R语言实现蛋白质示意图绘制

BiocManager::install("drawProteins")

##Uniprot数据的下载
drawProteins::get_features("Q04206")-> rel_json
 
##数据格式化处理
drawProteins::feature_to_dataframe(rel_json)-> rel_data

##绘制结构图
draw_canvas(rel_data)-> p
p <-draw_chains(p, rel_data)
p <-draw_domains(p, rel_data)

##去除结构图的背景
library(ggplot2)
p <- p +theme_bw(base_size = 20) + # white background
    theme(panel.grid.minor=element_blank(),
        panel.grid.major=element_blank()) +
    theme(axis.ticks = element_blank(),
        axis.text.y = element_blank()) +
theme(panel.border = element_blank())

##添加转录激活域

draw_regions(p, rel_data)

##motif和核定位序列绘制
draw_motif(p, rel_data)

##磷酸位点的标注

draw_phospho(p, rel_data, size = 8)

##完整的信息展示
draw_canvas(rel_data) -> p
p <- draw_chains(p, rel_data)
p <- draw_domains(p, rel_data)
p <- draw_regions(p, rel_data)
p <- draw_motif(p, rel_data)
p <- draw_phospho(p, rel_data, size = 8)
 
# white backgnd & change text size
p <- p + theme_bw(base_size = 20) +
   theme(panel.grid.minor=element_blank(),
       panel.grid.major=element_blank()) +
    theme(axis.ticks =element_blank(),
        axis.text.y =element_blank()) +
    theme(panel.border =element_blank())
##add title
rel_subtitle <- paste0("circles = phosphorylationsites\n",
                "RHD =Rel Homology Domain\nsource:Uniprot")
p <- p + labs(title = "Rel A/p65", subtitle = rel_subtitle)

##多个蛋白质域的绘制

prot_data <- drawProteins::get_features("Q04206 Q01201Q04864 P19838 Q00653")
prot_data <- drawProteins::feature_to_dataframe(prot_data)
   
p <- draw_canvas(prot_data)
p <- draw_chains(p, prot_data)
p <- draw_domains(p, prot_data)
p <- draw_repeat(p, prot_data)
p <- draw_motif(p, prot_data)
p <- draw_phospho(p, prot_data, size = 8)
 
# background and y-axis
p <- p + theme_bw(base_size = 20) + # white backgnd & changetext size
   theme(panel.grid.minor=element_blank(),
       panel.grid.major=element_blank()) +
    theme(axis.ticks =element_blank(),
        axis.text.y =element_blank()) +
    theme(panel.border =element_blank())
 
# add titles
rel_subtitle <- paste0("circles = phosphorylationsites\n",
                "RHD =Rel Homology Domain\nsource:Uniprot")
 
p <- p + labs(title = "Schematic of human NF-kappaBproteins",
                subtitle =rel_subtitle)
 
 
# move legend to top
p <- p + theme(legend.position="top") +labs(fill="")