Coloring the graph of PCA clusters in R

Question

I have some biological data that look like this: 2 different types of clusters (A and B):

                Cluster_ID       A1      A2      A3       B1       B2      B3
 5  chr5:100947454..100947489,+   3.31322  7.52365  3.67255  21.15730  8.732710 17.42640
12 chr5:101227760..101227782,+   1.48223  3.76182  5.11534  15.71680  4.426170 13.43560
29 chr5:102236093..102236457,+  15.60700 10.38260 12.46040   6.85094 15.551400  7.18341

I clear the data:

CAGE<-read.table("CAGE_expression_matrix.txt", header=T)
CAGE_data <- as.data.frame(CAGE)

#Remove clusters with 0 expression for all 6 samples
CAGE_filter <- CAGE[rowSums(abs(CAGE[,2:7]))>0,]

#Filter whole file to keep only clusters with at least 5 TPM in at least 3 files
CAGE_filter_more <- CAGE_filter[apply(CAGE_filter[,2:7] >= 5,1,sum) >= 3,]
CAGE_data <- as.data.frame(CAGE_filter_more)

After that, the data size decreases from 6981 clusters to 599.

Then I continue to apply PCA:

#Get data dimensions

dim(CAGE_data)
PCA.CAGE<-prcomp(CAGE_data[,2:7], scale.=TRUE) 
summary(PCA.CAGE)

I want to create a PCA data graph, label each sample and color the samples depending on their type (A or B.) Thus, for each graph there should be two colors for the text labels.

This is what I tried, to erroneous results:

qplot(PC1, PC2, colour = CAGE_data, geom=c("point"), label=CAGE_data, data=as.data.frame(PCA.CAGE$x))

ggplot(data=PCA.CAGE, aes(x=PCA1, y=PCA2, colour=CAGE_filter_more, label=CAGE_filter_more)) + geom_point() + geom_text()

qplot(PCA.CAGE[1:3], PCA.CAGE[4:6], label=colnames(PC1, PC2, PC3), geom=c("point", "text"))

Errors appear as such:

  > qplot(PCA.CAGE$x[,1:3],PCA.CAGE$x[4:6,], xlab="Data 1", ylab="Data 2")

  Error: Aesthetics must either be length one, or the same length as the dataProblems:PCA.CAGE$x[4:6, ]

  > qplot(PC1, PC2, colour = CAGE_data, geom=c("point"), label=CAGE_data,    data=as.data.frame(PCA.CAGE$x))

  Don't know how to automatically pick scale for object of type data.frame.   Defaulting to continuous
  Don't know how to automatically pick scale for object of type data.frame. Defaulting to continuous
  Error: Aesthetics must either be length one, or the same length as the dataProblems:CAGE_data, CAGE_data

 > ggplot(data=PCA.CAGE, aes(x=PCA1, y=PCA2, colour=CAGE_filter_more,      label=CAGE_filter_more)) + geom_point() + geom_text()

 Error: ggplot2 doesn't know how to deal with data of class 

Answer 1

( , ). , 3 ( A B). PCA 6 , 6 , () 6 . (). ( ), . iris.

pca   <- prcomp(iris[,1:4], scale.=TRUE)
clust <- kmeans(pca$x[,1:2], centers=3)$cluster
library(ggbiplot)
ggbiplot(pca, groups=factor(clust)) + xlim(-3,3)

, PCA 4 iris. pca$x - , . , k-mean clust. ggibplot(...) .