", "Chimp"), scaled = TRUE,
                           fill = c("orange", "green"),
                           cex = 1.5,
                           cat.cex = 1.5,
                           cat.pos = c(320, 25),
                           cat.dist = .05) 

Past versions of unnamed-chunk-45-1.png

both5sm_same= both5sm %>% filter(ChimpPAS==HumanPAS)
nrow(both5sm_same)

[1] 1145

both5sm_diff= both5sm %>% filter(ChimpPAS!=HumanPAS)
nrow(both5sm_diff)

[1] 15

location for same:

same5=ggplot(both5sm_same,aes(x=ChimpLoc,fill=ChimpLoc)) +geom_bar(stat = "count") +scale_fill_brewer(palette = "Dark2")+ labs(title="Matched Gene Matched PAS .5", y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
same5

Past versions of unnamed-chunk-47-1.png

both5sm_diff

      ChimpPAS    gene ChimpLoc    HumanPAS HumanLoc
1   human21024   CKS1B     utr3  human21027      end
2   human48359   PGAM1     utr3  human48357   intron
3   human60067    FTH1     utr3  human60068      cds
4   human68171    DDX6     utr3  human68160     utr3
5  chimp137870    TMC8     utr3 human151981     utr3
6  human162402  MFSD12     utr3 human162401     utr3
7  chimp182091   MAT2A     utr3 human184286      cds
8  human205442   RBCK1     utr3 human205434     utr3
9  chimp163919  IFNGR2     utr3 human215583   intron
10 chimp165747     LSS     utr3 human217562   intron
11 human225614   RPL32     utr3 human225615     utr3
12 human250766   NCBP2     utr3 chimp224588      cds
13 human324647 NSUN5P1     utr5 human324646     utr5
14 chimp308202   FABP5     utr3 human345717      cds
15 human366498 SLC27A4   intron human366500     utr3

ggplot(BothDom5, aes(x=nPAS, fill=set)) + geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="Number of PAS per gene with .5 difference",y="genes")

Past versions of unnamed-chunk-49-1.png

HumanDom5_smLab= HumanDom5 %>% anti_join(ChimpDom5,by = "gene") %>% mutate(Set="Human")
ChimpDom5_smLab=  ChimpDom5 %>% anti_join(HumanDom5,by = "gene") %>% mutate(Set="Chimp")
BothDom5_smLab=HumanDom5_smLab %>% bind_rows(ChimpDom5_smLab)
diffgenes5=ggplot(BothDom5_smLab,aes(x=loc, fill=Set))+ geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") +   labs(title="Non Matched: 0.5", y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
diffgenes5

Past versions of unnamed-chunk-50-1.png

BothDom5_prop= BothDom5 %>% group_by(set, loc) %>% summarise(nLoc=n()) %>% ungroup() %>% group_by(set) %>% mutate(nSet=sum(nLoc), prop=nLoc/nSet)

proploc5=ggplot(BothDom5_prop, aes(x=loc,by=set, fill=set,y=prop)) + geom_bar(stat="identity",position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.5",y="Proportion",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")

BothDom5_smLab_prop=BothDom5_smLab%>% group_by(set, loc) %>% summarise(nLoc=n()) %>% ungroup() %>% group_by(set) %>% mutate(nSet=sum(nLoc), prop=nLoc/nSet)
propDiff5=ggplot(BothDom5_smLab_prop, aes(x=loc,by=set, fill=set,y=prop)) + geom_bar(stat="identity",position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.5: Different Genes",y="Proportion",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")

40% difference

HumanDom4=read.table("../data/DomDefGreaterX/Human_.4_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Human4") %>% inner_join(PASnumHuman, by="gene")
nrow(HumanDom4)

[1] 1833

ChimpDom4=read.table("../data/DomDefGreaterX/Chimp_.4_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Chimp4") %>% inner_join(PASnumChimp, by="gene")
nrow(ChimpDom4)

[1] 2478

BothDom4=HumanDom4 %>% bind_rows(ChimpDom4)
genloc4=ggplot(BothDom4, aes(x=loc, fill=set)) + geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.4",y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
genloc4

Past versions of unnamed-chunk-53-1.png

HumanDom4_sm=HumanDom4 %>% select(PAS, gene, loc) %>% rename(HumanPAS=PAS, HumanLoc=loc)
ChimpDom4_sm=ChimpDom4 %>% select(PAS, gene, loc)%>% rename(ChimpPAS=PAS, ChimpLoc=loc)

both4sm=ChimpDom4_sm %>% inner_join(HumanDom4_sm, by="gene")
nrow(both4sm)

[1] 1565

grid.newpage()
venn.plot4 <- draw.pairwise.venn(area1 = length(HumanDom4_sm$gene),
                           area2 = length(ChimpDom4_sm$gene),
                           cross.area = nrow(both4sm),
                           c("Human", "Chimp"), scaled = TRUE,
                           fill = c("orange", "green"),
                           cex = 1.5,
                           cat.cex = 1.5,
                           cat.pos = c(320, 25),
                           cat.dist = .05) 

Past versions of unnamed-chunk-55-1.png

both4sm_same= both4sm %>% filter(ChimpPAS==HumanPAS)
nrow(both4sm_same)

[1] 1543

both4sm_diff= both4sm %>% filter(ChimpPAS!=HumanPAS)
nrow(both4sm_diff)

[1] 22

location for same:

same4=ggplot(both4sm_same,aes(x=ChimpLoc,fill=ChimpLoc)) +geom_bar(stat = "count") +scale_fill_brewer(palette = "Dark2")+ labs(title="Matched Gene Matched PAS .4", y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
same4

Past versions of unnamed-chunk-57-1.png

22 is enough to start to plot:

both4sm_diff_g= both4sm_diff %>% select(gene, HumanLoc, ChimpLoc) %>% gather('Species', 'Loc', -gene)
diffDom4=ggplot(both4sm_diff_g, aes(x=Loc, fill=Species))+ geom_bar(stat="count",position = "dodge") +scale_fill_brewer(palette = "Dark2")+ labs(y='Genes', title="Different Dominant PAS: 0.4",x="") +theme(axis.text.x = element_text(angle = 90),legend.position = "none")
diffDom4

Past versions of unnamed-chunk-58-1.png

ggplot(BothDom4, aes(x=nPAS, fill=set)) + geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="Number of PAS per gene with .4 difference",y="genes")

Past versions of unnamed-chunk-59-1.png

HumanDom4_smLab= HumanDom4 %>% anti_join(ChimpDom4,by = "gene") %>% mutate(Set="Human")
ChimpDom4_smLab=  ChimpDom4 %>% anti_join(HumanDom4,by = "gene") %>% mutate(Set="Chimp")
BothDom4_smLab=HumanDom4_smLab %>% bind_rows(ChimpDom4_smLab)
diffgenes4=ggplot(BothDom4_smLab,aes(x=loc, fill=Set))+ geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") +  labs(title="Non Matched: 0.4", y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
diffgenes4

BothDom4_prop= BothDom4 %>% group_by(set, loc) %>% summarise(nLoc=n()) %>% ungroup() %>% group_by(set) %>% mutate(nSet=sum(nLoc), prop=nLoc/nSet)

proploc4=ggplot(BothDom4_prop, aes(x=loc,by=set, fill=set,y=prop)) + geom_bar(stat="identity",position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.4",y="Proportion",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")

BothDom4_smLab_prop=BothDom4_smLab%>% group_by(set, loc) %>% summarise(nLoc=n()) %>% ungroup() %>% group_by(set) %>% mutate(nSet=sum(nLoc), prop=nLoc/nSet)
propDiff4=ggplot(BothDom4_smLab_prop, aes(x=loc,by=set, fill=set,y=prop)) + geom_bar(stat="identity",position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.4: Different Genes",y="Proportion",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")

30% difference

HumanDom3=read.table("../data/DomDefGreaterX/Human_.3_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Human3") %>% inner_join(PASnumHuman, by="gene")
nrow(HumanDom3)

[1] 2403

ChimpDom3=read.table("../data/DomDefGreaterX/Chimp_.3_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Chimp3") %>% inner_join(PASnumChimp, by="gene")
nrow(ChimpDom3)

[1] 3127

BothDom3=HumanDom3 %>% bind_rows(ChimpDom3)
genloc3=ggplot(BothDom3, aes(x=loc, fill=set)) + geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.3",y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
genloc3

Past versions of unnamed-chunk-63-1.png

HumanDom3_sm=HumanDom3 %>% select(PAS, gene, loc) %>% rename(HumanPAS=PAS, HumanLoc=loc)
ChimpDom3_sm=ChimpDom3 %>% select(PAS, gene, loc)%>% rename(ChimpPAS=PAS, ChimpLoc=loc)

both3sm=ChimpDom3_sm %>% inner_join(HumanDom3_sm, by="gene")
nrow(both3sm)

[1] 2069

grid.newpage()
venn.plot3 <- draw.pairwise.venn(area1 = length(HumanDom3_sm$gene),
                           area2 = length(ChimpDom3_sm$gene),
                           cross.area = nrow(both3sm),
                           c("Human", "Chimp"), scaled = TRUE,
                           fill = c("orange", "green"),
                           cex = 1.5,
                           cat.cex = 1.5,
                           cat.pos = c(320, 25),
                           cat.dist = .05) 

Past versions of unnamed-chunk-65-1.png

both3sm_same= both3sm %>% filter(ChimpPAS==HumanPAS)
nrow(both3sm_same)

[1] 2031

both3sm_diff= both3sm %>% filter(ChimpPAS!=HumanPAS)
nrow(both3sm_diff)

[1] 38

location for same:

same3=ggplot(both3sm_same,aes(x=ChimpLoc,fill=ChimpLoc)) +geom_bar(stat = "count") +scale_fill_brewer(palette = "Dark2")+ labs(title="Matched Gene Matched PAS .3", y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
same3

Past versions of unnamed-chunk-67-1.png

both3sm_diff_g= both3sm_diff %>% select(gene, HumanLoc, ChimpLoc) %>% gather('Species', 'Loc', -gene)
diffDom3=ggplot(both3sm_diff_g, aes(x=Loc, fill=Species))+ geom_bar(stat="count",position = "dodge") +scale_fill_brewer(palette = "Dark2")+ labs(y='Genes', title="Different Dominant PAS: 0.3",x="") +theme(axis.text.x = element_text(angle = 90),legend.position = "none")
diffDom3

ggplot(BothDom3, aes(x=nPAS, fill=set)) + geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="Number of PAS per gene with .3 difference",y="genes")

Past versions of unnamed-chunk-69-1.png

HumanDom3_smLab= HumanDom3 %>% anti_join(ChimpDom3,by = "gene") %>% mutate(Set="Human")
ChimpDom3_smLab=  ChimpDom3 %>% anti_join(HumanDom3,by = "gene") %>% mutate(Set="Chimp")
BothDom3_smLab=HumanDom3_smLab %>% bind_rows(ChimpDom3_smLab)
diffgenes3=ggplot(BothDom3_smLab,aes(x=loc, fill=Set))+ geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") +   labs(title="Non Matched: 0.3", y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
diffgenes3

BothDom3_prop= BothDom3 %>% group_by(set, loc) %>% summarise(nLoc=n()) %>% ungroup() %>% group_by(set) %>% mutate(nSet=sum(nLoc), prop=nLoc/nSet)

proploc3=ggplot(BothDom3_prop, aes(x=loc,by=set, fill=set,y=prop)) + geom_bar(stat="identity",position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.3",y="Proportion",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")

BothDom3_prop= BothDom3 %>% group_by(set, loc) %>% summarise(nLoc=n()) %>% ungroup() %>% group_by(set) %>% mutate(nSet=sum(nLoc), prop=nLoc/nSet)

proploc3=ggplot(BothDom3_prop, aes(x=loc,by=set, fill=set,y=prop)) + geom_bar(stat="identity",position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.3",y="Proportion",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")

BothDom3_smLab_prop=BothDom3_smLab%>% group_by(set, loc) %>% summarise(nLoc=n()) %>% ungroup() %>% group_by(set) %>% mutate(nSet=sum(nLoc), prop=nLoc/nSet)
propDiff3=ggplot(BothDom3_smLab_prop, aes(x=loc,by=set, fill=set,y=prop)) + geom_bar(stat="identity",position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.3: Different Genes",y="Proportion",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")

20% difference

HumanDom2=read.table("../data/DomDefGreaterX/Human_.2_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Human2") %>% inner_join(PASnumHuman, by="gene")
nrow(HumanDom2)

[1] 3183

ChimpDom2=read.table("../data/DomDefGreaterX/Chimp_.2_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Chimp2") %>% inner_join(PASnumChimp, by="gene")
nrow(ChimpDom2)

[1] 3969

BothDom2=HumanDom2 %>% bind_rows(ChimpDom2)
genloc2=ggplot(BothDom2, aes(x=loc, fill=set)) + geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.2",y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
genloc2

Past versions of unnamed-chunk-74-1.png

HumanDom2_sm=HumanDom2 %>% select(PAS, gene, loc) %>% rename(HumanPAS=PAS, HumanLoc=loc)
ChimpDom2_sm=ChimpDom2 %>% select(PAS, gene, loc)%>% rename(ChimpPAS=PAS, ChimpLoc=loc)

both2sm=ChimpDom2_sm %>% inner_join(HumanDom2_sm, by="gene")
nrow(both2sm)

[1] 2711

grid.newpage()
venn.plot2 <- draw.pairwise.venn(area1 = length(HumanDom2_sm$gene),
                           area2 = length(ChimpDom2_sm$gene),
                           cross.area = nrow(both2sm),
                           c("Human", "Chimp"), scaled = TRUE,
                           fill = c("orange", "green"),
                           cex = 1.5,
                           cat.cex = 1.5,
                           cat.pos = c(320, 25),
                           cat.dist = .05) 

Past versions of unnamed-chunk-76-1.png

both2sm_same= both2sm %>% filter(ChimpPAS==HumanPAS)
nrow(both2sm_same)

[1] 2634

both2sm_diff= both2sm %>% filter(ChimpPAS!=HumanPAS)
nrow(both2sm_diff)

[1] 77

location for same:

same2=ggplot(both2sm_same,aes(x=ChimpLoc,fill=ChimpLoc)) +geom_bar(stat = "count") +scale_fill_brewer(palette = "Dark2")+ labs(title="Matched Gene Matched PAS .2", y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
same2

Past versions of unnamed-chunk-78-1.png

both2sm_diff_g= both2sm_diff %>% select(gene, HumanLoc, ChimpLoc) %>% gather('Species', 'Loc', -gene)
diffDom2=ggplot(both2sm_diff_g, aes(x=Loc, fill=Species))+ geom_bar(stat="count",position = "dodge") +scale_fill_brewer(palette = "Dark2")+  labs(y='Genes', title="Different Dominant PAS: 0.2",x="") +theme(axis.text.x = element_text(angle = 90),legend.position = "none")
diffDom2

Past versions of unnamed-chunk-79-1.png

ggplot(BothDom2, aes(x=nPAS, fill=set)) + geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="Number of PAS per gene with .2 difference",y="genes")

HumanDom2_smLab= HumanDom2 %>% anti_join(ChimpDom2,by = "gene") %>% mutate(Set="Human")
ChimpDom2_smLab=  ChimpDom2 %>% anti_join(HumanDom2,by = "gene") %>% mutate(Set="Chimp")
BothDom2_smLab=HumanDom2_smLab %>% bind_rows(ChimpDom2_smLab)
diffgenes2=ggplot(BothDom2_smLab,aes(x=loc, fill=Set))+ geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") +  labs(title="Non Matched: 0.2", y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
diffgenes2

BothDom2_prop= BothDom2 %>% group_by(set, loc) %>% summarise(nLoc=n()) %>% ungroup() %>% group_by(set) %>% mutate(nSet=sum(nLoc), prop=nLoc/nSet)

proploc2=ggplot(BothDom2_prop, aes(x=loc,by=set, fill=set,y=prop)) + geom_bar(stat="identity",position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.2",y="Proportion",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")

BothDom2_smLab_prop=BothDom2_smLab%>% group_by(set, loc) %>% summarise(nLoc=n()) %>% ungroup() %>% group_by(set) %>% mutate(nSet=sum(nLoc), prop=nLoc/nSet)
propDiff2=ggplot(BothDom2_smLab_prop, aes(x=loc,by=set, fill=set,y=prop)) + geom_bar(stat="identity",position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.2: Different Genes",y="Proportion",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")

10% difference

HumanDom1=read.table("../data/DomDefGreaterX/Human_.1_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Human1") %>% inner_join(PASnumHuman, by="gene")
nrow(HumanDom1)

[1] 4417

ChimpDom1=read.table("../data/DomDefGreaterX/Chimp_.1_dominantPAS.txt", col.names = MetaCol,stringsAsFactors = F) %>% mutate(set="Chimp1") %>% inner_join(PASnumChimp, by="gene")
nrow(ChimpDom1)

[1] 5254

BothDom1=HumanDom1 %>% bind_rows(ChimpDom1)
genloc1=ggplot(BothDom1, aes(x=loc, fill=set)) + geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.1",y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none") 

genloc1

HumanDom1_sm=HumanDom1 %>% select(PAS, gene, loc) %>% rename(HumanPAS=PAS, HumanLoc=loc)
ChimpDom1_sm=ChimpDom1 %>% select(PAS, gene, loc)%>% rename(ChimpPAS=PAS, ChimpLoc=loc)

both1sm=ChimpDom1_sm %>% inner_join(HumanDom1_sm, by="gene")
nrow(both1sm)

[1] 3814

grid.newpage()
venn.plot1 <- draw.pairwise.venn(area1 = length(HumanDom1_sm$gene),
                           area2 = length(ChimpDom1_sm$gene),
                           cross.area = nrow(both1sm),
                           c("Human", "Chimp"), scaled = TRUE,
                           fill = c("orange", "green"),
                           cex = 1.5,
                           cat.cex = 1.5,
                           cat.pos = c(320, 25),
                           cat.dist = .05) 

both1sm_same= both1sm %>% filter(ChimpPAS==HumanPAS)
nrow(both1sm_same)

[1] 3542

both1sm_diff= both1sm %>% filter(ChimpPAS!=HumanPAS)
nrow(both1sm_diff)

[1] 272

location for same:

same1=ggplot(both1sm_same,aes(x=ChimpLoc,fill=ChimpLoc)) +geom_bar(stat = "count") +scale_fill_brewer(palette = "Dark2")+ labs(title="Matched Gene Matched PAS .1", y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
same1

both1sm_diff_g= both1sm_diff %>% select(gene, HumanLoc, ChimpLoc) %>% gather('Species', 'Loc', -gene)
diffDom1=ggplot(both1sm_diff_g, aes(x=Loc, fill=Species))+ geom_bar(stat="count",position = "dodge") +scale_fill_brewer(palette = "Dark2")+ labs(y='PAS', title="Location for Different Dominant PAS at 10% difference") +labs(y='Genes', title="Different Dominant PAS: 0.1",x="") +theme(axis.text.x = element_text(angle = 90),legend.position = "none")
diffDom1

ggplot(BothDom1, aes(x=nPAS, fill=set)) + geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="Number of PAS per gene with .1 difference",y="genes")

HumanDom1_smLab= HumanDom1 %>% anti_join(ChimpDom1,by = "gene") %>% mutate(Set="Human")
ChimpDom1_smLab=  ChimpDom1 %>% anti_join(HumanDom1,by = "gene") %>% mutate(Set="Chimp")
BothDom1_smLab=HumanDom1_smLab %>% bind_rows(ChimpDom1_smLab)
diffgenes1=ggplot(BothDom1_smLab,aes(x=loc, fill=Set))+ geom_bar(stat="count", position = "dodge") + scale_fill_brewer(palette = "Dark2") +  labs(title="Non Matched: 0.1", y="genes",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")
diffgenes1

BothDom1_prop= BothDom1 %>% group_by(set, loc) %>% summarise(nLoc=n()) %>% ungroup() %>% group_by(set) %>% mutate(nSet=sum(nLoc), prop=nLoc/nSet)

proploc1=ggplot(BothDom1_prop, aes(x=loc,by=set, fill=set,y=prop)) + geom_bar(stat="identity",position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.1",y="Proportion",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")

BothDom1_smLab_prop=BothDom1_smLab%>% group_by(set, loc) %>% summarise(nLoc=n()) %>% ungroup() %>% group_by(set) %>% mutate(nSet=sum(nLoc), prop=nLoc/nSet)
propDiff1=ggplot(BothDom1_smLab_prop, aes(x=loc,by=set, fill=set,y=prop)) + geom_bar(stat="identity",position = "dodge") + scale_fill_brewer(palette = "Dark2") + labs(title="0.1: Different Genes",y="Proportion",x="")+theme(axis.text.x = element_text(angle = 90),legend.position = "none")