getDAregion.Rd
Cluster the DA cells retained from Step 1 and Step 2 of DA-seq to obtain spatially coherent DA regions.
getDAregion(X, da.cells, cell.labels, labels.1, labels.2, prune.SNN = 1/15, resolution = 0.05, group.singletons = F, min.cell = NULL, do.plot = T, plot.embedding = NULL, size = 0.5, do.label = F, ...)
X | size N-by-p matrix, input merged dataset of interest after dimension reduction |
---|---|
da.cells | output from getDAcells() or updateDAcells() |
cell.labels | size N vector, labels for each input cell |
labels.1 | vector, label name(s) that represent condition 1 |
labels.2 | vector, label name(s) that represent condition 2 |
prune.SNN | parameter for Seurat function FindNeighbors(), default 1/15 |
resolution | parameter for Seurat function FindClusters(), default 0.05 |
group.singletons | parameter for Seurat function FindClusters(), default True |
min.cell | integer, number of cells below which a DA region will be removed as outliers, default NULL, use minimum k value in k-vector |
do.plot | a logical value to indicate whether to return ggplot objects showing the results, default True |
plot.embedding | size N-by-2 matrix, 2D embedding for the cells |
size | cell size to use in the plot, default 0.5 |
do.label | a logical value to indicate whether to label each DA region with text, default False |
... | other parameters to pass to Seurat FindClusters() |
a list of results
DA region label for each cell from the whole dataset, '0' represents non-DA cells.
a table showing DA score and p-value for each DA region
ggplot object showing DA regions on plot.embedding