Plot of 2D CA projection of the data.
ca_biplot.Rd
Plots the first 2 dimensions of the rows and columns in the same plot.
Usage
ca_biplot(
obj,
xdim = 1,
ydim = 2,
princ_coords = 1,
row_labels = NULL,
col_labels = NULL,
type = "plotly",
...
)
# S4 method for cacomp
ca_biplot(
obj,
xdim = 1,
ydim = 2,
princ_coords = 1,
row_labels = NULL,
col_labels = NULL,
type = "plotly",
...
)
# S4 method for Seurat
ca_biplot(
obj,
xdim = 1,
ydim = 2,
princ_coords = 1,
row_labels = NULL,
col_labels = NULL,
type = "plotly",
...,
assay = Seurat::DefaultAssay(obj),
slot = "counts"
)
# S4 method for SingleCellExperiment
ca_biplot(
obj,
xdim = 1,
ydim = 2,
princ_coords = 1,
row_labels = NULL,
col_labels = NULL,
type = "plotly",
...,
assay = "counts"
)
Arguments
- obj
An object of class "cacomp" with the relevant standardized and principal coordinates calculated, or alternatively an object of class "Seurat" or "SingleCellExperiment" with a dim. reduction named "CA" saved.
- xdim
Integer. The dimension for the x-axis. Default 1.
- ydim
Integer. The dimension for the y-axis. Default 2.
- princ_coords
Integer. If 1 then principal coordinates are used for the rows, if 2 for the columns. Default 1 (rows).
- row_labels
Numeric vector. Indices for the rows for which a label should be added (label should be stored in rownames). Default NULL.
- col_labels
Numeric vector. Indices for the columns for which a label should be added (label should be stored in colnames). Default NULL (no columns).
- type
String. Type of plot to draw. Either "ggplot" or "plotly". Default "plotly".
- ...
Further arguments.
- assay
SingleCellExperiment assay for recomputation
- slot
Seurat assay slot from which to get matrix.
Details
Choosing type "plotly" will generate an interactive html plot with the package plotly. Type "ggplot" generates a static plot. Depending on whether `princ_coords` is set to 1 or 2 either the principal coordinates of either the rows (1) or the columns (2) are chosen. For the other the standard coordinates are plotted (assymetric biplot). Labels for rows and columns should be stored in the row and column names respectively.
Examples
# Simulate counts
cnts <- mapply(function(x){rpois(n = 500, lambda = x)},
x = sample(1:100, 50, replace = TRUE))
rownames(cnts) <- paste0("gene_", 1:nrow(cnts))
colnames(cnts) <- paste0("cell_", 1:ncol(cnts))
# Run correspondence analysis
ca <- cacomp(obj = cnts, princ_coords = 3)
#> Warning:
#> Parameter top is >nrow(obj) and therefore ignored.
ca_biplot(ca)