Order metacells by RNA marker clustering — mc_order_by

order the metacells using the RNA marker clustering. See get_rna_marker_matrix for more information. When force_cell_type is TRUE and atac_mc@metadata has a field named "cell_type", the columns are only ordered only within each cell type.

Usage

mc_order_by_rna(
  atac_mc,
  markers = NULL,
  force_cell_type = TRUE,
  rm_zeros = TRUE,
  epsilon = 0.00001,
  ...
)

Arguments

atac_mc

a McPeaks/McTracks object with RNA expression (using add_mc_rna)

markers

a list of marker genes. If NULL - the function uses get_rna_markers with default parameters which can be overridden using the ellipsis ....

force_cell_type

do not split cell types when ordering the metacells. Default: TRUE

rm_zeros

remove genes with no RNA expression in any metacell. Default: TRUE

epsilon

regularization factor added to the log normalized expression

...

Arguments passed on to get_rna_marker_matrix