Bycon

* complete refactoring of plot code as `ByconPlot` class
* renamed library `bycon_plot.py`

* new `services/samplesPlotter` entry point
- currently specific for file uploads (handling of DB calls see below)
* completed the integration of the new `bycon` plotting
* new `plotCytoregionLabels` plot labeling parameter
- [/beacon/biosamples/?plotGroupBy=icdot&filters=pgx:icdom-95003&plotCytoregionLabels=8q,9p11p12&plotGeneSymbols=MYCN&output=histoplot&limit=500](http://progenetix.org/beacon/biosamples/?plotGroupBy=icdot&filters=pgx:icdom-95003&plotCytoregionLabels=8q,9p11p12&plotGeneSymbols=MYCN&output=histoplot&limit=500)

* added method to subset samples for multi-histogram generation using the `groupBy`
parameter for matching of `filter_definitions` classes
- [/beacon/biosamples/?groupBy=icdot&filters=pgx:icdom-95003&plotGeneSymbols=MYCN&output=histoplot&limit=100](http://progenetix.org/beacon/biosamples/?groupBy=icdot&filters=pgx:icdom-95003&plotGeneSymbols=MYCN&output=histoplot&limit=100)
* removal of deprecated `cgitb` use & replacing it w/ a simple _Exception_/traceback
wrapper
* expansion of the [plotting documentation](http://bycon.progenetix.org/plotting/)
* move of the plot arguments parsing to `cgi_parsing.py`

* more plotting: now histograms and samples - if >3 - get a dendrogram to indicate
the clustering results
- clustering can be suppressed by `&plotClusterResults=false`

--------------------------------------------------------------------------------

2023 01-04

* plotting & clustering of samples
- [/beacon/analyses/?filters=pgx:icdom-95003&plot_labelcol_width=0&plot_filter_empty_samples=y&plotGeneSymbols=MYCN&plot_samplestrip_height=1&output=samplesplot&limit=500](http://progenetix.org/beacon/analyses/?filters=pgx:icdom-95003&plot_labelcol_width=0&plot_filter_empty_samples=y&plotGeneSymbols=MYCN&plot_samplestrip_height=1&output=samplesplot&limit=500)

* more plot_utils goodness - staggered labels
- [/services/intervalFrequencies/?plotChros=2,8,9,17&labels=8:120000000-123000000:Some+Interesting+Region&plot_gene_symbols=MYCN,REL,TP53,MTAP,CDKN2A,MYC,ERBB2,CDK1&filters=pgx:icdom-85003&output=histoplot](http://progenetix.org/services/intervalFrequencies/?plotChros=2,8,9,17&labels=8:120000000-123000000:Some+Interesting+Region&plot_gene_symbols=MYCN,REL,TP53,MTAP,CDKN2A,MYC,ERBB2,CDK1&filters=pgx:icdom-85003&output=histoplot)
- [/beacon/biosamples/?datasetIds=examplez,progenetix,cellz&referenceName=9&variantType=DEL&start=21500000&start=21975098&end=21967753&end=22500000&filters=NCIT:C3058&output=histoplot&plotGeneSymbols=CDKN2A,MTAP,EGFR,BCL6](http://progenetix.org/beacon/biosamples/?datasetIds=examplez,progenetix,cellz&referenceName=9&variantType=DEL&start=21500000&start=21975098&end=21967753&end=22500000&filters=NCIT:C3058&output=histoplot&plotGeneSymbols=CDKN2A,MTAP,EGFR,BCL6)