MVP.PCAplot {rMVP} | R Documentation |
PCA Plot
MVP.PCAplot(PCA, memo = "MVP", col = NULL, pch = NULL, class = NULL, legend.pos = "topright", Ncluster = 1, plot3D = FALSE, file.type = "pdf", dpi = 300, box = FALSE, file.output = TRUE, outpath = getwd(), verbose = TRUE)
PCA |
Principal component analysis result, 2-column matrix |
memo |
the prefix of the output image file. |
col |
colors for each cluster |
pch |
Either an integer specifying a symbol or a single character to be
used as the default in plotting points. See |
class |
the class of all individuals, for example: "breed", "location" |
legend.pos |
position of legend. default is "topright" |
Ncluster |
cluster number |
plot3D |
(DEPRECATED)if TRUE, plot PC figure in 3D format, it can be only used in windows and mac operation system, "rgl" package should be installed beforehead |
file.type |
Character. Options are jpg, pdf, and tiff |
dpi |
Number. Dots per inch for .jpg and .tiff files |
box |
Logical value. If TRUE, the border line of Manhattan plot will be added |
file.output |
Logical value. If TRUE, the figures will be generated. |
outpath |
Effective only when file.output = TRUE, determines the path of the output file |
verbose |
whether to print detail. |
Output file: MVP.PCA_2D.<type>
genoPath <- system.file("extdata", "06_mvp-impute", "mvp.imp.geno.desc", package = "rMVP") geno <- attach.big.matrix(genoPath) pca <- MVP.PCA(M=geno) MVP.PCAplot(PCA=pca, Ncluster=3, class=NULL, col=c("red", "green", "yellow"), file.output=FALSE, pch=19)