09 7 / 2014

Polar bear #polarbear (在 宜得利家居)

Polar bear #polarbear (在 宜得利家居)

28 6 / 2014

by Studio English

by Studio English

24 6 / 2014

勇於嘗試 #化學芒果霜淇淋 🍦🍦 (在 全家便利商店興安店)

勇於嘗試 #化學芒果霜淇淋 🍦🍦 (在 全家便利商店興安店)

24 6 / 2014

4ub:

Show individ variation after ANNOWAR
After exome sequencing, variant calling and annotation there is a need to show variation. Here is an example - we can see stops, synonymous and non synonymous variants and their population frequencies if they are. Frequencies are getting higher from center to border.
Here is some R code:
## genomic ranges and circos
library("BSgenome.Hsapiens.UCSC.hg19")
library('ggbio')
seqlengths(Hsapiens)[1:25]
names(seqlengths(Hsapiens)[1:25])
ideo19<-GRanges(seqnames = names(seqlengths(Hsapiens)[1:24]), ranges = IRanges(start=1, width = seqlengths(Hsapiens)[1:24]))
seqlevels(ideo19)<-names(seqlengths(Hsapiens)[1:24])
seqlengths(ideo19)<-seqlengths(Hsapiens)[1:24]

nonsyn<-GRanges(seqnames=annovar$Chr[annovar$ExonicFunc =='nonsynonymous SNV'],ranges=IRanges(start=annovar$Start[annovar$ExonicFunc =='nonsynonymous SNV'],width=1),strand='+',freq=annovar$ESP5400_ALL[annovar$ExonicFunc =='nonsynonymous SNV'],seqlengths=seqlengths(Hsapiens)[1:24])

syn<-GRanges(seqnames=annovar$Chr[annovar$ExonicFunc =='synonymous SNV'],ranges=IRanges(start=annovar$Start[annovar$ExonicFunc =='synonymous SNV'],width=1),strand='+',freq=annovar$ESP5400_ALL[annovar$ExonicFunc =='synonymous SNV'],seqlengths=seqlengths(Hsapiens)[1:24])
                  
st<-GRanges(seqnames=annovar$Chr[annovar$ExonicFunc =='stopgain SNV'],ranges=IRanges(start=annovar$Start[annovar$ExonicFunc =='stopgain SNV'],width=1),strand='+',freq=annovar$ESP5400_ALL[annovar$ExonicFunc =='stopgain SNV'],seqlengths=seqlengths(Hsapiens)[1:24])

ggplot() + layout_circle(ideo19, geom = "ideo", fill = "gray70", radius = 39, trackWidth = 2) + layout_circle(ideo19, geom = "text", aes(label = seqnames), vjust = 0, radius = 40, trackWidth = 5,size = 5) + layout_circle(nonsyn, geom= 'point',size=1, aes(x=start,y=freq,color='Nonsynonimous'),radius = 29, trackWidth = 10,size = 15,grid=T,grid.background='white',grid.line='black',grid.n=3) + layout_circle(syn, geom= 'point',size=1, aes(x=start,y=freq,color='Synonymous'),radius = 19, trackWidth = 10,size = 15,grid=T,grid.background='white',grid.line='black',grid.n=3) + layout_circle(st, geom= 'point',size=3, aes(x=start,y=freq,color='Stopgain'),radius = 9, trackWidth = 10,size = 15,grid=T,grid.background='white',grid.line='black',grid.n=3) + ggtitle("Variation")

4ub:

Show individ variation after ANNOWAR

After exome sequencing, variant calling and annotation there is a need to show variation. Here is an example - we can see stops, synonymous and non synonymous variants and their population frequencies if they are. Frequencies are getting higher from center to border. Here is some R code:

## genomic ranges and circos
library("BSgenome.Hsapiens.UCSC.hg19")
library('ggbio')
seqlengths(Hsapiens)[1:25]
names(seqlengths(Hsapiens)[1:25])
ideo19<-GRanges(seqnames = names(seqlengths(Hsapiens)[1:24]), ranges = IRanges(start=1, width = seqlengths(Hsapiens)[1:24]))
seqlevels(ideo19)<-names(seqlengths(Hsapiens)[1:24])
seqlengths(ideo19)<-seqlengths(Hsapiens)[1:24]

nonsyn<-GRanges(seqnames=annovar$Chr[annovar$ExonicFunc =='nonsynonymous SNV'],ranges=IRanges(start=annovar$Start[annovar$ExonicFunc =='nonsynonymous SNV'],width=1),strand='+',freq=annovar$ESP5400_ALL[annovar$ExonicFunc =='nonsynonymous SNV'],seqlengths=seqlengths(Hsapiens)[1:24])

syn<-GRanges(seqnames=annovar$Chr[annovar$ExonicFunc =='synonymous SNV'],ranges=IRanges(start=annovar$Start[annovar$ExonicFunc =='synonymous SNV'],width=1),strand='+',freq=annovar$ESP5400_ALL[annovar$ExonicFunc =='synonymous SNV'],seqlengths=seqlengths(Hsapiens)[1:24])
                  
st<-GRanges(seqnames=annovar$Chr[annovar$ExonicFunc =='stopgain SNV'],ranges=IRanges(start=annovar$Start[annovar$ExonicFunc =='stopgain SNV'],width=1),strand='+',freq=annovar$ESP5400_ALL[annovar$ExonicFunc =='stopgain SNV'],seqlengths=seqlengths(Hsapiens)[1:24])

ggplot() + layout_circle(ideo19, geom = "ideo", fill = "gray70", radius = 39, trackWidth = 2) + layout_circle(ideo19, geom = "text", aes(label = seqnames), vjust = 0, radius = 40, trackWidth = 5,size = 5) + layout_circle(nonsyn, geom= 'point',size=1, aes(x=start,y=freq,color='Nonsynonimous'),radius = 29, trackWidth = 10,size = 15,grid=T,grid.background='white',grid.line='black',grid.n=3) + layout_circle(syn, geom= 'point',size=1, aes(x=start,y=freq,color='Synonymous'),radius = 19, trackWidth = 10,size = 15,grid=T,grid.background='white',grid.line='black',grid.n=3) + layout_circle(st, geom= 'point',size=3, aes(x=start,y=freq,color='Stopgain'),radius = 9, trackWidth = 10,size = 15,grid=T,grid.background='white',grid.line='black',grid.n=3) + ggtitle("Variation")

20 6 / 2014

Go Go @shawn1002 🍻🍻 (在 DNArails HQ 1.0)

Go Go @shawn1002 🍻🍻 (在 DNArails HQ 1.0)

20 6 / 2014

是有多好吃,來試試!#nagi #ramen (在 ラーメン凪ramen Nagi 台灣(西門店ximen))

是有多好吃,來試試!#nagi #ramen (在 ラーメン凪ramen Nagi 台灣(西門店ximen))

18 6 / 2014

#BJ4 #Hoegaarden (在 DNArails HQ 1.0)

#BJ4 #Hoegaarden (在 DNArails HQ 1.0)

18 6 / 2014

I&#8217;m wired! #dnarails (在 DNArails HQ 1.0)

I’m wired! #dnarails (在 DNArails HQ 1.0)

16 6 / 2014

阿根廷與波赫之戰,看完大家都倒了 #2014worldcup #brasil2014 #fifaworldcup (在 DNArails HQ 1.0)

阿根廷與波赫之戰,看完大家都倒了 #2014worldcup #brasil2014 #fifaworldcup (在 DNArails HQ 1.0)

16 6 / 2014

2014生醫生農選秀賽,今年用公司名義再挑戰一次 #garageplus #epoch #生醫生農選秀 (在 Garage+ Campus)

2014生醫生農選秀賽,今年用公司名義再挑戰一次 #garageplus #epoch #生醫生農選秀 (在 Garage+ Campus)

13 6 / 2014

#chochoco 喜餅 ☕️ (在 DNArails HQ 1.0)

#chochoco 喜餅 ☕️ (在 DNArails HQ 1.0)

13 6 / 2014

越積越多,什麼時候開來喝啊 (在 DNArails HQ 1.0)

越積越多,什麼時候開來喝啊 (在 DNArails HQ 1.0)

13 6 / 2014

Michael 你醉了嗎! (在 DNArails HQ 1.0)

Michael 你醉了嗎! (在 DNArails HQ 1.0)

13 6 / 2014

超爽der!#tarami #果凍 (在 DNArails HQ 1.0)

超爽der!#tarami #果凍 (在 DNArails HQ 1.0)

12 6 / 2014

辦公室有維納斯女神啊!#venus (在 DNArails HQ 1.0)

辦公室有維納斯女神啊!#venus (在 DNArails HQ 1.0)