写个包 metaplot 绘制 m6A peak 分布

引言
使用 Guitar 包绘制 m6A peak 分布时间耗时较长,且经常会发生一些搞不清楚的报错。在去年完成了基础框架的搭建,不如把这些代码打包一下。
安装

install.packages(“devtools”)

devtools::install_github(“junjunlab/metaplot”)

or

remotes::install_github(“junjunlab/metaplot”)
使用
使用 prepare_features来准备特征文件。
library(metaplot)
library(ggplot2)

test

feature_anno <- prepare_features(gtf_file = “Homo_sapiens.GRCh38.111.gtf.gz”)
metaPlot 来进行可视化。
meta <- metaPlot(bed_file = “ed.rep1_summits.bed”,
features_anno = feature_anno)
返回的结果包含了数据和图。
df_data <- meta$data

check

head(df_data,3)

type rel_pos group_names

1 CDS 1.422274 ed.rep1_summits.bed

2 UTR3 2.546256 ed.rep1_summits.bed

3 UTR3 2.365882 ed.rep1_summits.bed

图形:

plot

meta$plot

scale_region 归一化特征区域长度。
meta <- metaPlot(bed_file = “ed.rep1_summits.bed”,
features_anno = feature_anno,
scale_region = T)

meta$plot

多个样本展示。
meta <- metaPlot(bed_file = list(“ed.rep1_summits.bed”,
“pa.rep1_summits.bed”),
group_names = c(“ed”,”pa”),
features_anno = feature_anno)

meta$plot

分面展示。
meta <- metaPlot(bed_file = list(“ed.rep1_summits.bed”,
“pa.rep1_summits.bed”),
group_names = c(“ed”,”pa”),
features_anno = feature_anno,
facet = T)

meta$plot +
theme(strip.background = element_blank(),
strip.text = element_text(face = “bold”,size = rel(1.1)))

展示个 METTL3 敲除的看看。
feature_anno <- prepare_features(gtf_file = “hg19.ncbiRefSeq.gtf.gz”,
features_name = c(“5UTR”,”CDS”,”3UTR”))

meta <- metaPlot(bed_file = list(“GSE211588_control12_merge.narrowPeak”,
“GSE211588_koMETTL3_12_merge.narrowPeak”),
group_names = c(“Control”,”METTL3 KO”),
features_anno = feature_anno)

meta$plot

画个 m1A 和 m6A 的分布。
feature_anno <- prepare_features(gtf_file = “hg19.ncbiRefSeq.gtf.gz”,
features_name = c(“5UTR”,”CDS”,”3UTR”))

meta <- metaPlot(bed_file = list(“GSE102493_Ctrl_m6A.narrowPeak”,
“m1A-peaks.bed”),
group_names = c(“m6A”,”m1A”),
features_anno = feature_anno)

meta$plot

meta <- metaPlot(bed_file = list(“GSE102493_Ctrl_m6A.narrowPeak”,
“m1A-peaks.bed”),
group_names = c(“m6A”,”m1A”),
features_anno = feature_anno,
scale_region = T)

meta$plot

结尾
路漫漫其修远兮,吾将上下而求索。
欢迎加入生信交流群。加我微信我也拉你进 微信群聊 老俊俊生信交流群 (微信交流群需收取 20 元入群费用,一旦交费,拒不退还!(防止骗子和便于管理)) 。QQ 群可免费加入, 记得进群按格式修改备注哦。