Project a metacell object on a reference

This will take each cell in the query object and find its to correlated metacell in the reference, then generating figures showing detailed comparison of how each metacell in the query is distributed in the atlas, and how the pool of all cells in the query MC compare to the pool of their best match projections

mcell_proj_on_atlas(
  mat_id,
  mc_id,
  atlas,
  fig_cmp_dir,
  ten2mars = T,
  gene_name_map = NULL,
  recolor_mc_id = NULL,
  plot_all_mcs = F,
  md_field = NULL,
  max_entropy = 2,
  burn_cor = 0.6
)

Arguments

mat_id: id of metacell object ina scdb
mc_id: id of metacell object ina scdb
atlas: an object generated by mcell_gen_atlas
fig_cmp_dir: name of directory to put figures per MC
ten2mars: should gene mapping be attmpeted using standard MARS-seq to 10x naming convetnion
gene_name_map: if this is dedining a named vector query_name[ref_name], then the name conversion between the query and reference will be determined using it
recolor_mc_id: if this is specified, the atlas colors will be projected on the query MCCs and updated to the scdb object named recolor_mc
md_field: metadata field too use as additional factor for plotting subsets
plot_all_mc: set this to T if you want a plot per metacell to show comparison of query pooled umi's and projected pooled umis.

Project a metacell object on a reference "atlas"

Arguments