Generated PCA baisc plots, including screen plot, biplot and pairs plot.

PCABasic(
  pca,
  x = "PC1",
  y = "PC2",
  explain.threshold = 90,
  loading.num = 5,
  loading.label.size = 3,
  loading.label.color = "red",
  colby = NULL,
  pair.pc = 5,
  pair.label.size = 14,
  legend.pos = c("right", "bottom", "top", "left", "none")
)

Arguments

pca	PCA results of `PCA`.
x	The principal component to display on the x axis. Default: PC1.
y	The principal component to display on the y axis. Default: PC2.
explain.threshold	The threshold of explained variance. Default: 90.
loading.num	Select loading gene number based on absolute ordered variable loading for each PC in the biplot. Default: 5.
loading.label.size	Size of loading label. Default: 3.
loading.label.color	Color of loading label. Default: red.
colby	Group information to color samples. Default: NULL.
pair.pc	The principal components to be included in the plot. Default: 5.
pair.label.size	Size of p rincipal component label. Default: 14.
legend.pos	Position of legend ('top', 'bottom', 'left', 'right', 'none'). Default: right.

Value

A ggplot2 object.

Examples

library(DESeq2)
library(DEbPeak)
count.file <- system.file("extdata", "snon_count.txt", package = "DEbPeak")
meta.file <- system.file("extdata", "snon_meta.txt", package = "DEbPeak")
count.matrix <- read.table(file = count.file, header = TRUE, sep = "\t")
meta.info <- read.table(file = meta.file, header = TRUE)
dds <- DESeq2::DESeqDataSetFromMatrix(countData = count.matrix, colData = meta.info, design = ~condition)
#> Warning: some variables in design formula are characters, converting to factors
keep.genes <- rowSums(DESeq2::counts(dds, normalized = FALSE)) >= 10
dds <- dds[keep.genes, ]
pca_res <- PCA(deobj = dds, transform.method = "rlog")
#> Differential expression analysis with DESeq2!
#> Use all genes for PCA!
PCABasic(pca_res, colby = "condition")
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.
#> $screen
#> 
#> $biplot
#> 
#> $pairs
#>