For column names from ClonotypeSearchSummary.FIELDS_AG
For column names from ClonotypeSearchSummary.FIELDS_MHC_A
For column names from ClonotypeSearchSummary.FIELDS_MHC_B
Counters are stored in
final Map<String, Map<String, ClonotypeCounter>> columnSequenceCounters
Access is the following e.g. for FIELDS_AG = ["antigen.species", "antigen.gene"]:
columnSequenceCounters.getAt("antigen.species") will list species->counter (first circle of starburst), e.g. "HIV"->1
For the second circle we access columnSequenceCounters.getAt("antigen.species\tantigen.gene") that will list "HIV\tgag"->1 and "HIV\tpol"->2 counts for both genes of HIV in database.
If there is a specific JSON format for starburst I can simplify the access.
Each counter has unique, reads and frequency counts. Maybe we can make a switch to re-draw the chart under each of those options
There is also a ClonotypeSearchSummary.totalCounter (total) and ClonotypeSearchSummary.notFoundCounter (not annotated) that can be shown as bars for unique, reads and frequency at the same time.
Starburst charts
To generate the summary one should call
Now we have 3 charts possible:
ClonotypeSearchSummary.FIELDS_AGClonotypeSearchSummary.FIELDS_MHC_AClonotypeSearchSummary.FIELDS_MHC_BCounters are stored in
Access is the following e.g. for
FIELDS_AG = ["antigen.species", "antigen.gene"]:columnSequenceCounters.getAt("antigen.species")will listspecies->counter(first circle of starburst), e.g."HIV"->1For the second circle we access
columnSequenceCounters.getAt("antigen.species\tantigen.gene")that will list"HIV\tgag"->1and"HIV\tpol"->2counts for both genes of HIV in database.If there is a specific JSON format for starburst I can simplify the access.
Each counter has
unique,readsandfrequencycounts. Maybe we can make a switch to re-draw the chart under each of those optionsThere is also a
ClonotypeSearchSummary.totalCounter(total) andClonotypeSearchSummary.notFoundCounter(not annotated) that can be shown as bars forunique,readsandfrequencyat the same time.