Entering edit mode
6.8 years ago
1769mkc
★
1.2k
Im trying to make a 3D PCA but i m not sure if its really working or not i cannot label my sample which i intend to here is my code anyone can help or any suggestion how can i label my samples in my final plot.
d <- read.csv("~/analysis/gene_fpkm/PRIMARY_AUX_ATPASE.csv",header = TRUE)
names(d)
model <- prcomp(t(d[,-1]), scale=TRUE)
plotPCA <- function(x, nGroup) {
n <- ncol(x)
}
fit <- hclust(dist(x), method="complete")
groups <- cutree(fit, k=nGroup)
if(n == 3) { # 3d plot
plot3d(x, col=groups, type="s", size=1, axes=F)
axes3d(edges=c("x--", "y--", "z"), lwd=3, axes.len=2, labels = TRUE)
mtext3d(text)
grid3d("x")
grid3d("y")
grid3d("z")
} else { # 2d plot
maxes <- apply(abs(x), 2, max)
rangeX <- c(-maxes[1], maxes[1])
rangeY <- c(-maxes[2], maxes[2])
plot(x, col=groups, pch=19, xlab=colnames(x)[1], ylab=colnames(x)[2], xlim=rangeX, ylim=rangeY)
lines(c(0,0), rangeX*2)
lines(rangeY*2, c(0,0))
}
}
plotPCA(model$x[,1:3], 5)
this is the code im running i cannot label my sample in which comes in the final 3D pca .any suggestion or help would be highly appreciated