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library(wesanderson)
library(magrittr)
library(tidyverse)
library(clusterProfiler)
数据清洗
pal <- wes_palette("Zissou1", 100, type = "continuous")
load("data.RData")kegg <- read.delim("Kegg.xls") %>%
select(2,3,6) %>%
separate(`GeneRatio`,into="GeneRatio",sep="/") %>%
arrange(desc(p.adjust))
kegg$Description <- factor(kegg$Description,levels=kegg$Description,ordered = T)
条形图
ggplot(kegg,aes(Description,GeneRatio,fill=p.adjust))+
geom_col()+
scale_fill_gradientn(colours=pal)+
coord_flip()+
scale_x_discrete(expand = c(0, 0)) +
theme_test()+
theme(axis.title = element_blank(),
axis.text=element_text(color="black"),
legend.key=element_blank(),
legend.title = element_text(color="black",size=10),
legend.text = element_text(color="black",size=8),
legend.spacing.x=unit(0.1,'cm'),
legend.key.width=unit(0.5,'cm'),
legend.key.height=unit(0.5,'cm'),
legend.background=element_blank(),
legend.box.margin = margin(1,1,1,1),
legend.position = c(0.99,0),legend.justification = c(0.99,0))
散点图
read.delim("Kegg.xls") %>%
select(2,3,6) %>%
separate(`GeneRatio`,into=c("A","B"),sep="/") %>%
mutate(A=as.numeric(A),B=as.numeric(B)) %>%
mutate(count=A/B) %>%
ggplot(aes(count,fct_reorder(Description,count)))+
geom_point(aes(size=A,color=p.adjust))+
scale_color_gradientn(colours=pal)+
guides(size=guide_legend(title="Count"))+
theme_test()+
theme(axis.title = element_blank(),
axis.text=element_text(color="black"),
legend.key=element_blank(),
legend.title = element_text(color="black",size=10),
legend.text = element_text(color="black",size=8),
legend.spacing.x=unit(0.1,'cm'),
legend.key.width=unit(0.5,'cm'),
legend.key.height=unit(0.5,'cm'),
legend.background=element_blank(),
legend.box.margin = margin(1,1,1,1))
网络图
目前还是依靠cnetplot函数来绘制网络图，后期希望能用ggplot2实现
cnetplot(dd,
foldChange = geneList,
showCategory = 3,
node_label = "none", # category | gene | all | none
circular = TRUE,
colorEdge = TRUE)+
theme_test()+
theme(axis.title = element_blank(),
axis.ticks = element_blank(),
axis.text=element_blank())
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