(GDC correlation) new mass chart types for quick access to Mutation-Diagnosis or similar

[xzhou82]

4 plots have been added. more could be added later depends on feedback
please test at http://localhost:3000/?noheader=1&gdccorrelation=1&filter0={%22op%22:%22in%22,%22content%22:{%22field%22:%22cases.primary_site%22,%22value%22:[%22brain%22,%22breast%22]}}, with master code, please let me know issues

url has a default filter to restrict case size and make the plot run faster. delete filter0= for much slower response

[xzhou82]

• BUG at geneV chart, add gene exp as term2 breaks in TermSettingApi.ts
• inconvenience: on clicking CNV vs Exp chart btn, gene search box focus disappears in 1 second
• BUG selecting age term breaks. this was fixed but breaks again with mismatched tw.q.type and term.bins (fails with case.diagnoses.age_at_diagnosis, which has tw.q.type='regular-bin' but term.bins.default.type='custom-bin')
• allow to customize sandbox header name for launched plot
• mutation gene search to support region in addition to gene names
• gene exp-survival should default to q.mode=binary to show up to 3 curves rather than many curves from regular bin
• gene exp violin list sample breaks
• barchart click bar label to show menu for standard behavior
• bar clicking to List sample to add gdc portal case links
• after searching gene for mutation/cnv, it runs two /categories and one /barsql before chart is shown. very slow for geneset
• summary chart using cnv categories (gain/loss etc) should use common.mclass[].color but not auto-assigned colors
• when using geneVariant, barchart List sample may show actual gene mutation for each sample to be informative. even better when geneVariant is geneset, the List sample shows both gene & mutation for each sample
• genevariant geneset barchart List sample not working for gdc
• SearchHandler.init() should accept customization e.g. to check CNV but not SNV/indel by default
• for survival-related chart type, clicking a survival term pill should disable Edit as there's nothing to edit. for gdc, nice to also disable Replace as gdc has just one survival term
• in gdc, survival plot launched from Survival chart btn can show Year in xlab, but not from exp-survival chart button
• ds will define optional unit for gene exp and make it available to client at termdbConfig.queries.geneExp.unit. summary charts and whereever using geneExp term should show unit || 'expression'
• violin brush and List sample menu behavior should be same as barchart List sample
• SLOPPY VIOLIN - server-side tick plot looks fuzzy and should be made crisper; rename config menu option Symbol size to Tick Size
• SLOPPY VIOLIN - List sample table should not hardcode "Action>View" column. only do it when sampleView is in allowedChartTypes
• SLOPPY VIOLIN - plot width param not observed
• RIDICULUS VIOLIN - get rid of convertViolinData();new violinRenderer should directly work with vocabApi.getViolinPlotData result without
• violin by genemut violin with smaller cohort should not span all to max; List sample breaks (does this mean that a violin plot should end at its max value, not at the max value across all plots? List sample seems to work fine)
• violin fails to show alert msg when there's no sample due to filtering
• violin w/survival list sample breaks
• violin term2=cat groupsetting List sample won't show data
• violin plot lacks "Loading..." indicator (Seems to already have this indicator)
• violin: gene exp & gene mut List sample breaks
• violin drag tooltip placement bug: at link drag to right end, the tooltip will show up at window bottom left
• GDC gene exp less than 1 line violin link brush and List to get this err
• select2Term should yield tw but not term so facet works with geneV
• BUG barchart list sample fails for term2=survival (works with gdc, issue only occurs with TermdbTest due to sampleType)
• genesearch tooltip stays after hitting enter
• BUG numeric termsetting custom bin label is no longer shown
• BUG numeric termsetting custom bin label not auto populated after entering a break value in textarea at link
• BUG tdbtest xyz barchart list sample breaks (issue is specific to TermdbTest, as barchart list sample works for gdc)
• reduce excessive white space on left of survival plot
• (Airen) scatter: will be nice for the plot not to "flash" when clicking the lasso button
• (Airen) scatter: at dynamic scatter using two terms for X/Y, lasso and List sample table should also include X/Y term values
• in summarizeMutationDiagnosis.ts for snvindel, searching coordinate in gene search box breaks
• geneset edit ui add an optional new INPUT for geneset name; enable this field for genevariant tw edit ui (when geneset radio btn is selected). on selecting a msigdb geneset, the msigdb term name should populate to this new INPUT in geneset edit ui; then it becomes the genevariant term name. this is user friendly and solves a headache of summary chart getting crazy term name of comma-joined string (Done in branch)
• geneVariant gene list max size should limit to 100 to ensure performance. if need to apply this limit on both client & back (Done in branch)
• Survival: at risk counts - click -> move up/down not working
• Survival: at risk counts - click -> color -> should add submit button
• Survival: 95% CI – Suggest spelling out (95% Confidence Interval) (Done in branch)
• Survival: Mouseover missing for 95% CI, Censored Symbol, and Default color. Also, Mouseover fades too fast to be able to read, especially for Survival Time Visualized. (Done in branch)
• Survival: Changing the Time Factor and Unit works, but it may result in incorrect information (e.g., Change Time Unit to Days. Days are displayed but the values are still years)
• Survival: Not sure what the default color does. It did not appear to change any color when a new color was selected
• Survival: Would be nice to have a reset option and not just an undo
• improve scatter tests