pcaTCGA: Plot Two Main Components of Principal Component Analysis

In RTCGA/RTCGA: The Cancer Genome Atlas Data Integration

Plot Two Main Components of Principal Component Analysis

Description

Plots Two Main Components of Principal Component Analysis

Usage

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,
  ggtheme = theme_RTCGA(),
  ...
)

Arguments

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.
ggtheme	a ggtheme to be used (set to NULL, if using ggthemr package)
...	Further arguments passed to prcomp.

Value

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.

ggbiplot

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.

Issues

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.

Author(s)

Marcin Kosinski, [e-mail]

See Also

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

Other RTCGA: RTCGA-package, boxplotTCGA(), checkTCGA(), convertTCGA(), datasetsTCGA, downloadTCGA(), expressionsTCGA(), heatmapTCGA(), infoTCGA(), installTCGA(), kmTCGA(), mutationsTCGA(), readTCGA(), survivalTCGA(), theme_RTCGA()

Examples

## 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

## End(Not run)

RTCGA/RTCGA documentation built on Nov. 1, 2022, 8:15 p.m.