diff --git a/scirpy/_tools/_clonotypes.py b/scirpy/_tools/_clonotypes.py index ebfa809b0..b2ad61d13 100644 --- a/scirpy/_tools/_clonotypes.py +++ b/scirpy/_tools/_clonotypes.py @@ -20,10 +20,10 @@ _common_doc = """\ receptor_arms One of the following options: - * `"TRA"` - only consider TRA sequences - * `"TRB"` - only consider TRB sequences - * `"all"` - both TRA and TRB need to match - * `"any"` - either TRA or TRB need to match + * `"VJ"` - only consider :term:`VJ` sequences + * `"VDJ"` - only consider :term:`VDJ` sequences + * `"all"` - both VJ and VDJ need to match + * `"any"` - either VJ or VDJ need to match If `"any"`, two distances are combined by taking their minimum. If `"all"`, two distances are combined by taking their maximum. This is motivated @@ -35,10 +35,10 @@ dual_ir One of the following options: - * `"primary_only"` - only consider most abundant pair of TRA/TRB chains - * `"any"` - consider both pairs of TRA/TRB sequences. Distance must be below + * `"primary_only"` - only consider most abundant pair of :term:`VJ/VDJ` chains + * `"any"` - consider both pairs of :term:`VJ/VDJ` sequences. Distance must be below cutoff for any of the chains. - * `"all"` - consider both pairs of TRA/TRB sequences. Distance must be below + * `"all"` - consider both pairs of :term:`VJ/VDJ` sequences. Distance must be below cutoff for all of the chains. Distances are combined as for `receptor_arms`.