get_coord: get_coord
| get_coord | R Documentation |
get_coord
Description
Extract coordinates (e.g. from dimensionality reduction) from bio datasets, optionally with annotations to help plotting them with ggplot2 package.
Usage
get_coord(x, coord.name = NULL, add.cols = TRUE, add.exprs = NULL, ...)
## S3 method for class 'SingleCellExperiment'
get_coord(x, coord.name = NULL, add.cols = TRUE, add.exprs = FALSE, ...)
## S3 method for class 'CellDataSet'
get_coord(x, coord.name = "A", add.cols = TRUE, add.exprs = FALSE, ...)
## S3 method for class 'seurat'
get_coord(x, coord.name = "tsne", add.cols = TRUE, add.exprs = FALSE, ...)
## S3 method for class 'Seurat'
get_coord(
x,
coord.name = NULL,
add.cols = TRUE,
add.exprs = FALSE,
assay = NULL,
slot = "data",
...
)
Arguments
x |
object to obtain coordinates. |
coord.name |
name of the holder for coordinates. |
add.cols |
logical; whether to annotate each coordinate with column data (i.e. colData). |
add.exprs |
if not NULL a list of genes to add counts obtained with get_expression(). |
... |
arguments passed down to methods. |
assay |
name of assay for Seurat objects. |
slot |
name of slot for Seurat objects. |
Value
A data.frame object.
