PCA

library(ggpubr)

library(ggthemes)

library(gmodels)


data<- read.csv('Documents.csv',sep = ",",header = T, row.names = 1)
head(data) 
##      CK_1  CK_2  CK_3  ff_1  ff_2  ff_3  X2_1  X2_2  X2_3
## A1 0.997 0.826 0.963 1.154 1.209 1.251 0.849 0.964 0.785
## A2 0.899 0.933 0.828 1.174 1.197 1.248 0.927 0.870 0.924
## A3 0.956 0.918 0.985 1.102 1.166 1.123 0.942 0.916 0.892
## A4 0.847 0.800 0.879 1.014 1.181 1.073 1.139 1.019 1.047
## A5 0.807 0.860 0.860 1.197 1.132 1.157 0.995 1.008 0.984
## A6 0.802 0.848 0.831 1.181 1.293 1.333 1.017 0.859 0.836


pca.info <- fast.prcomp(data)  #计算PCA
head(pca.info$rotation)
         PC1           PC2          PC3         PC4         PC5         PC6       PC7        PC8         PC9
## CK_1 -0.2457120 -0.3916791546 -0.184711326  0.25556333 -0.20855518  0.54288907 0.3400128 -0.4720976  0.10036671
## CK_2 -0.2398894 -0.3979242732  0.001259835 -0.33241476 -0.41773793 -0.40334507 0.3048059  0.1126560 -0.48043521
## CK_3 -0.2433020 -0.4086936533  0.197493608  0.07863573  0.61132026 -0.14806624 0.3678744  0.3210061  0.30752843
## ff_1  0.4738034 -0.0073809534  0.484306510 -0.45144249  0.09074063 -0.00211779 0.3169145 -0.4679174  0.09738058
## ff_2  0.4663091  0.0005589496  0.144334086  0.65148767  0.04900114 -0.03443670 0.3033427  0.1083170 -0.47953163
## ff_3  0.4743796 -0.0060860825 -0.615903649 -0.19285910 -0.13489913  0.02689424 0.3756398  0.3213497  0.30838793


pca.data <- data.frame(sample = rownames(pca.info$rotation),
                       
                       Type = c(rep("ck", 3), rep("FF", 3),rep("x2",3)),  
                       
                       pca.info$rotation)#设置各个分组的样本数

#开始画图

ggscatter(pca.data, x = "PC1", y = "PC2",
          
          color = "Type",
          
          ellipse = T,
          
          size = 2, palette = c("mediumaquamarine", "violet","tomato"),     #可以修改点的大小和颜色，颜色代码可以去网上搜索
          
          label = "sample", repel = TRUE, main = "PCA plot") + theme_base()                  

#可以修改图的名称，label = "sample"用于显示各个点对应的样本名

#由于每个组的点数码太少，所以不能进行eclipse画图（即用圈圈把同一组画在一起）。 Too few points to calculate an ellipse

image.png

参考：https://mp.weixin.qq.com/s?__biz=MzI2ODUwOTcxMQ==&mid=2247484946&idx=1&sn=8916c2d770a59cfc87b078dfd148fdb3&chksm=eaef3172dd98b864e676221afd21af85cc18e6eb25eb9b99d504b62166bb0ca014a5dea66e30&mpshare=1&scene=23&srcid=0202pdfkqYOU9Qqg22GScb8Y&sharer_sharetime=1643771106893&sharer_shareid=a4cfed7e97e053f52fa6e29dfbc89cfe#rd