PAS descriptive plots

Last updated: 2019-09-04

Checks: 6 1

Knit directory: apaQTL/analysis/

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Unstaged changes:
    Modified:   analysis/NuclearSpecAPAqtl.Rmd
    Modified:   analysis/PrematureTermQTL.Rmd
    Modified:   analysis/Readdistagainstfeatures.Rmd
    Modified:   analysis/compareAnnotatedpas.Rmd
    Modified:   analysis/overlapapaqtlsandeqtls.Rmd
    Modified:   analysis/rerunQTL_changePC.Rmd
    Modified:   analysis/version15bpfilter.Rmd
    Modified:   code/BothFracDTPlotGeneRegions.sh
    Modified:   code/Snakefile
    Modified:   code/SnakefilefiltPAS
    Modified:   code/apaQTLCorrectPvalMakeQQ.R
    Modified:   code/apaQTL_Nominal.sh
    Modified:   code/apaQTL_permuted.sh
    Modified:   code/apaQTLsnake.err
    Modified:   code/bam2bw.sh
    Modified:   code/bed2saf.py
    Modified:   code/cluster.json
    Modified:   code/clusterfiltPAS.json
    Modified:   code/config.yaml
    Modified:   code/environment.yaml
    Modified:   code/makePheno.py
    Modified:   code/mergeAllBam.sh
    Modified:   code/mergeByFracBam.sh
    Modified:   code/mergePeaks.sh
    Modified:   code/peakFC.sh
    Modified:   code/snakemake.batch
    Modified:   code/snakemakePAS.batch
    Modified:   code/snakemakefiltPAS.batch
    Modified:   code/submit-snakemake.sh
    Modified:   code/submit-snakemakePAS.sh
    Modified:   code/submit-snakemakefiltPAS.sh
    Deleted:    code/test.txt
    Modified:   data/MetaDataSequencing.txt
    Deleted:    docs/figure/PASdescriptiveplots.Rmd/figure1D-1.pdf
    Deleted:    reads_graphs.Rmd

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File	Version	Author	Date	Message
Rmd	5984fad	brimittleman	2019-09-04	update for new filter condition
html	1419181	brimittleman	2019-08-01	Build site.
Rmd	a66cd73	brimittleman	2019-08-01	fig1D pdf
html	dc5e7d0	brimittleman	2019-07-16	Build site.
Rmd	66c1c27	brimittleman	2019-07-16	remove white space between bars
html	96d85de	brimittleman	2019-07-07	Build site.
html	b6aa8cb	brimittleman	2019-07-02	Build site.
Rmd	d30bbd0	brimittleman	2019-07-02	use only protien coding
html	b3cbd22	brimittleman	2019-06-21	Build site.
Rmd	d11ce2b	brimittleman	2019-06-21	fix plots
html	660979c	brimittleman	2019-06-13	Build site.
Rmd	02b669e	brimittleman	2019-06-13	fix big bug
html	0dbb65b	brimittleman	2019-05-22	Build site.
Rmd	d3df9c3	brimittleman	2019-05-22	fix plots
html	6af55a2	brimittleman	2019-05-21	Build site.
Rmd	2fd13bb	brimittleman	2019-05-21	add location plots
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html	1fb7086	brimittleman	2019-04-23	Build site.

In this analysis I will create discriptive plots for the PAS identified in the 54 LCLs.

library(workflowr)

This is workflowr version 1.4.0
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()

library(reshape2)


Attaching package: 'reshape2'

The following object is masked from 'package:tidyr':

    smiths

library(cowplot)


Attaching package: 'cowplot'

The following object is masked from 'package:ggplot2':

    ggsave

Peaks per gene:

I want to plot how many genes have 0, 1, 2 and more than 2 PAS in the set. I need to join my PAS with the annotation to find out how many genes have 0 PAS.

pas=read.table("../data/PAS/APAPAS_GeneLocAnno.5perc.bed", header = F, stringsAsFactors = F, col.names = c("Chr", "start", "end", "PeakID", "score", "strand")) %>% separate(PeakID, into=c("peaknum", "geneAnno"), sep=":") %>% separate(geneAnno, into=c("Gene", "Loc"),sep="_")
pasbygene= pas %>% group_by(Gene) %>% summarise(PAS=n())

annotation=read.table("../../genome_anotation_data/refseq.ProteinCoding.bed", col.names = c("chr", "start", "end", "Gene", "score", "strand")) %>% dplyr::select(Gene) %>% unique()

PASallgene=annotation %>% left_join(pasbygene, by="Gene") %>% replace_na(list(PAS=0))

Warning: Column `Gene` joining factor and character vector, coercing into
character vector

#group with 0,1,2,more than 2
PASallgene_grouped=PASallgene %>% mutate(Zero=ifelse(PAS==0,1, 0), One=ifelse(PAS==1,1,0), Multiple=ifelse(PAS>1,1,0))

Plot this:

Genes=c(sum(PASallgene_grouped$Zero),sum(PASallgene_grouped$One),sum(PASallgene_grouped$Multiple))
PAS=c("Zero", "One", "Multiple")
AllPAS=c(sum(PASallgene_grouped$Zero),sum(PASallgene_grouped$One),sum(PASallgene_grouped$Multiple))
GenebyPAS=as.data.frame(cbind(PAS,AllPAS))
GenebyPAS$AllPAS=as.numeric(as.character(GenebyPAS$AllPAS))

allPASplot=ggplot(GenebyPAS, aes(x="",y=AllPAS, fill=PAS)) + geom_bar(stat="identity", width=.5) + scale_fill_brewer(palette="GnBu") + labs(title="Identified PAS per Gene", y="Genes",x="All Indentified PAS")
allPASplot

Version	Author	Date
b6aa8cb	brimittleman	2019-07-02
660979c	brimittleman	2019-06-13
74a1372	brimittleman	2019-04-24
012892d	brimittleman	2019-04-24
1fb7086	brimittleman	2019-04-23

ggsave(allPASplot, file="../output/GeneswithAPApotentialAllPAS.png", width=3, height=5)

Subset and get stats for UTR

pasUTR=pas %>% filter(Loc=="utr3") %>% group_by(Gene) %>% summarise(PAS=n())

pasUTR_allgene=annotation %>% full_join(pasUTR, by="Gene") %>% replace_na(list(PAS=0))

Warning: Column `Gene` joining factor and character vector, coercing into
character vector

PASUTRallgene_grouped=pasUTR_allgene %>% mutate(Zero=ifelse(PAS==0,1, 0), One=ifelse(PAS==1,1,0), Multiple=ifelse(PAS>1,1,0))


GenesUTR=c(sum(PASUTRallgene_grouped$Zero),sum(PASUTRallgene_grouped$One),sum(PASUTRallgene_grouped$Multiple))
UTR=c(sum(PASUTRallgene_grouped$Zero),sum(PASUTRallgene_grouped$One),sum(PASUTRallgene_grouped$Multiple))
GenebyPASUTR=as.data.frame(cbind(PAS,UTR))
GenebyPASUTR$UTR=as.numeric(as.character(GenebyPASUTR$UTR))

ggplot(GenebyPASUTR, aes(x="",y=UTR, fill=PAS)) + geom_bar(stat="identity")

Version	Author	Date
b6aa8cb	brimittleman	2019-07-02
660979c	brimittleman	2019-06-13
74a1372	brimittleman	2019-04-24
012892d	brimittleman	2019-04-24
1fb7086	brimittleman	2019-04-23

Subset and get stats for Intron

pasIntron=pas %>% filter(Loc=="intron" | Loc=='utr3') %>% group_by(Gene) %>% summarise(PAS=n())

pasIntron_allgene=annotation %>% full_join(pasIntron, by="Gene") %>% replace_na(list(PAS=0))

Warning: Column `Gene` joining factor and character vector, coercing into
character vector

pasIntronallgene_grouped=pasIntron_allgene %>% mutate(Zero=ifelse(PAS==0,1, 0), One=ifelse(PAS==1,1,0), Multiple=ifelse(PAS>1,1,0))


UTRandIntron=c(sum(pasIntronallgene_grouped$Zero),sum(pasIntronallgene_grouped$One),sum(pasIntronallgene_grouped$Multiple))
GenebyPASIntron=as.data.frame(cbind(PAS,UTRandIntron))
GenebyPASIntron$UTRandIntron=as.numeric(as.character(GenebyPASIntron$UTRandIntron))

ggplot(GenebyPASIntron, aes(x="",y=UTRandIntron, fill=PAS)) + geom_bar(stat="identity")

Version	Author	Date
b6aa8cb	brimittleman	2019-07-02
660979c	brimittleman	2019-06-13
74a1372	brimittleman	2019-04-24
012892d	brimittleman	2019-04-24
1fb7086	brimittleman	2019-04-23

Make these side by side:

GenebyPASUTR_melt=melt(GenebyPASUTR, id.vars = "PAS", value.name = "Genes", variable.name = "Set")

GenebyPAS_melt=melt(GenebyPAS, id.vars = "PAS", value.name = "Genes", variable.name = "Set")

GenebyPASIntron_melt=melt(GenebyPASIntron, id.vars = "PAS", value.name = "Genes", variable.name = "Set")

GenebyPAStoplot=rbind(GenebyPAS_melt,GenebyPASUTR_melt,GenebyPASIntron_melt)

geneswithAPA=ggplot(GenebyPAStoplot, aes(x=Set,y=Genes, fill=PAS, by=Set)) + geom_bar(stat="identity")+ scale_fill_brewer(palette="YlGnBu") + labs(title="Genes with APA poential")

geneswithAPA

Version	Author	Date
b6aa8cb	brimittleman	2019-07-02
660979c	brimittleman	2019-06-13
74a1372	brimittleman	2019-04-24
012892d	brimittleman	2019-04-24
1fb7086	brimittleman	2019-04-23

ggsave(geneswithAPA, file="../output/GeneswithAPApotential.png")

Saving 7 x 5 in image

GenebyPAStoplot

       PAS          Set Genes
1     Zero       AllPAS  6550
2      One       AllPAS  4198
3 Multiple       AllPAS  8495
4     Zero          UTR  7463
5      One          UTR  7466
6 Multiple          UTR  5024
7     Zero UTRandIntron  6868
8      One UTRandIntron  5672
9 Multiple UTRandIntron  8015

Location of PAS

PAS_loc=pas %>% group_by(Loc) %>% summarise(nPAS=n())
loclabel=c("Coding", "Downstream", "Intronic", "3' UTR", "5' UTR")
PASLocPlot=ggplot(PAS_loc, aes(x=Loc, y=nPAS, fill=Loc)) + geom_bar(stat="identity",width=.5)+ scale_fill_brewer(palette = "YlGnBu") + labs(x="Gene location", y="Number of identified PAS", title="Location distribution for identified PAS") + theme(legend.position = "none")+ scale_x_discrete(labels= loclabel)+theme(axis.text.x = element_text(angle = 90, hjust = 1))
PASLocPlot

Version	Author	Date
660979c	brimittleman	2019-06-13
74a1372	brimittleman	2019-04-24
012892d	brimittleman	2019-04-24

ggsave(PASLocPlot, file="../output/PASlocation.png")

Saving 7 x 5 in image

Number of genes with apa by cutoff

I want to make a script that takes a cuttoff and tells me how many gens have 0,1, >1 PAS. This way I can put these together to make stacked barplots:

I can make the plot for total then again for nuclear.

The annotaiton is annotation:

totapaanno=read.table("../data/phenotype/APApeak_Phenotype_GeneLocAnno.Total.fc",header = T,stringsAsFactors = F) 
indiv=colnames(totapaanno)[2:53]
totapanum=read.table("../data/phenotype/APApeak_Phenotype_GeneLocAnno.Total.CountsOnlyNumeric",header = F, col.names = indiv) 
totapa_mean=rowMeans(totapanum)
totapaMeananno=as.data.frame(cbind(ID=totapaanno$chrom, meanUsage=totapa_mean))
totapaMeananno$meanUsage=as.numeric(as.character(totapaMeananno$meanUsage))
totapaMeananno$ID=as.character(totapaMeananno$ID)

write.table(totapaMeananno, file="../data/PAS/TotalPASMeanUsage.txt", col.names = T, row.names = F, quote=F,sep="\t")

genesbycuttoff_tot=function(fraction){
  totapaMeananno_filt=totapaMeananno %>% filter(meanUsage >=fraction) %>% separate(ID, into=c("chrom", "start","end", "peakID"),sep=":") %>% separate(peakID, into=c("Gene","loc", "strand", "peak"),sep="_") %>% group_by(Gene) %>% summarise(PAS=n())
  PASallgene=annotation %>% full_join(totapaMeananno_filt, by="Gene") %>% replace_na(list(PAS=0))
  PASallgene_cat=PASallgene %>% mutate(Category=ifelse(PAS==0,"Zero", ifelse(PAS==1, "One", "Multiple"))) %>% group_by(Category) %>% summarise(NPer=n())
return(PASallgene_cat$NPer)
}

#multiple, one, zero 
categories=c("Multiple_PAS", "One_PAS", "Zero_PAS")
FullDF=as.data.frame(cbind(categories))
cutoffs=seq(from=0, to=.5, by=.05)
for (val in cutoffs[1:10])
{
FullDF=cbind(FullDF,val=genesbycuttoff_tot(val))
}

Warning: Expected 4 pieces. Additional pieces discarded in 3 rows [12630,
12631, 12632].

Warning: Column `Gene` joining factor and character vector, coercing into
character vector

Warning: Expected 4 pieces. Additional pieces discarded in 3 rows [4597,
4598, 4599].

Warning: Column `Gene` joining factor and character vector, coercing into
character vector

Warning: Expected 4 pieces. Additional pieces discarded in 3 rows [3413,
3414, 3415].

Warning: Column `Gene` joining factor and character vector, coercing into
character vector

Warning: Expected 4 pieces. Additional pieces discarded in 2 rows [2856,
2857].

Warning: Column `Gene` joining factor and character vector, coercing into
character vector

Warning: Expected 4 pieces. Additional pieces discarded in 2 rows [2508,
2509].

Warning: Column `Gene` joining factor and character vector, coercing into
character vector

Warning: Expected 4 pieces. Additional pieces discarded in 1 rows [2223].

Warning: Column `Gene` joining factor and character vector, coercing into
character vector

Warning: Expected 4 pieces. Additional pieces discarded in 1 rows [1985].

Warning: Column `Gene` joining factor and character vector, coercing into
character vector

Warning: Expected 4 pieces. Additional pieces discarded in 1 rows [1789].

Warning: Column `Gene` joining factor and character vector, coercing into
character vector

Warning: Expected 4 pieces. Additional pieces discarded in 1 rows [1641].

Warning: Column `Gene` joining factor and character vector, coercing into
character vector

Warning: Expected 4 pieces. Additional pieces discarded in 1 rows [1520].

Warning: Column `Gene` joining factor and character vector, coercing into
character vector

colnames(FullDF)=c("Category",cutoffs[1:10])

Melt:

fullDF_melt=melt(FullDF,id.vars = "Category",variable.name = "Cutoff", value.name = "NGenes") %>% mutate(propGene=NGenes/nrow(annotation))


totalPropgenes=ggplot(fullDF_melt,aes(x=Cutoff, y=propGene, by=Category, fill=Category)) + geom_bar(width=1, stat="identity") + labs(title="Total Fraction", y="Proportion of 19,243 genes", x="Usage Filter cutoff") + theme(axis.text.x = element_text(angle = 90, hjust =1)) + scale_x_discrete(name="Usage Filter cutoff", breaks=c("0","0.1","0.2", "0.3", "0.4","0.5"))+  theme(text = element_text(size=16),legend.position = "bottom")+scale_fill_brewer(name = "", labels = c("Multiple PAS", "One PAS", "Zero Identified PAS"),palette="Dark2")

totalPropgenes

Version	Author	Date
dc5e7d0	brimittleman	2019-07-16
96d85de	brimittleman	2019-07-07
b6aa8cb	brimittleman	2019-07-02
b3cbd22	brimittleman	2019-06-21
660979c	brimittleman	2019-06-13
0dbb65b	brimittleman	2019-05-22
a88eedf	brimittleman	2019-05-20

Nuclear:

nucapaanno=read.table("../data/phenotype/APApeak_Phenotype_GeneLocAnno.Nuclear.fc",header = T,stringsAsFactors = F) 

nucapanum=read.table("../data/phenotype/APApeak_Phenotype_GeneLocAnno.Nuclear.CountsOnlyNumeric",header = F, col.names = indiv) 
nucapa_mean=rowMeans(nucapanum)
nucapaMeananno=as.data.frame(cbind(ID=nucapaanno$chrom, meanUsage=nucapa_mean))
nucapaMeananno$meanUsage=as.numeric(as.character(nucapaMeananno$meanUsage))
nucapaMeananno$ID=as.character(nucapaMeananno$ID)
write.table(nucapaMeananno, file="../data/PAS/NuclearPASMeanUsage.txt", col.names = T, row.names = F, quote=F,sep="\t")

genesbycuttoff_nuc=function(fraction){
  nucapaMeananno_filt=nucapaMeananno %>% filter(meanUsage >=fraction) %>% separate(ID, into=c("chrom", "start","end", "peakID"),sep=":") %>% separate(peakID, into=c("Gene","loc", "strand", "peak"),sep="_") %>% group_by(Gene) %>% summarise(PAS=n())
  PASallgene=annotation %>% full_join(nucapaMeananno_filt, by="Gene") %>% replace_na(list(PAS=0))
  PASallgene_cat=PASallgene %>% mutate(Category=ifelse(PAS==0,"Zero", ifelse(PAS==1, "One", "Multiple"))) %>% group_by(Category) %>% summarise(NPer=n())
return(PASallgene_cat$NPer)
}

#multiple, one, zero 
FullDFNuc=as.data.frame(cbind(categories))
for (val in cutoffs[1:10])
{
FullDFNuc=cbind(FullDFNuc,val=genesbycuttoff_nuc(val))
}

Warning: Expected 4 pieces. Additional pieces discarded in 3 rows [12630,
12631, 12632].

Warning: Column `Gene` joining factor and character vector, coercing into
character vector

Warning: Expected 4 pieces. Additional pieces discarded in 3 rows [5138,
5139, 5140].

Warning: Column `Gene` joining factor and character vector, coercing into
character vector

Warning: Expected 4 pieces. Additional pieces discarded in 3 rows [3674,
3675, 3676].

Warning: Column `Gene` joining factor and character vector, coercing into
character vector

Warning: Expected 4 pieces. Additional pieces discarded in 3 rows [2980,
2981, 2982].

Warning: Column `Gene` joining factor and character vector, coercing into
character vector

Warning: Expected 4 pieces. Additional pieces discarded in 2 rows [2546,
2547].

Warning: Column `Gene` joining factor and character vector, coercing into
character vector

Warning: Expected 4 pieces. Additional pieces discarded in 1 rows [2259].

Warning: Column `Gene` joining factor and character vector, coercing into
character vector

Warning: Expected 4 pieces. Additional pieces discarded in 1 rows [2012].

Warning: Column `Gene` joining factor and character vector, coercing into
character vector

Warning: Expected 4 pieces. Additional pieces discarded in 1 rows [1804].

Warning: Column `Gene` joining factor and character vector, coercing into
character vector

Warning: Expected 4 pieces. Additional pieces discarded in 1 rows [1640].

Warning: Column `Gene` joining factor and character vector, coercing into
character vector

Warning: Expected 4 pieces. Additional pieces discarded in 1 rows [1500].

Warning: Column `Gene` joining factor and character vector, coercing into
character vector

colnames(FullDFNuc)=c("Category",cutoffs[1:10])

FullDFNuc_melt=melt(FullDFNuc,id.vars = "Category",variable.name = "Cutoff", value.name = "NGenes") %>% mutate(propGene=NGenes/nrow(annotation))

nuclearPropgenes=ggplot(FullDFNuc_melt,aes(x=Cutoff, y=propGene, by=Category, fill=Category)) + geom_bar( width=1,stat="identity")  + labs(title="Nuclear Fraction",y="Proportion of 19,243 genes", x="Usage Filter cutoff") + scale_x_discrete(name="Usage Filter cutoff", breaks=c("0","0.1","0.2", "0.3", "0.4","0.5")) +  theme(text = element_text(size=16), legend.position = "bottom")+ scale_fill_brewer(name = "", labels = c("Multiple PAS", "One PAS", "Zero Identified PAS"),palette="Dark2")

nuclearPropgenes

Version	Author	Date
1419181	brimittleman	2019-08-01
b6aa8cb	brimittleman	2019-07-02
b3cbd22	brimittleman	2019-06-21
660979c	brimittleman	2019-06-13
a88eedf	brimittleman	2019-05-20

title_theme <- ggdraw() +
  draw_label("Proportion of Genes by PAS identification",  x = 0.28, hjust = 0,size=20, fontface="bold")

withouttitle=plot_grid(totalPropgenes,nuclearPropgenes, rel_widths = c(1, 1))
plot_grid(title_theme,withouttitle,ncol = 1, rel_heights = c(0.2, 1))

Version	Author	Date
dc5e7d0	brimittleman	2019-07-16
96d85de	brimittleman	2019-07-07

Location of PAS by filter

I will make these plots but the categories will be location of the PAS.

locbycutoff_tot=function(fraction){
  totapaMeananno_filt=totapaMeananno %>% filter(meanUsage >=fraction) %>% separate(ID, into=c("chrom", "start","end", "peakID"),sep=":") %>% separate(peakID, into=c("Gene","loc", "strand", "peak"),sep="_") %>% group_by(loc) %>% summarise(PerLoc=n()) %>%filter(loc!= "008559")
return(totapaMeananno_filt$PerLoc)
}

locations=c("cds", "end", "intron", "utr3", "utr5")
FullDF_loc=as.data.frame(cbind(locations))
cutoffs=seq(from=0, to=.5, by=.05)
for (val in cutoffs[1:10])
{
FullDF_loc=cbind(FullDF_loc,val=locbycutoff_tot(val))
}

Warning: Expected 4 pieces. Additional pieces discarded in 3 rows [12630,
12631, 12632].

Warning: Expected 4 pieces. Additional pieces discarded in 3 rows [4597,
4598, 4599].

Warning: Expected 4 pieces. Additional pieces discarded in 3 rows [3413,
3414, 3415].

Warning: Expected 4 pieces. Additional pieces discarded in 2 rows [2856,
2857].

Warning: Expected 4 pieces. Additional pieces discarded in 2 rows [2508,
2509].

Warning: Expected 4 pieces. Additional pieces discarded in 1 rows [2223].

Warning: Expected 4 pieces. Additional pieces discarded in 1 rows [1985].

Warning: Expected 4 pieces. Additional pieces discarded in 1 rows [1789].

Warning: Expected 4 pieces. Additional pieces discarded in 1 rows [1641].

Warning: Expected 4 pieces. Additional pieces discarded in 1 rows [1520].

colnames(FullDF_loc)=c("Location",cutoffs[1:10])

Melt:

FullDF_loc_melt=melt(FullDF_loc,id.vars = "Location",variable.name = "Cutoff", value.name = "NPas") %>% group_by(Cutoff) %>%  mutate(propPAS=NPas/sum(NPas))

totplotloc=ggplot(FullDF_loc_melt,aes(x=Cutoff, y=propPAS, by=Location, fill=Location)) + geom_bar(width=1, stat="identity")  + labs(title="Total Fraction",y="Proportion of PAS", x="Usage Filter cutoff")+ theme(axis.text.x = element_text(angle = 90, hjust = 1)) + scale_x_discrete(name="Usage Filter cutoff", breaks=c("0","0.1","0.2", "0.3", "0.4","0.5"))+  theme(text = element_text(size=16), legend.position = "bottom")+ scale_fill_brewer(name = "", labels = c("Coding", "5KB downstread", "Intronic", "3' UTR", "5' UTR"),palette="Dark2")+guides(fill=guide_legend(nrow=2,byrow=TRUE))

Nuclear

locbycutoff_nuc=function(fraction){
nucapaMeananno_filt=nucapaMeananno %>% filter(meanUsage >=fraction) %>% separate(ID, into=c("chrom", "start","end", "peakID"),sep=":") %>% separate(peakID, into=c("Gene","loc", "strand", "peak"),sep="_") %>% group_by(loc) %>% summarise(PerLoc=n()) %>%filter(loc!= "008559")
return(nucapaMeananno_filt$PerLoc)
}

NucFullDF_loc=as.data.frame(cbind(locations))
cutoffs=seq(from=0, to=.5, by=.05)
for (val in cutoffs)
{
NucFullDF_loc=cbind(NucFullDF_loc,val=locbycutoff_nuc(val))
}

Warning: Expected 4 pieces. Additional pieces discarded in 3 rows [12630,
12631, 12632].

Warning: Expected 4 pieces. Additional pieces discarded in 3 rows [5138,
5139, 5140].

Warning: Expected 4 pieces. Additional pieces discarded in 3 rows [3674,
3675, 3676].

Warning: Expected 4 pieces. Additional pieces discarded in 3 rows [2980,
2981, 2982].

Warning: Expected 4 pieces. Additional pieces discarded in 2 rows [2546,
2547].

Warning: Expected 4 pieces. Additional pieces discarded in 1 rows [2259].

Warning: Expected 4 pieces. Additional pieces discarded in 1 rows [2012].

Warning: Expected 4 pieces. Additional pieces discarded in 1 rows [1804].

Warning: Expected 4 pieces. Additional pieces discarded in 1 rows [1640].

Warning: Expected 4 pieces. Additional pieces discarded in 1 rows [1500].

Warning: Expected 4 pieces. Additional pieces discarded in 1 rows [1359].

colnames(NucFullDF_loc)=c("Location",cutoffs)

Melt:

NucFullDF_locMelt=melt(NucFullDF_loc,id.vars = "Location",variable.name = "Cutoff", value.name = "NPas") %>% group_by(Cutoff) %>%  mutate(propPAS=NPas/sum(NPas))

nucplotloc=ggplot(NucFullDF_locMelt,aes(x=Cutoff, y=propPAS, by=Location, fill=Location)) + geom_bar(width = 1, stat="identity") + labs(title="Nuclear Fraction",y="Proportion of PAS", x="Usage Filter cutoff")+ theme(axis.text.x = element_text(angle = 90, hjust = 1)) + scale_x_discrete(name="Usage Filter cutoff", breaks=c("0","0.1","0.2", "0.3", "0.4","0.5"))+  theme(text = element_text(size=16), legend.position = "bottom", legend.box="horizontal")+ scale_fill_brewer(name = "", labels = c("Coding", "5KB downstread", "Intronic", "3' UTR", "5' UTR"),palette="Dark2") + guides(fill=guide_legend(nrow=2,byrow=TRUE))

nucplotloc

Version	Author	Date
dc5e7d0	brimittleman	2019-07-16
96d85de	brimittleman	2019-07-07
b3cbd22	brimittleman	2019-06-21
660979c	brimittleman	2019-06-13
0dbb65b	brimittleman	2019-05-22
6af55a2	brimittleman	2019-05-21

Plot next to eachother

title_loc <- ggdraw() +
  draw_label("Location of Identified PAS",  x = 0.35, hjust = 0,size=20, fontface="bold")


locPlots=plot_grid(totplotloc,nucplotloc)


locPlotswtitle=plot_grid(title_loc,locPlots,ncol = 1, rel_heights = c(0.2, 1))

locPlotswtitle

Version	Author	Date
dc5e7d0	brimittleman	2019-07-16
96d85de	brimittleman	2019-07-07

Nuclear specific PAS (only identified at 5% in nuclear)

NucPAS=read.table("../data/PAS/NuclearPASMeanUsage.txt",header =T,stringsAsFactors = F ) %>% filter(meanUsage > 0.05)
TotPAS=read.table("../data/PAS/TotalPASMeanUsage.txt",header=T, stringsAsFactors = F) %>% filter(meanUsage>0.05) 


nucspecific=NucPAS %>% anti_join(TotPAS, by="ID")

totspecific=TotPAS %>% anti_join(NucPAS, by="ID")

nucspecific_sep=nucspecific %>% separate(ID, into=c("chr", "start", "end", "geneID"), sep=":") %>% separate(geneID, into=c("gene","loc", "strand","pas"),sep="_")

ggplot(nucspecific_sep, aes(x=loc)) +geom_bar(stat="count")

Version	Author	Date
1419181	brimittleman	2019-08-01

summary(nucspecific_sep$meanUsage)

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
0.05019 0.05788 0.06942 0.08064 0.09135 0.42500

nucspecific_sep %>% group_by(loc) %>% summarise(nLoc=n())

# A tibble: 5 x 2
  loc     nLoc
  <chr>  <int>
1 cds      308
2 end      659
3 intron  5339
4 utr3     409
5 utr5      56

nucspecific_sep_int=nucspecific_sep %>% filter(loc=="intron") 
summary(nucspecific_sep_int$meanUsage)

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
0.05019 0.05885 0.07096 0.08190 0.09288 0.38154

totspecific_sep=totspecific %>% separate(ID, into=c("chr", "start", "end", "geneID"), sep=":") %>% separate(geneID, into=c("gene","loc", "strand","pas"),sep="_")

ggplot(totspecific_sep, aes(x=loc)) +geom_bar(stat="count")

Version	Author	Date
1419181	brimittleman	2019-08-01

summary(totspecific_sep$meanUsage)

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
0.05019 0.05577 0.06385 0.07341 0.07976 0.30769

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] cowplot_0.9.4   reshape2_1.4.3  forcats_0.3.0   stringr_1.3.1  
 [5] dplyr_0.8.0.1   purrr_0.3.2     readr_1.3.1     tidyr_0.8.3    
 [9] tibble_2.1.1    ggplot2_3.1.1   tidyverse_1.2.1 workflowr_1.4.0

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         utf8_1.1.4         rlang_0.4.0       
[10] pillar_1.3.1       glue_1.3.0         withr_2.1.2       
[13] RColorBrewer_1.1-2 modelr_0.1.2       readxl_1.1.0      
[16] plyr_1.8.4         munsell_0.5.0      gtable_0.2.0      
[19] cellranger_1.1.0   rvest_0.3.2        evaluate_0.12     
[22] labeling_0.3       knitr_1.20         fansi_0.4.0       
[25] highr_0.7          broom_0.5.1        Rcpp_1.0.0        
[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        magrittr_1.5      
[40] lazyeval_0.2.1     crayon_1.3.4       whisker_0.3-2     
[43] pkgconfig_2.0.2    xml2_1.2.0         lubridate_1.7.4   
[46] assertthat_0.2.0   rmarkdown_1.10     httr_1.3.1        
[49] rstudioapi_0.10    R6_2.3.0           nlme_3.1-137      
[52] git2r_0.25.2       compiler_3.5.1

PAS descriptive plots

Briana Mittleman

4/23/2019

Peaks per gene:

Subset and get stats for UTR

Subset and get stats for Intron

Location of PAS

Number of genes with apa by cutoff

Location of PAS by filter