Highlight gene expression in UMAP embeddings, for example.
feat(obj, features, fast = NULL, verbose = TRUE, ...)A ggplot object (assembled by cowplot).
A cellpypes object, see section cellpypes Objects below.
A vector of genes (features) to colour by.
Set this to TRUE if you want fast plotting in spite of many cells
(using the scattermore package). If NULL (default), cellpypes decides
automatically and fast plotting is done for more than 10k cells, if FALSE
it always uses geom_point.
feat ignores gene names not present in your object and
warns you about them by default. verbose=FALSE will suppress the warning
(not recommended in interactive use).
Arguments passed to cowplot's plot_grid function, for example ncol or rel_widths.
A cellpypes object is a list with four slots:
raw (sparse) matrix with genes in rows, cells in columns
totalUMI the colSums of obj$raw
embed two-dimensional embedding of the cells, provided as data.frame or tibble with two columns and one row per cell.
neighbors index matrix with one row per cell and k columns, where k is the number of nearest neighbors (we recommend 15<k<100, e.g. k=50). Here are two ways to get the neighbors index matrix:
Use find_knn(featureMatrix)$idx, where featureMatrix could be
principal components, latent variables or normalized genes (features in
rows, cells in columns).
use as(seurat@graphs[["RNA_nn"]], "dgCMatrix")> .1 to extract
the kNN
graph computed on RNA. The > .1 ensures this also works with RNA_snn,
wknn/wsnn or any other
available graph – check with names(seurat@graphs).