[R] Principal componet plot from lower triangular matrix file
cm
mbnchakravarthy at gmail.com
Mon Nov 28 11:55:41 CET 2011
Hi,
I have a comma separated file with element names in first column like shown
below :
Name_1,0
Name_2,0.8878,0
Name_3,0.6777,0.7643,0
Name_4,0.9844,0.1234,0.1414,0
Original data is a 10000x10000 symmetric matrix (600 MB). To reduce file
size, I have minimized matrix to only lower triangle. Is there a (memory)
efficient way to 1) read file 2) compute first and second principal
components and 3) and plot first vs second PC's ?
In the past, I could do this by :
b <- read.csv("distance.csv", sep=",", head=F) # distance.csv file is
complete data matrix, so this command worked !!
my_matrix <- data.matrix(b)
pca2 <- princomp(my_matrix)
plot(pca2$scores[,1],pca2$scores[,2])
text(pca2$scores[,1],pca2$scores[,2],rownames(nba_matrix), cex=0.5, pos=1)
This time, I don't have a complete file. So, I was wondering, how to do this
?
Any help is much appreciated
TIA
M
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