R: Preprocess data

.preprocessData {SpatialCPie}

R Documentation

Preprocess data

Preprocesses input data for .makeServer.

.preprocessData(counts, margin, resolutions, assignmentFunction,
  coordinates = NULL)

`counts`	count matrix. `rownames` should correspond to genes and `colnames` should correspond to spot coordinates.
`margin`	which margin of the count matrix to cluster. Valid values are `c("spot", "sample", "gene", "feature")`.
`resolutions`	vector of resolutions to cluster.
`assignmentFunction`	function to compute cluster assignments. The function should have the following signature: integer (number of clusters) -> (m, n) feature matrix -> m-length vector (cluster assignment of each data point).
`coordinates`	optional `data.frame` with pixel coordinates for each spot. `rownames` should correspond to the `colnames` of `counts` and the columns `x` and `y` should specify the pixel coordinates of the spots.

list with the following elements:

$assignments: tidy assignments
$means: cluster means
$scores: cluster scores for each spot in each resolution
$colors: cluster colors
$coordinates: spot coordinates, either from coordinates or parsed from assignments
$featureName: name of the clustered feature (the "opposite" of margin)

[Package SpatialCPie version 1.3.4 Index]