Sequence logo
最后发布时间:2023-02-09 15:18:58
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CG、CHG 和 CHH 中甲基化 C 附近的 9bp 序列的序列特征分析
Logo plots of the sequences proximal to sites of CG, CHG, and CHH DNA methylation in each sequence context.
方式一
library(seqLogo)
mFile <- system.file("extdata/pwm1", package="seqLogo")
m <- read.table(mFile)
p <- makePWM(m)
png(file="a.png")
seqLogo(p, ic.scale=FALSE)
dev.off()
| V1 | V2 | V3 | V4 | V5 | V6 | V7 | V8 | |
|---|---|---|---|---|---|---|---|---|
| C | 0 | 0 | 0 | 0.3 | 0.2 | 0 | 0 | 0 |
| G | 0.8 | 0.2 | 0.8 | 0.3 | 0.4 | 0.2 | 0.8 | 0.2 |
| A | 0.2 | 0.8 | 0.2 | 0.4 | 0.3 | 0.8 | 0.2 | 0.8 |
| T | 0 | 0 | 0 | 0 | 0.1 | 0 | 0 | 0 |
https://bioconductor.org/packages/devel/bioc/vignettes/seqLogo/inst/doc/seqLogo.html
方式二
> seqs_dna$MA0001.1
[1] "CCATATATAG" "CCATATATAG" "CCATAAATAG" "CCATAAATAG" "CCATAAATAG"
[6] "CCATAAATAG" "CCATAAATAG" "CCATATATGG" "CCATATATGG" "CCAAATATAG"
[11] "CCAAATATAG" "CCAAATATAG" "CCATAAATGG" "CCATAAATGG" "CCATAAATGG"
[16] "CCATAAATGG" "CCAAAAATAG" "CCAAAAATAG" "CCAAAAATAG" "CCAAAAATAG"
[21] "CCAAAAATAG" "CCAAATATGG" "CCAAAAATGG" "CCAAAAATGG" "CCATTTATAG"
[26] "CCATTTATAG" "CCATTTATAG" "CCATTAATAG" "CCATTAATAG" "CCATTAATAG"
[31] "CCAATTATAG" "CCATTAATGG" "CCAATAATAG" "CCAATTATGG" "CCAAAATTAG"
[36] "CCAAAATTAG" "CCAAAATTAG" "CCACATATAG" "CCATTTTTAG" "CCATTTTTAG"
[41] "CCATTTTTAG" "CCATAAGTGG" "CTATATATAG" "CCATACATGG" "CTATAAATAG"
[46] "CTATAAATAG" "CCTAATATAG" "CCTAATATAG" "CCTAATATAG" "CCAAAACTAG"
[51] "CTAAATATAG" "CTAAATATAG" "CCATAAACAG" "CTAAAAATAG" "CTAAAAATAG"
[56] "CCTAAAATGG" "CCTAAAATGG" "CCAGATTTAG" "CCTTTTATAG" "CCTTTTATAG"
[61] "CCAAAAAAAG" "CCAAATAAGG" "CCAGAATTAG" "CCATTTCTGG" "CTAAATTTAG"
[66] "CCCGATATAG" "CCAAAAATAC" "CCATATTGGG" "CCGTTTTTAG" "CAATTTATAG"
[71] "CTAAAAGTAG" "CTAAAAGTAG" "CCATTTTAAG" "CCATTTTAAG" "CCATTTATGT"
[76] "CTGTAAATAG" "CCATTTTGGG" "CAATAATTAG" "CTCAAAATAG" "CCAATTTAGG"
[81] "CCAATTTAGG" "CCTAATACGG" "CTATATTAAG" "CTATAAATGT" "CCTTTTATGT"
[86] "CCCTTTTTCG" "CTAAAAGAAG" "CTATATTTGT" "CTATAATTGT" "CTACTTAAAG"
[91] "CCGAAAAATG" "CCTAAAGTGT" "CCTTTTCTAC" "CCCTCACAAG" "TAATTTCTCG"
[96] "GCACACAGAC" "TTAGGATTCG"
data(ggseqlogo_sample)
library(ggseqlogo)
library(ggplot2)
png(file="a.png")
ggplot() + geom_logo( seqs_dna$MA0001.1 ) + theme_logo()
dev.off()
https://omarwagih.github.io/ggseqlogo/
https://github.com/kkdey/Logolas
