{"id":1533,"date":"2025-04-23T21:11:53","date_gmt":"2025-04-23T13:11:53","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=1533"},"modified":"2025-04-23T21:19:38","modified_gmt":"2025-04-23T13:19:38","slug":"%e8%bd%ac%e5%bd%95%e7%bb%84%e9%ab%98%e7%ba%a7%e7%bb%98%e5%9b%be-%e5%b7%ae%e5%bc%82%e7%81%ab%e5%b1%b1%e5%9b%be%e8%bf%9b%e9%98%b6%e7%89%88","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2025\/04\/23\/%e8%bd%ac%e5%bd%95%e7%bb%84%e9%ab%98%e7%ba%a7%e7%bb%98%e5%9b%be-%e5%b7%ae%e5%bc%82%e7%81%ab%e5%b1%b1%e5%9b%be%e8%bf%9b%e9%98%b6%e7%89%88\/","title":{"rendered":"\u8f6c\u5f55\u7ec4\u9ad8\u7ea7\u7ed8\u56fe-\u5dee\u5f02\u706b\u5c71\u56fe\u8fdb\u9636\u7248"},"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
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\u6bd4\u8f83\u8f6c\u5f55\u7ec4\u662f\u6bcf\u4e2a\u751f\u4fe1\u4eba\u5165\u95e8\u7684\u7b2c\u4e00\u8bfe\uff0c\u4f46\u662f\u5728\u5982\u4eca\u5377\u79d1\u7814\u7ed8\u56fe\u7684\u5e74\u4ee3\uff0c\u4f20\u7edf\u7684\u56fe\u5df2\u7ecf\u4e0d\u80fd\u6ee1\u8db3\u9876\u520a\u7684\u9700\u6c42\u4e86\uff0c\u56e0\u6b64\u4eca\u5929\u51b3\u5b9a\u6765\u66f4\u65b0\u8f6c\u5f55\u7ec4\u7684\u9ad8\u7ea7\u7ed8\u56fe\u7279\u522b\u677f\u5757\uff0c\u5305\u62ec\u5dee\u5f02\u5206\u6790\u706b\u5c71\u56fe\uff0c\u529f\u80fd\u5bcc\u96c6\u5206\u6790\u56fe\u7b49\u7b49\u3002\u4eca\u5929\u6765\u8fdb\u884c\u8f6c\u5f55\u7ec4\u7684\u7b2c\u4e00\u5f20\u56fe\uff0c\u5dee\u5f02\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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2. \u8f93\u5165\u6587\u4ef6<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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xlsx\u683c\u5f0f\u7684\u77e9\u9635\u6587\u4ef6\uff0c1-5\u5217\u5206\u522b\u4e3a\uff0c\u57fa\u56e0ID\u3001\u57fa\u56e0\u540d\u3001Log2FC\u3001p adj\u548c\u5dee\u5f02\u7c7b\u578b\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\n\n\n\t\n\n\t\n\t\n\t\n\t
gene_id<\/th>GeneSymbol<\/th>log2FoldChange<\/th>padj<\/th>change<\/th>\n<\/tr>\n<\/thead>\n
ENSMUSG00000015340<\/td>Cybb<\/td>3.798364673<\/td>2.16399E-89<\/td>Up<\/td>\n<\/tr>\n
ENSMUSG00000026177<\/td>Slc11a1<\/td>3.926648494<\/td>5.57001E-88<\/td>Up<\/td>\n<\/tr>\n
ENSMUSG00000022586<\/td>Ly6i<\/td>7.112341161<\/td>7.2439E-80<\/td>Up<\/td>\n<\/tr>\n
ENSMUSG00000028581<\/td>Laptm5<\/td>3.228974154<\/td>1.32924E-78<\/td>Up<\/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
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3. \u7ed8\u56fe<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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####—-load R Package—-####<\/span><\/p>\n

library(tidyverse)
library(ggrepel)
library(ggfun)
library(grid)
library(readxl)<\/p>\n

####—-load Data—-####
df <- read_xlsx(path = “Input\/DEG.xlsx”)<\/p>\n

####—-MODIFIED PART START—-####
# \u9700\u8981\u9ad8\u4eae\u7684\u57fa\u56e0
gene_list <- c(“Laptm5”, “Eps8l2”)<\/p>\n

# \u7b5b\u9009\u76ee\u6807\u57fa\u56e0\u6570\u636e
target_genes <- df %>%
filter(GeneSymbol %in% gene_list) # \u7cbe\u786e\u5339\u914d\u57fa\u56e0\u540d\u79f0<\/p>\n

####—-Plot—-####
p <- ggplot(data=df,
aes(x=log2FoldChange,
y=-log10(padj)))+
geom_point(alpha=0.6, aes(size = -log10(padj), color=log2FoldChange))+
scale_color_gradientn(colours = c(“#2166ac”, “#4393c3″,”#ffffbf”, “#de77ae”, “#c51b7d”),
values = seq(0, 1, 0.2)) +
# \u9ad8\u4eae\u76ee\u6807\u57fa\u56e0\u70b9
geom_point(data = target_genes,
aes(x = log2FoldChange, y = -log10(padj), size = -log10(padj)),
shape = 21, color = “#000000”, fill = “#ff7f00”) +
# \u76ee\u6807\u57fa\u56e0\u6807\u7b7e
geom_text_repel(data = target_genes,
aes(x = log2FoldChange, y = -log10(padj), label = GeneSymbol),
nudge_x = 0.5,
box.padding = 0.5,
nudge_y = 1,
segment.curvature = -0.1,
segment.ncp = 3,
segment.angle = 20
) +
####—-MODIFIED PART END—-####
scale_size(range = c(2,10),
guide = guide_legend(override.aes = list(fill = NA)))+
scale_y_continuous(expand = expansion(mult = c(0.1, 0.2))) +
xlim(c(-6, 6)) +
geom_vline(xintercept = c(-1.5, 1.5), lty = 4, col = “black”, lwd = 0.8) +
geom_hline(yintercept = -log10(0.05), lty = 4, col = “black”, lwd = 0.8) +
xlab(‘log2 fold change’)+
ylab(‘-log10 padj’)+
theme_bw() +
theme(plot.title = element_text(size = 15,hjust = 0.5),
legend.background = element_roundrect(color = ‘#808080’,linetype = 1),
axis.text = element_text(size = 12.5, color = “#000000”),
axis.title = element_text(size = 15, color = “#000000”)
) +
coord_cartesian(clip = “off”) +
annotation_custom(
grob = grid::segmentsGrob(
y0 = unit(-10, “pt”),
y1 = unit(-10, “pt”),
arrow = arrow(angle = 45, length = unit(.2, “cm”), ends = “first”),
gp = grid::gpar(lwd = 3, col = “#74add1”)
),
xmin = -3,
xmax = -5,
ymin = 95,
ymax = 95
) +
annotation_custom(
grob = grid::textGrob(
label = “Down\\n(634)”, # \u4e0b\u8c03\u57fa\u56e0\u7684\u6570\u91cf
gp = grid::gpar(col = “#74add1”)
),
xmin = -3,
xmax = -5,
ymin = 97,
ymax = 97
) +
annotation_custom(
grob = grid::segmentsGrob(
y0 = unit(-10, “pt”),
y1 = unit(-10, “pt”),
arrow = arrow(angle = 45, length = unit(.2, “cm”), ends = “last”),
gp = grid::gpar(lwd = 3, col = “#d73027”)
),
xmin = 3,
xmax = 5,
ymin = 95,
ymax = 95
) +
annotation_custom(
grob = grid::textGrob(
label = “Up\\n(2075)”, # \u4e0a\u8c03\u7684\u57fa\u56e0\u6570\u91cf
gp = grid::gpar(col = “#d73027”)
),
xmin = 3,
xmax = 5,
ymin = 97,
ymax = 97
)<\/p>\n

ggsave(filename = “custom_volcano_plot_S2.pdf”,
plot = p,
height = 8,
width = 8.5)<\/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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4. \u7ed3\u679c<\/h2>\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\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 \u6bd4\u8f83\u8f6c\u5f55\u7ec4\u662f\u6bcf\u4e2a\u751f\u4fe1\u4eba\u5165\u95e8\u7684\u7b2c\u4e00\u8bfe\uff0c\u4f46\u662f\u5728\u5982\u4eca\u5377\u79d1\u7814\u7ed8\u56fe\u7684\u5e74\u4ee3\uff0c\u4f20\u7edf\u7684\u56fe\u5df2\u7ecf\u4e0d\u80fd\u6ee1\u8db3\u9876\u520a\u7684\u9700\u6c42\u4e86\uff0c … \u9605\u8bfb\u66f4\u591a<\/a><\/p>\n","protected":false},"author":1,"featured_media":1535,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_crdt_document":"","footnotes":""},"categories":[12,9],"tags":[],"class_list":["post-1533","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-12","category-9"],"acf":[],"yoast_head":"\n\u8f6c\u5f55\u7ec4\u9ad8\u7ea7\u7ed8\u56fe-\u5dee\u5f02\u706b\u5c71\u56fe\u8fdb\u9636\u7248 - \u5c0f\u9a6c\u751f\u4fe1\u65e5\u8bb0<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, 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