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Zea maize GO

news 2025/6/25 3:44:28

1.涉及到新旧基因组的转化 B73v4_to_B73v5

（davidbioinformatics只支持新版基因组）

MaizeGDB Map文件下载https://download.maizegdb.org/Pan-genes/B73_gene_xref/

小处理脚本（制作map文件）

import pandas as pd# 读取CSV文件
f_standard = pd.read_csv(r"B73v4_to_B73v5.tsv")# 分割数据
f_standard = f_standard.iloc[:,0].str.split('\t', expand=True)# 添加列名
f_standard.columns = ['V4', 'V5']  # 直接给DataFrame添加列名# 保存为TSV文件
f_standard.to_csv(r"Map.tsv",sep='\t',        # 使用tab作为分隔符index=False)     # 不保存索引

脚本2（v4.0 2 V5.0）

import pandas as pd# 读取数据
input = pd.read_csv('input', header=None)
map_ = pd.read_csv("Map.tsv", sep='\t')input.columns = ['V4']# 合并数据框，指定用于合并的列名
new_ = pd.merge(input, map_,left_on='V4',      # input数据框用于匹配的列right_on='V4',     # map_数据框用于匹配的列how='left')        # 保留input中的所有行new_.to_csv("MergedResult.csv", index=False)

可以直接复制V5列

打开

DAVID Functional Annotation Tools

选自己需要的（如这里是三个GO途径）别的里面有Kegg

下载即可

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2024年11月20日18:26:41

在原先的结果文件上补充一个气泡权重与富集基因数目的气泡图(常用)
R

# 加载必要的包
library(ggplot2)
library(dplyr)# 读取TSV文件
data <- read.delim("GO_P_re.tsv", header = TRUE, sep = "\t")
#data <- read.delim("test2.tsv", header = TRUE, sep = "\t")
# setwd("GOKEGG/GO")
# 数据处理 - 修改为需要的格式
go_data <- data.frame(category = case_when(grepl("BP", data$Category) ~ "BP",grepl("MF", data$Category) ~ "MF",grepl("CC", data$Category) ~ "CC"),ID = sub("GO:", "", sub("~.*", "", sub(".*GO:", "GO:", data$Term))), # 提取GO IDterm = sub(".*~", "", data$Term), # 提取描述pvalue = as.numeric(data$PValue), # P值count = as.numeric(data$Count), # 基因数量gene_ratio = as.numeric(data$Fold.Enrichment) # 使用Fold Enrichment作为基因比率
)# 创建气泡图
p <- ggplot(go_data,aes(x = gene_ratio,y = term)
) +geom_point(aes(size = count,color = pvalue)) +scale_color_gradient(low = "red",high = "blue") +scale_size_continuous(range = c(3, 12)) + # 增大气泡的最小和最大尺寸facet_grid(category ~ .,scales = "free_y",space = "free_y") +labs(x = "Gene Ratio",y = "GO term",title = "GO Enrichment",color = "PValue",size = "Count") +theme_bw() +theme(axis.text.y = element_text(size = 10,angle = 45,hjust = 1),axis.text.x = element_text(size = 8,angle = 45,hjust = 1),strip.text = element_text(size = 10),legend.title = element_text(size = 10),legend.text = element_text(size = 8),plot.title = element_text(size = 12, hjust = 0.5),panel.spacing = unit(0, "lines"),# 减少面板之间的间距plot.margin = margin(t = 20, r = 20, b = 30, l = 20, unit = "pt")#边距调整)print(p)# 保存图片
ggsave("GO__bubble.png", width = 12, height = 8) # 减小了高度，使图形更紧凑