plot_pca | R Documentation |
This function plots a low-dimensional projection of an omic data matrix using principal component analysis.
plot_pca( dat, group = NULL, covar = NULL, top = NULL, pcs = c(1L, 2L), label = FALSE, pal_group = "npg", pal_covar = "Blues", size = NULL, alpha = NULL, title = "PCA", legend = "right", hover = FALSE, D3 = FALSE )
dat |
Omic data matrix or matrix-like object with rows corresponding to
probes and columns to samples. It is strongly recommended that data be
filtered and normalized prior to plotting. Raw counts stored in |
group |
Optional character or factor vector of length equal to sample size, or up to two such vectors organized into a list or data frame. Supply legend title(s) by passing a named list or data frame. |
covar |
Optional continuous covariate. If non- |
top |
Optional number (if > 1) or proportion (if < 1) of most variable probes to be used for PCA. |
pcs |
Vector specifying which principal components to plot. Must be of
length two unless |
label |
Label data points by sample name? Defaults to |
pal_group |
String specifying the color palette to use if |
pal_covar |
String specifying the color palette to use if |
size |
Point size. |
alpha |
Point transparency. |
title |
Optional plot title. |
legend |
Legend position. Must be one of |
hover |
Show sample name by hovering mouse over data point? If |
D3 |
Render plot in three dimensions? |
This function plots the samples of an omic data matrix in a two- or three-dimensional principal component subspace. Axis labels include the percentage of variance explained by each component. PCA is an easy and popular projection method that can aid in identifying clusters, detecting outliers, and visualizing the latent structure of a dataset.
By default, plot_pca
performs singular value decomposition on the
complete dat
matrix. Limit the PCA to only the most variable probes by
using the top
argument.
Hotelling, H. (1933). Analysis of a complex of variables into principal components. Journal of Educational Psychology, 24(6): 414:441.
Pearson, K. (1901). On lines and planes of closest fit to systems of points in space. Philosophical Magazine, 2(11): 559–572.
plotPCA
, plot_mds
,
plot_tsne
mat <- matrix(rnorm(1000 * 5), nrow = 1000, ncol = 5) plot_pca(mat) library(DESeq2) dds <- makeExampleDESeqDataSet() dds <- rlog(dds) plot_pca(dds, group = colData(dds)$condition)
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