aggregate_cell_types: Aggregates the pixel occurrences for each cell type in the...
In dmcable/RCTD: SpatialeXpressionR: Cell type identification and cell type-specific differential expression in spatial transcriptomics
aggregate_cell_types R Documentation
Aggregates the pixel occurrences for each cell type in the RCTD object
Description
The difference with count_cell_types is that this function does not filter out pixels
based on total cell type weight, as occurs in the CSIDE algorithm.
Usage
aggregate_cell_types(myRCTD, barcodes, doublet_mode = T)
Arguments
barcodes
the barcodes, or pixel names, of the SpatialRNA object to be used when counting cell types.
doublet_mode
(default TRUE) if TRUE, uses RCTD doublet mode weights. Otherwise, uses RCTD full mode weights
RCTD
an RCTD object with annotated cell types e.g. from the run.RCTD function.
Value
a named vector of number of pixel occurrences for each cell type
dmcable/RCTD documentation built on Feb. 24, 2024, 11:03 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
| aggregate_cell_types | R Documentation |
Aggregates the pixel occurrences for each cell type in the RCTD object
Description
The difference with count_cell_types is that this function does not filter out pixels
based on total cell type weight, as occurs in the CSIDE algorithm.
Usage
aggregate_cell_types(myRCTD, barcodes, doublet_mode = T)
Arguments
barcodes |
the barcodes, or pixel names, of the |
doublet_mode |
(default TRUE) if TRUE, uses RCTD doublet mode weights. Otherwise, uses RCTD full mode weights |
RCTD |
an |
Value
a named vector of number of pixel occurrences for each cell type
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.