chmAddPCA | R Documentation |
Add PCA coordinates as hidden covariate bars to an axis of an NG-CHM. One hidden covariate bar is added for each PCA coordinate (up to ndim coordinates). Coordinates are given names 'BASENAME.coordinate.N', where BASENAME is specified by the parameter basename (default "PC") and N ranges from 1 to the number of added covariate bars.
chmAddPCA(hm, axis, prc, basename = "PC", ndim = 2)
hm |
The NGCHM to add the coordinates to. |
axis |
The NGCHM axis ("row" or "column") to add the coordinates to. |
prc |
Principal component coordinates (output of |
ndim |
The maximum number of coordinates to add. |
baseName |
The prefix to use for the coordinate names. |
The NGCHM with added coordinates.
chmAddTSNE()
chmAddUMAP()
chmAddUWOT()
chmAddReducedDim()
prc <- prcomp(TCGA.GBM.EXPR); hm <- chmNew ("gbm", TCGA.GBM.EXPR); hm <- chmAddPCA(hm, "column", prc);
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