{"id":1544,"date":"2025-05-06T21:13:20","date_gmt":"2025-05-06T13:13:20","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=1544"},"modified":"2025-05-06T21:18:30","modified_gmt":"2025-05-06T13:18:30","slug":"%e8%bd%ac%e5%bd%95%e7%bb%84%e9%ab%98%e7%ba%a7%e7%bb%98%e5%9b%be-%e5%a4%9a%e7%bb%84%e5%b7%ae%e5%bc%82%e5%9f%ba%e5%9b%a0%e7%81%ab%e5%b1%b1%e5%9b%be","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2025\/05\/06\/%e8%bd%ac%e5%bd%95%e7%bb%84%e9%ab%98%e7%ba%a7%e7%bb%98%e5%9b%be-%e5%a4%9a%e7%bb%84%e5%b7%ae%e5%bc%82%e5%9f%ba%e5%9b%a0%e7%81%ab%e5%b1%b1%e5%9b%be\/","title":{"rendered":"\u8f6c\u5f55\u7ec4\u9ad8\u7ea7\u7ed8\u56fe-\u591a\u7ec4\u5dee\u5f02\u57fa\u56e0\u706b\u5c71\u56fe"},"content":{"rendered":"\t\t
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1. \u524d\u8a00<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t

\u6700\u8fd1\u770b\u5230\u4e86\u8bba\u6587\u4e2d\u90fd\u628a\u591a\u7ec4\u7684\u5dee\u5f02\u5206\u6790\u706b\u5c71\u56fe\u5206\u4e3a\u591a\u4e2a\u56fe\u5c55\u793a\uff0c\u867d\u7136\u6ca1\u4ec0\u4e48\u95ee\u9898\uff0c\u4f46\u662f\u611f\u89c9\u8ffd\u6c42\u9876\u520a\u8fd9\u6837\u7684\u8bdd\u6709\u4e9bLow\uff0c\u6240\u4ee5\u6765\u7ed8\u5236\u4e00\u4e2a\u591a\u7ec4\u7684\u5dee\u5f02\u57fa\u56e0\u706b\u5c71\u56fe\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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\n\t\t\t\t\t

2.\u8f93\u5165\u6587\u4ef6<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
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\n\n\n\n\t\n\n\t\n\t\n\t\n\t
SYMBOL<\/th>log2FoldChange<\/th>change<\/th>group<\/th>\n<\/tr>\n<\/thead>\n
SERPINE1<\/td>-1.102974389<\/td>Down<\/td>12h_vs_0h<\/td>\n<\/tr>\n
HSPA1A<\/td>0.87030297<\/td>Up<\/td>12h_vs_0h<\/td>\n<\/tr>\n
HSPA1B<\/td>0.883833938<\/td>Up<\/td>12h_vs_0h<\/td>\n<\/tr>\n
SOD2<\/td>-0.606522079<\/td>Down<\/td>12h_vs_0h<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t

3. \u7ed8\u56fe<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t

rm(list = ls())<\/p>

####—-load R Package—-####
library(tidyverse)
library(ggrepel)
library(ggfun)<\/p>

####—-load Data—-####
all_deg <- read.csv(file = “\u4f18\u5316\u540e\u7684\u8f93\u5165\u6587\u4ef6\/test.csv”)<\/p>

# ================================================
# \u65b0\u589e\uff1a\u5b9a\u4e49\u9700\u8981\u9ad8\u4eae\u7684\u57fa\u56e0\u5217\u8868\uff08\u66ff\u6362\u4e3a\u5b9e\u9645\u57fa\u56e0\u540d\u79f0\uff09
gene_list <- c(“HSPA1B”)
# ================================================<\/p>

####—-plot—-####
p <- ggplot(data = all_deg) +
# \u6b63\u5e38\u57fa\u56e0\uff08\u7070\u8272\u80cc\u666f\uff09
geom_jitter(data = all_deg %>%
dplyr::filter(change == “Normal”),
aes(x = group, y = log2FoldChange,
color = change, size = abs(log2FoldChange),
alpha = abs(log2FoldChange)),
width = 0.4) +
# \u5dee\u5f02\u57fa\u56e0\uff08\u4e0a\/\u4e0b\u8c03\uff09
geom_jitter(data = all_deg %>%
dplyr::filter(change != “Normal”),
aes(x = group, y = log2FoldChange,
color = change, size = abs(log2FoldChange),
alpha = abs(log2FoldChange)),
width = 0.4) +
# ================================================
# \u4fee\u6539\uff1a\u6839\u636e\u57fa\u56e0\u5217\u8868\u9ad8\u4eae\u6307\u5b9a\u57fa\u56e0\uff08\u539f\u7b5b\u9009\u524d15\u540d\u7684\u90e8\u5206\uff09
geom_jitter(
data = all_deg %>% dplyr::filter(SYMBOL %in% gene_list), # \u7b5b\u9009\u57fa\u56e0\u5217\u8868
aes(x = group, y = log2FoldChange, size = abs(log2FoldChange)),
width = 0.4,
shape = 21,
fill = “#dd1c77” # \u9ad8\u4eae\u989c\u8272
) +
geom_text_repel(
data = all_deg %>% dplyr::filter(SYMBOL %in% gene_list), # \u7b5b\u9009\u57fa\u56e0\u5217\u8868
aes(x = group, y = log2FoldChange, label = SYMBOL)
) +
# ================================================
# \u4ee5\u4e0b\u4ee3\u7801\u4fdd\u6301\u539f\u6837
geom_tile(aes(x = group, y = 0, fill = group), height = 0.4) +
geom_text(data = all_deg %>%
dplyr::select(group) %>%
dplyr::distinct(group, .keep_all = T),
aes(x = group, y = 0, label = group),
size = 6) +
geom_hline(yintercept = c(-log2(1.5), log2(1.5))) +
scale_y_continuous(limits = c(-5, 5)) +
scale_size(range = c(1,15)) +
scale_alpha(range = c(0.1, 1)) +
scale_color_manual(values = c(“Up” = “#f46d43”,
“Normal” = “#bdbdbd”,
“Down” = “#3288bd”)) +
scale_fill_manual(values = c(‘#8dd3c7′,’#ffffb3′,’#bebada’,’#fb8072′,’#80b1d3′)) +
theme_bw() +
theme(
axis.text = element_text(color = “#000000”, size = 12),
axis.title = element_text(color = “#000000”, size = 15),
panel.grid = element_blank(),
legend.background = element_roundrect(color = “#969696”)
)<\/p>

# \u4fdd\u5b58\u56fe\u7247
ggsave(filename = “test.pdf”,
plot = p,
height = 12,
width = 12)<\/p>

####—-sessionInfo—-####
sessionInfo()<\/p>

# \u4fdd\u5b58\u6570\u636e\uff08\u53ef\u9009\uff09
write.csv(x = all_deg, file = “test.csv”, row.names = FALSE)<\/p>

# \u8bbe\u7f6e\u5de5\u4f5c\u8def\u5f84\uff08\u6839\u636e\u5b9e\u9645\u8def\u5f84\u4fee\u6539\uff09
setwd(“F:\/\u6a21\u4eff\u4e2d\u53ef\u89c6\u5316\/…”)<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t

4. \u7ed3\u679c<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\"\"\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"

1. \u524d\u8a00 \u6700\u8fd1\u770b\u5230\u4e86\u8bba\u6587\u4e2d\u90fd\u628a\u591a\u7ec4\u7684\u5dee\u5f02\u5206\u6790\u706b\u5c71\u56fe\u5206\u4e3a\u591a\u4e2a\u56fe\u5c55\u793a\uff0c\u867d\u7136\u6ca1\u4ec0\u4e48\u95ee\u9898\uff0c\u4f46\u662f\u611f\u89c9\u8ffd\u6c42\u9876\u520a\u8fd9\u6837\u7684\u8bdd\u6709 … \u9605\u8bfb\u66f4\u591a<\/a><\/p>\n","protected":false},"author":1,"featured_media":1546,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_crdt_document":"","footnotes":""},"categories":[9],"tags":[],"class_list":["post-1544","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-9"],"acf":[],"yoast_head":"\n\u8f6c\u5f55\u7ec4\u9ad8\u7ea7\u7ed8\u56fe-\u591a\u7ec4\u5dee\u5f02\u57fa\u56e0\u706b\u5c71\u56fe - \u5c0f\u9a6c\u751f\u4fe1\u65e5\u8bb0<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"http:\/\/www.majunpeng.com\/index.php\/2025\/05\/06\/\u8f6c\u5f55\u7ec4\u9ad8\u7ea7\u7ed8\u56fe-\u591a\u7ec4\u5dee\u5f02\u57fa\u56e0\u706b\u5c71\u56fe\/\" \/>\n<meta property=\"og:locale\" content=\"zh_CN\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"\u8f6c\u5f55\u7ec4\u9ad8\u7ea7\u7ed8\u56fe-\u591a\u7ec4\u5dee\u5f02\u57fa\u56e0\u706b\u5c71\u56fe - \u5c0f\u9a6c\u751f\u4fe1\u65e5\u8bb0\" \/>\n<meta property=\"og:description\" content=\"1. \u524d\u8a00 \u6700\u8fd1\u770b\u5230\u4e86\u8bba\u6587\u4e2d\u90fd\u628a\u591a\u7ec4\u7684\u5dee\u5f02\u5206\u6790\u706b\u5c71\u56fe\u5206\u4e3a\u591a\u4e2a\u56fe\u5c55\u793a\uff0c\u867d\u7136\u6ca1\u4ec0\u4e48\u95ee\u9898\uff0c\u4f46\u662f\u611f\u89c9\u8ffd\u6c42\u9876\u520a\u8fd9\u6837\u7684\u8bdd\u6709 ... \u9605\u8bfb\u66f4\u591a\" \/>\n<meta property=\"og:url\" content=\"http:\/\/www.majunpeng.com\/index.php\/2025\/05\/06\/\u8f6c\u5f55\u7ec4\u9ad8\u7ea7\u7ed8\u56fe-\u591a\u7ec4\u5dee\u5f02\u57fa\u56e0\u706b\u5c71\u56fe\/\" \/>\n<meta property=\"og:site_name\" content=\"\u5c0f\u9a6c\u751f\u4fe1\u65e5\u8bb0\" \/>\n<meta property=\"article:published_time\" content=\"2025-05-06T13:13:20+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2025-05-06T13:18:30+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/05\/test_1-scaled.png\" \/>\n\t<meta property=\"og:image:width\" content=\"2560\" \/>\n\t<meta property=\"og:image:height\" content=\"2560\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/png\" \/>\n<meta name=\"author\" content=\"majunpeng\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"\u4f5c\u8005\" \/>\n\t<meta name=\"twitter:data1\" content=\"majunpeng\" \/>\n\t<meta name=\"twitter:label2\" 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