View source: R/preprocessing.R
ReadAkoya | R Documentation |
Read and Load Akoya CODEX data
ReadAkoya(
filename,
type = c("inform", "processor", "qupath"),
filter = "DAPI|Blank|Empty",
inform.quant = c("mean", "total", "min", "max", "std")
)
LoadAkoya(
filename,
type = c("inform", "processor", "qupath"),
fov,
assay = "Akoya",
...
)
filename |
Path to matrix generated by upstream processing. |
type |
Specify which type matrix is being provided.
|
filter |
A pattern to filter features by; pass |
inform.quant |
When |
fov |
Name to store FOV as |
assay |
Name to store expression matrix as |
... |
Ignored |
ReadAkoya
: A list with some combination of the following values
“matrix
”: a
sparse matrix with expression data; cells
are columns and features are rows
“centroids
”: a data frame with cell centroid
coordinates in three columns: “x”, “y”, and “cell”
“metadata
”: a data frame with cell-level meta data;
includes all columns in filename
that aren't in
“matrix
” or “centroids
”
When type
is “inform
”, additional expression matrices
are returned and named using their segmentation type (eg.
“nucleus”, “membrane”). The “Entire Cell” segmentation
type is returned in the “matrix
” entry of the list
LoadAkoya
: A Seurat
object
This function uses
progressr to
render status updates and progress bars. To enable progress updates, wrap
the function call in with_progress
or run
handlers(global = TRUE)
before running
this function. For more details about progressr, please read
vignette("progressr-intro")
This function requires the data.table package to be installed
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