install.packages(\u201cggplot2\u201d)<\/p>\n
install.packages(\u201ctidyverse\u201d)<\/p>\n
install.packages(\u201cdevtools\u201d)<\/p>\n
devtools::install_github(“Hy4m\/linkET”, force = TRUE)<\/p>\n
- \n
- \u8f7d\u5165\u9700\u8981\u7684R\u5305<\/li>\n<\/ol>\n
library(devtools)<\/p>\n
library(ggplot2)<\/p>\n
library(tidyverse)<\/p>\n
library(linkET)<\/p>\n
- \n
- \u4ee3\u7801\u5c55\u793a<\/li>\n<\/ol>\n
#\u8bfb\u53d6\u6570\u636e<\/p>\n
varechem<-read.csv(file=”varechem.csv”,row.names=1)<\/p>\n
![\"Dingtalk_20230218120002\"](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/dingtalk_20230218120002.jpeg?resize=640%2C154\")
<\/p>\nvarespec<-read.csv(file=”varespec.csv”,row.names=1)<\/p>\n
![\"Dingtalk_20230218120043\"](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/dingtalk_20230218120043.jpeg?resize=640%2C180\")
<\/p>\n# mantel test<\/p>\n
mantel <- mantel_test(varespec, varechem, # \u4f20\u5165\u9700\u8981\u68c0\u6d4b\u7684\u4e24\u4e2a\u77e9\u9635<\/p>\n
mantel_fun = ‘mantel’,<\/p>\n
spec_select = list(Spec01 = 1:7,<\/p>\n
Spec02 = 8:18,<\/p>\n
Spec03 = 19:37,<\/p>\n
Spec04 = 38:44)) %>%<\/p>\n
mutate(r = cut(r, breaks = c(-Inf, 0.2, 0.4, Inf),<\/p>\n
labels = c(“< 0.2”, “0.2 – 0.4”, “>= 0.4”)),<\/p>\n
p = cut(p, breaks = c(-Inf, 0.01, 0.05, Inf),<\/p>\n
labels = c(“< 0.01”, “0.01 – 0.05”, “>= 0.05”)))<\/p>\n
#\u8ba1\u7b97\u73af\u5883\u56e0\u5b50\u76f8\u5173\u6027\u7cfb\u6570\uff1a<\/p>\n
cor2 <- correlate(varechem)<\/p>\n
#\u7ed8\u5236\u76f8\u5173\u6027\u70ed\u56fe<\/p>\n
p1<- qcorrplot(cor2,<\/p>\n
grid_col = “grey50”,<\/p>\n
grid_size = 0.2,<\/p>\n
type = “upper”,<\/p>\n
diag = FALSE) +<\/p>\n
geom_square() +<\/p>\n
scale_fill_gradientn(colours = c(“#610214”, “#d05646”, “#f5f4f4”, “#569cc7”, “#0b3b71”<\/p>\n
),limits = c(-1, 1))<\/p>\n
#\u6dfb\u52a0\u663e\u8457\u6027\u6807\u7b7e\uff1a<\/p>\n
p2 <- p1+<\/p>\n
geom_mark(size = 4,<\/p>\n
only_mark = T,<\/p>\n
sig_level = c(0.05, 0.01, 0.001),<\/p>\n
sig_thres = 0.05,<\/p>\n
colour = ‘white’)<\/p>\n
#\u5728\u76f8\u5173\u6027\u70ed\u56fe\u4e0a\u6dfb\u52a0mantel\u8fde\u7ebf\uff1a<\/p>\n
p3<- p2+<\/p>\n
geom_couple(data = mantel,<\/p>\n
aes(colour = p, size = r),<\/p>\n
curvature = nice_curvature())+<\/p>\n
scale_size_manual(values = c(0.5, 1.2, 2)) + #\u8fde\u7ebf\u7c97\u7ec6<\/p>\n
scale_colour_manual(values = c(“#d85c01”, “#29d300”, “#A2A2A288”<\/p>\n
)) + #\u8fde\u7ebf\u914d\u8272<\/p>\n
#\u4fee\u6539\u56fe\u4f8b\uff1a<\/p>\n
guides(size = guide_legend(title = “Mantel r”,<\/p>\n
override.aes = list(colour = “grey35”),<\/p>\n
order = 2),<\/p>\n
colour = guide_legend(title = “Mantel p”,<\/p>\n
override.aes = list(size = 3),<\/p>\n
order = 1),<\/p>\n
fill = guide_colorbar(title = “Pearson r”, order = 3))<\/p>\n
![\"Dingtalk_20230218115112\"](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/dingtalk_20230218115112.jpeg?resize=640%2C613\")
<\/p>\n\u5c0f\u679c\u611f\u89c9\u6548\u679c\u8fd8\u4e0d\u9519\uff0c\u8be5\u5305\u4e0eggplot2\u8bed\u6cd5\u517c\u5bb9\uff0c\u5728\u7ed8\u56fe\u7684\u540c\u65f6\u53ef\u4ee5\u5b66\u4e60\u76f8\u5173\u7684ggplot2\u7684\u7ed8\u56fe\u77e5\u8bc6\uff0c\u503c\u5f97\u63a8\u8350\uff0c\u4eca\u5929\u5c0f\u679c\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\u4e86\uff0c\u6709\u9700\u8981\u7684\u53ef\u4ee5\u501f\u9274\u5b66\u4e60\uff0c\u4e0b\u671f\u518d\u89c1\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"
\u4eca\u5929\u5c0f\u679c\u60f3\u5b66\u4e60\u5229\u7528linkET\u5305\u6765\u7ed8\u5236mantel test\u76f8\u5173\u6027\u70ed\u56fe\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a \u5b89\u88c5\u9700\u8981\u7684R\u5305 insta […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29207"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=29207"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29207\/revisions"}],"predecessor-version":[{"id":29211,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29207\/revisions\/29211"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=29207"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=29207"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=29207"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}
- \u4ee3\u7801\u5c55\u793a<\/li>\n<\/ol>\n