Plots Two Main Components of Principal Component Analysis

pcaTCGA(x, group.names, title = "", return.pca = FALSE, scale = TRUE, center = TRUE, var.scale = 1, obs.scale = 1, ellipse = TRUE, circle = TRUE, var.axes = FALSE, alpha = 0.8, add.lines = TRUE, ...)

- x
- A
`data.frame`

or`matrix`

containing i.e. expressions information. See expressionsTCGA. - group.names
- Names of group variable to use in labels of the plot.
- title
- The title of a plot.
- return.pca
- Should return pca object additionaly to pca plot?
- scale
- As in prcomp.
- center
- As in prcomp.
- var.scale
- As in
`ggbiplot`

. - obs.scale
- As in
`ggbiplot`

. - ellipse
- As in
`ggbiplot`

. - circle
- As in
`ggbiplot`

. - var.axes
- As in
`ggbiplot`

. - alpha
- As in
`ggbiplot`

. - add.lines
- Should axis lines be added to plot.
- ...
- Further arguments passed to prcomp.

If `return.pca = TRUE`

then a list containing a PCA plot (of class `ggplot`

) and a `pca`

model, the result of prcomp function.
If not, then only PCA plot is returned.

This function is based on https://github.com/vqv/ggbiplot
which had to be copied to RTCGA because `Bioconductor`

does not support
remote dependencies from `GitHub`

.

If you have any problems, issues or think that something is missing or is not clear please post an issue on https://github.com/RTCGA/RTCGA/issues.

RTCGA website http://rtcga.github.io/RTCGA/articles/Visualizations.html.

Other RTCGA: `RTCGA-package`

,
`boxplotTCGA`

, `checkTCGA`

,
`convertTCGA`

, `createTCGA`

,
`datasetsTCGA`

, `downloadTCGA`

,
`expressionsTCGA`

, `heatmapTCGA`

,
`infoTCGA`

, `installTCGA`

,
`kmTCGA`

, `mutationsTCGA`

,
`readTCGA`

, `survivalTCGA`

,
`theme_RTCGA`

## Not run: ------------------------------------ # library(dplyr) # ## RNASeq expressions # library(RTCGA.rnaseq) # expressionsTCGA(BRCA.rnaseq, OV.rnaseq, HNSC.rnaseq) %>% # rename(cohort = dataset) %>% # filter(substr(bcr_patient_barcode, 14, 15) == "01") -> BRCA.OV.HNSC.rnaseq.cancer # # pcaTCGA(BRCA.OV.HNSC.rnaseq.cancer, "cohort") # pcaTCGA(BRCA.OV.HNSC.rnaseq.cancer, "cohort", add.lines = FALSE) # pcaTCGA(BRCA.OV.HNSC.rnaseq.cancer, "cohort", return.pca = TRUE) -> pca.rnaseq # pca.rnaseq$plot # pca.rnaseq$pca ## ---------------------------------------------