written in front
The traditional volcano map can only show two sets of differences, but if we incorporate the idea of the Manhattan map into the volcano map, we can show multiple sets of differences in one volcano map. The idea comes from the Cell article.
Traditional heatmap:
Two types of volcano maps have been updated this time:
Clustered volcano map:
Only the difference between the two groups is made, but the OTUs with similar trends are clustered, and the differences of different clustering modules are displayed according to the categories. It is convenient for us to find a large class of modules with similar differences for subsequent analysis.
Multiple groups of volcano maps:
Since the traditional volcano map shows the difference between two groups, we adjust and display the results of the pairwise difference analysis of multiple groups into one picture, so as to better observe the differences between different groups.
Actual Combat - Multi-clustering Volcano Map
library(ggClusterNet)
library(tidyverse)
library(phyloseq)
data(ps)
# 准备脚本-函数来自三人成师第一版，目前更新到第五版本
source("./EdgerSuper.R")
source("./EdgerSuper2.R")
source("./Mui.cluster-group.volcano.R")
# source("./Plot.CompareWithCK.R",encoding = "utf-8")
group1 = c("OE","WT")
b= data.frame(group1)
diffpath.1 = "./"
res = EdgerSuper(ps = ps,group = "Group",artGroup =b,
j = "OTU",
path = diffpath.1
)
head(res)
result = Mui.cluster.volcano(res = res)
p = result[[1]]
pp = result[[2]]
p
ggsave("cs.pdf",p,width = 8,height = 6)Actual Combat - Multiple Volcano Maps
#----多组火山图#------
diffpath.1 = "./result_cs"
dir.create(diffpath.1)
# 本-函数来自三人成师第一版，目前更新到第五版本
res = EdgerSuper2 (ps = ps,group = "Group",artGroup =NULL,
j = "OTU",
path = diffpath.1
)
head(res)
result = Mui.Group.volcano (res = res)
p = result[[2]]pggsave("cs4.pdf",p5,width = 12,height = 6,limitsize = FALSE)猜你喜欢iMeta简介 高引文章 高颜值绘图imageGP 网络分析iNAP
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