一键运行
可以一步执行整个功能模块
runDEG(
obj,
dir = ".",
prefix = "2-runDEG",
parallel = TRUE,
qc = TRUE
)
模块分解运行
进行差异分析
degResolve(object, dir = ".",
prefix = "2-DEG",
parallel = FALSE,
qc = TRUE)
上下调分组
degGroup(obj)
结果整理
degSummary(
obj,
dir = ".",
prefix = "2-runDEG",
PointVolcanoParam = list(gene = 10, light = NULL, light_color = "#24ac56",
light_label_color = "#24ac56", expend = c(0.12, 0.12))
)
该模块衍生可视化工具
火山图
PointVolcano(
object,
which,
category = "H",
gene,
light = NULL,
light_color = "#24ac56",
light_label_color = "#24ac56",
expend = c(0.12, 0.12)
)
top 差异基因的表达量热图
DEGtopHeatmap(
object,
which,
top = 50,
filename = NA,
show_gene = TRUE,
palette = RColorBrewer::brewer.pal(3, "Set2")[1:2],
...
)
多种方法的差异基因 Venn 图
## venn
## check deg results
test <- deg_here(data_deg)
ok <- names(test)[which(test == TRUE)]
## except merge
main <- setdiff(ok,"merge")
index <- c(setdiff(label(data_deg),label_ns(data_deg)),"diff")
## 提取差异基因
geneSets <- lapply(main, function(x){
geneSymbol_list <- hyper_GS(object = data_deg,which = x,type = "SYMBOL")
})
names(geneSets) <- main
## 创建绘图数据
geneSets_ls <- list()
for (i in index){
tmp <- lapply(main, function(x){geneSets[[x]][[i]]})
names(tmp) <- main
geneSets_ls[[i]] <- tmp
}
## 绘图
p_list <- lapply(seq_along(geneSets_ls), function(x){
DEGvenn(geneSets = geneSets_ls[[x]])
})
## 拼图
p_l <- aplot::plot_list(gglist = p_list,labels = index)
## 存图
venn_file = "vennplot.pdf"
ggplot2::ggsave(filename = venn_file,plot = p_l,device = cairo_pdf,width = 4.5*length(index),height = 4.5)