样本数据PCA分析

article/2025/7/9 1:32:26

PCA分析及画图

library(ggpubr)
library(ggplot2)
library(ggthemes)
data1<-read.table('./100klist.txt',header = 1)[,1:4]
head(data1)BCD_rep1 BCD_rep2 CK_rep1 CK_rep2
1   0.1987   0.2036  0.1807  0.2062
2   0.2133   0.2169  0.2040  0.2140
3   0.1943   0.1965  0.1862  0.1902
4   0.1051   0.1005  0.0928  0.1072
5   0.1627   0.1546  0.1453  0.1488
6   0.1283   0.1322  0.1123  0.1270pca.info <- prcomp(data1,scale=F)
#显示PCA计算结果
head(pca.info$rotation)
percentage<-round(pca.info$sdev / sum(pca.info$sdev) * 100,2)
# df_pcs <-data.frame(pca.info$x, Species = iris$Species) 
percentage<-paste(c("PC1","PC2"),"(", paste(as.character(percentage), "%", ")", sep=""))
pca.data <- data.frame(sample = rownames(pca.info$rotation),# type=c(rep("0h",3),rep("0.5h",3),rep("1h",3),rep("2h",3),rep("4h",3),rep("8h",3),#        rep("0h",3),rep("0.5h",3),rep("1h",3),rep("2h",3),rep("4h",3),rep("8h",3)),Sample = c(rep("BCD",2),rep("CK",2)),pca.info$rotation)  #sample 设置形状，type设置颜色
#绘图
table(pca.data$Sample)
pca.data$Sample<- factor(pca.data$Sample,levels= c('BCD','CK'),ordered = TRUE)
ggscatter(pca.data,x = "PC1",y = "PC2",label = "sample",color = "Sample",ellipse = F ,size = 4) +#,shape = "Sample"theme_bw()+xlab(percentage[1]) + ylab(percentage[2])+scale_color_brewer(type="seq",palette="Set1")+# guides(color = guide_legend(title = ''))+theme(axis.title = element_text(face = "bold",size = "19",color = "black"),axis.text.x = element_text(face = "bold",color = "black",angle = 0,size = 15,  hjust = 0.5, vjust = 0.5),axis.text.y = element_text(face = "bold",size = 15,color = "black"),# strip.text.y = element_text(face = 'bold',size = 10,colour = 'white'),####设置分面的的title框的形状\字体# strip.text.x = element_text(face = 'bold',size = 10,colour = 'white'),strip.text.x = element_text( face="bold",size = 16),#size=8,angle=75legend.text = element_text(size = 14,face = "bold"),legend.title = element_text(size = 14,face = "bold"),legend.position ='top',strip.text.y = element_text( face="bold",size = 16),panel.grid.major.y = element_blank(),panel.grid.minor.y = element_blank(),panel.grid.major.x = element_blank(),panel.grid.minor.x = element_blank(),panel.border = element_rect(colour = "black", fill=NA, size=1.5),strip.background = element_rect(colour = "white", fill = "grey"))