3D PCA plot.

PCA3D(
  pca,
  x = "PC1",
  y = "PC2",
  z = "PC3",
  color.key = NULL,
  color = NULL,
  cex = 1.5,
  col = "black",
  ticktype = "detailed",
  bty = "g",
  box = TRUE,
  theta = 140,
  phi = 20,
  d = 3,
  colkey = FALSE,
  label.size = 0.5,
  legend.pos = "bottom",
  legend.horiz = TRUE,
  legend.inset = -0.1,
  legend.bg = "white",
  legend.bty = "n",
  legend.ncol = NULL,
  main = NULL,
  ...
)

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.
z	The principal component to display on the z axis. Default: PC3.
color.key	Group to color the points. When set NULL, select first column of metadata. Default: NULL.
color	Colors used. When set NULL, select color from Set1 of `RColorBrewer` package. Default: NULL.
cex	Point size. Default: 1.5.
col	Point edge color. Default: black.
ticktype	Axis ticktype, chosen from: detailed and simple. Default: detailed.
bty	The type of the box, the default draws only the back panels, chosen from: f, b, b2, g, bl, bl2, u, n. Default: g.
box	Should the bounding box for the surface be displayed. Default: TRUE.
theta	Angles defining the viewing direction. `theta` gives the azimuthal direction. Default: 140.
phi	Angles defining the viewing direction. `phi` gives the colatitude direction. Default: 20.
d	a value which can be used to vary the strength of the perspective transformation. Values of d greater than 1 will lessen the perspective effect and values less and 1 will exaggerate it. Default: 3.
colkey	`colkey`. Default: FALSE.
label.size	Label font size. Default: 0.5.
legend.pos	Legend position. Default: bottom.
legend.horiz	Logical; if TRUE, set the legend horizontally rather than vertically (specifying horiz overrides the ncol specification). Default: TRUE.
legend.inset	Inset distance(s) from the margins as a fraction of the plot region when legend is placed by keyword. Default: -0.1.
legend.bg	The background color for the legend box. Note that this is only used if bty != "n". Default: white.
legend.bty	The type of box to be drawn around the legend, chosen from 0 and n. Default: n.
legend.ncol	The number of columns in which to set the legend items. Default: NULL (set the legend horizontally).
main	Title of the plot. Default: NULL.
...	Parameters for `scatter3D`.

Value

3D PCA plot.

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!
PCA3D(pca = pca_res, color.key = "condition", main = "3D PCA")