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updating service links
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@mbaudis
mbaudis committed Oct 10, 2024
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14 changes: 7 additions & 7 deletions docs/common/plotting.md
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Expand Up @@ -40,7 +40,7 @@ Examples link to or are embedded from **{{api_site_label}}**.
There are two possibilities to plot CNV histograms through the Progenetix API w/o using the user interface:

1. direct visualization of pre-computed collations, e.g. publications or diagnosttic entities
* [services/collationPlots/?datasetIds={{config.api_dataset_ids}}&id=NCIT:C4443]({{config.api_web_root}}/services/collationPlots/?datasetIds={{config.api_dataset_ids}}&id=NCIT:C4443)
* [services/collationplots/?datasetIds={{config.api_dataset_ids}}&filters=NCIT:C4443]({{config.api_web_root}}/services/collationplots/?datasetIds={{config.api_dataset_ids}}&filters=NCIT:C4443)
2. a services API query in Beacon format, with the added option `&plotType=histoplot`
(which is actually the fallback so not strictly needed...)
* [services/sampleplots?limit=200&datasetIds={{config.api_dataset_ids}}&referenceName=refseq:NC_000009.12&variantType=EFO:0030067&start=21500000,21975098&end=21967753,22500000&filters=NCIT:C3058&output=histoplot]({{config.api_web_root}}/services/sampleplots?limit=200&datasetIds={{config.api_dataset_ids}}&referenceName=refseq:NC_000009.12&variantType=EFO:0030067&start=21500000,21975098&end=21967753,22500000&filters=NCIT:C3058&output=histoplot)
Expand All @@ -56,21 +56,21 @@ Please **use option 1** if accessing complete entities (i.e. only using a single

* customized plot for glioblastoma CNV frequencies, limited to chromosomes 7, 9
and 10 and
- `services/collationPlots/?datasetIds={{config.api_dataset_ids}}&id=NCIT:C3058&plotPars=plotChros=7,9,10::size_plotimage_w_px=640`
- `services/collationplots/?datasetIds={{config.api_dataset_ids}}&filters=NCIT:C3058&plotPars=plotChros=7,9,10::size_plotimage_w_px=640`

![]({{config.api_web_root}}/services/collationPlots/?datasetIds={{config.api_dataset_ids}}&id=NCIT:C3058&plotPars=plotChros=7,9,10::size_plotimage_w_px=640)
![]({{config.api_web_root}}/services/collationplots/?datasetIds={{config.api_dataset_ids}}&filters=NCIT:C3058&plotPars=plotChros=7,9,10::size_plotimage_w_px=640)

* plot with modified maximum Y - `value_plot_y_max` (histogram's maximum value
in percent) and some custom label
- `services/collationPlots/?id=pgx:icdom-80703&plotPars=value_plot_y_max=50::plot_region_labels=5:0-48000000:Frequent+5p+gain,8:127735434-127742951:MYC::plot_marker_font_size=12`
- `services/collationplots/?filters=pgx:icdom-80703&plotPars=value_plot_y_max=50::plot_region_labels=5:0-48000000:Frequent+5p+gain,8:127735434-127742951:MYC::plot_marker_font_size=12`

![]({{config.api_web_root}}/services/collationPlots/?datasetIds={{config.api_dataset_ids}}&id=pgx:icdom-80703&plotPars=value_plot_y_max=50::plot_region_labels=5:0-48000000:Frequent+5p+gain,8:127735434-127742951:MYC::plot_marker_font_size=12)
![]({{config.api_web_root}}/services/collationplots/?datasetIds={{config.api_dataset_ids}}&filters=pgx:icdom-80703&plotPars=value_plot_y_max=50::plot_region_labels=5:0-48000000:Frequent+5p+gain,8:127735434-127742951:MYC::plot_marker_font_size=12)

* as above, but plastering some cancer driver genes on the plot by their gene
symbols (`plot_gene_symbols`):
- `services/collationPlots/?datasetIds={{config.api_dataset_ids}}&id=pgx:icdom-80703&plotPars=value_plot_y_max=50::plot_gene_symbols=MYC,MYCN,REL,ERBB2,TP53,CCND1,EGFR,BCL2,RB1::plot_marker_font_size=10`
- `services/collationplots/?datasetIds={{config.api_dataset_ids}}&filters=pgx:icdom-80703&plotPars=value_plot_y_max=50::plot_gene_symbols=MYC,MYCN,REL,ERBB2,TP53,CCND1,EGFR,BCL2,RB1::plot_marker_font_size=10`

![]({{config.api_web_root}}/services/collationPlots/?datasetIds={{config.api_dataset_ids}}&id=pgx:icdom-80703&plotPars=value_plot_y_max=50::plot_gene_symbols=MYC,MYCN,REL,ERBB2,TP53,CCND1,EGFR,BCL2,RB1::plot_marker_font_size=10)
![]({{config.api_web_root}}/services/collationplots/?datasetIds={{config.api_dataset_ids}}&filters=pgx:icdom-80703&plotPars=value_plot_y_max=50::plot_gene_symbols=MYC,MYCN,REL,ERBB2,TP53,CCND1,EGFR,BCL2,RB1::plot_marker_font_size=10)


### Sample Strip Plots
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8 changes: 4 additions & 4 deletions docs/news/2022-02-18-excluding-reference-samples.md
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Expand Up @@ -13,11 +13,11 @@ a term we had introduced into the Experimental Factor Ontology - are excluded fr
pre-computed histograms. However, when e.g. calling up samples from publications
using the search panel referencve samples will be included unless specifically excluded.

![](http://progenetix.org/cgi/PGX/cgi/collationPlots.cgi?datasetIds=progenetix&id=PMID:22824167)
<div style="font-size: 0.8em;">Pre-computed CNV Frequencies for <a href="http://progenetix.org/publication/?id=PMID:22824167">PMID:22824167</a>, now ommitting reference samples by default</div>
![](http://progenetix.org/services/collationplots/?datasetIds=progenetix&filters=PMID:22824167)
<div style="font-size: 0.8em;">Pre-computed CNV Frequencies for <a href="http://progenetix.org/publication/?filters=PMID:22824167">PMID:22824167</a>, now ommitting reference samples by default</div>

<!--more-->

![](http://progenetix.org/beacon/biosamples?datasetIds=progenetix&filters=PMID:22824167&output=histoplot)
<div style="font-size: 0.8em;">All samples for <a href="http://progenetix.org/publication/?id=PMID:22824167">PMID:22824167</a> were used when just retrieving by PMID</div>
![](http://progenetix.org/services/samplesplot?datasetIds=progenetix&filters=PMID:22824167&plotType=histoplot)
<div style="font-size: 0.8em;">All samples for <a href="http://progenetix.org/publication/?filters=PMID:22824167">PMID:22824167</a> were used when just retrieving by PMID</div>

44 changes: 9 additions & 35 deletions docs/progenetix-data-review.md
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Expand Up @@ -7,57 +7,31 @@ added to Progenetix in the first place. Please check & comment when done.

Large bias towards deletions. Is (probably) from cDNA arrays (since Pollack/Stanford)? Baseline/threshold correction?

![](http://progenetix.org/cgi/PGX/cgi/collationPlots.cgi?datasetIds=progenetix&id=PMID:19383354)
![](http://progenetix.org/services/collationplots/?datasetIds=progenetix&filters=PMID:19383354)

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

* [ ] **2022-05-27: [PMID:27257180](http://progenetix.org/publication/?id=PMID:27257180)**

This mostly looks like noise?

![](http://progenetix.org/cgi/PGX/cgi/collationPlots.cgi?datasetIds=progenetix&id=PMID:27257180)
![](http://progenetix.org/services/collationplots/?datasetIds=progenetix&filters=PMID:27257180)

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

* [ ] **2022-04-04 [pgx:icdom-84421](http://progenetix.org/subset/?datasetIds=progenetix&id=pgx:icdom-84421)**

The samples are highly skewed towards deletion...

![](http://progenetix.org/cgi/PGX/cgi/collationPlots.cgi?datasetIds=progenetix&id=pgx:icdom-84421)

--------------------------------------------------------------------------------
<!--
* [X] **2022-02-07 [PMID:16737909](http://progenetix.org/publication/?id=PMID:16737909)**
* [X] **2022-02-07 [PMID:16790082](http://progenetix.org/publication/?id=PMID:16790082)**
Excluded due to lacking CNV annotations (source file w/ complex karyotypes but
not parsed correctly in FMP).
* [X] **2022-02-02 [PMID:17934521](http://progenetix.org/publication/?id=PMID:17934521)**
* SOLVED 2022-02-02: the 12 samples w/ platform geo:GPL5055 have _only_ chr1 probes; **removed**. The other 96 arrays (like the exaample below) are GPL5056 and have also genome covering probes
* odd provenance; the samples have been tagged - and seem to correspond - to [GSE7428](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7426) with the data per sample on the
server corresponding to the **chr 1 only** arrays from GEO
* however, the stored variants & summary profile indicate nice whole-genome CNV profiles
* have to look-up provenance; maybe mix of annotations (from where?) and arrays?
![](http://progenetix.org/cgi/PGX/cgi/collationPlots.cgi?datasetIds=progenetix&id=PMID:17934521)
* This example really looks like a combination of whole-chromosome CNVs & array for chr1:
![](http://progenetix.org/cgi/PGX/cgi/singlePlot.cgi?analysisIds=pgxcs-kftw94yk&datasetIds=progenetix)
-->
![](http://progenetix.org/services/collationplots/?datasetIds=progenetix&filters=pgx:icdom-84421)

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

* [ ] **2022-01-19 [PMID:24454681](http://progenetix.org/publication/?id=PMID:24454681)**

* noisy

![](http://progenetix.org/cgi/PGX/cgi/collationPlots.cgi?datasetIds=progenetix&id=PMID:24454681)
![](http://progenetix.org/services/collationplots/?datasetIds=progenetix&filters=PMID:24454681)


--------------------------------------------------------------------------------
Expand All @@ -66,15 +40,15 @@ server corresponding to the **chr 1 only** arrays from GEO

* very biased towards deletion

![](http://progenetix.org/cgi/PGX/cgi/collationPlots.cgi?datasetIds=progenetix&id=geo:GSE58579)
![](http://progenetix.org/services/collationplots/?datasetIds=progenetix&filters=geo:GSE58579)

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

* [ ] **2022-01-18 [PMID:23583283](http://progenetix.org/publication/?id=PMID:23583283)**
* [ ] **2022-01-18 [PMID:23583283](http://progenetix.org/publication/?filters=PMID:23583283)**

* noisy and biased to deletion

![](http://progenetix.org/cgi/PGX/cgi/collationPlots.cgi?datasetIds=progenetix&id=PMID:23583283)
![](http://progenetix.org/services/collationplots/?datasetIds=progenetix&id=PMID:23583283)

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

Expand All @@ -91,7 +65,7 @@ server corresponding to the **chr 1 only** arrays from GEO

* baseline shifted towards deletions

![](http://progenetix.org/cgi/PGX/cgi/collationPlots.cgi?datasetIds=progenetix&id=PMID:22962301)
![](http://progenetix.org/services/collationplots/?datasetIds=progenetix&filters=PMID:22962301)

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

Expand All @@ -101,6 +75,6 @@ server corresponding to the **chr 1 only** arrays from GEO
* AFAIK was from methylation arrays & kept for DIPG project?
* review / discard / select samples?

![](http://progenetix.org/cgi/PGX/cgi/collationPlots.cgi?datasetIds=progenetix&id=PMID:23417712)
![](http://progenetix.org/services/collationplots/?datasetIds=progenetix&filters=PMID:23417712)

--------------------------------------------------------------------------------
6 changes: 3 additions & 3 deletions docs/use-cases.md
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Expand Up @@ -70,7 +70,7 @@ external project such as TCGA

This data can be accessed through the Progenetix API in data and image format.

![Example CNV histogram with custom parameters](http://progenetix.org/cgi/PGX/cgi/collationPlots.cgi?id=NCIT:C7376&-size_plotarea_h_px=40&-value_plot_y_max=50&-colorschema=bluered&plotChros=1,3,9,17,22)
![Example CNV histogram with custom parameters](http://progenetix.org/services/collationplots/?filters=NCIT:C7376&-size_plotarea_h_px=40&-value_plot_y_max=50&-colorschema=bluered&plotChros=1,3,9,17,22)

Interval frequencies are per default stored in a 1Mb binned format. More
information about the API use can be found [in the IntervalFrequencies API documentation](services.md#pgxseg-segment-cnv-frequencies).
Expand Down Expand Up @@ -134,8 +134,8 @@ added (single) collation code.

##### Examples

* [progenetix.org/services/collationplots/?id=pgx:icdom-85003](http://progenetix.org/services/collationplots/?id=pgx:icdom-85003)
* [progenetix.org/services/collationplots/?id=PMID:22824167](http://progenetix.org/services/collationplots/?id=PMID:22824167)
* [progenetix.org/services/collationplots/?filters=pgx:icdom-85003](http://progenetix.org/services/collationplots/?filters=pgx:icdom-85003)
* [progenetix.org/services/collationplots/?filters=PMID:22824167](http://progenetix.org/services/collationplots/?filters=PMID:22824167)

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

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2 changes: 1 addition & 1 deletion src/hooks/api.js
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Expand Up @@ -413,7 +413,7 @@ export function useGeneSymbol({ geneId }) {
}

export function subsetHistoBaseLink(id, datasetIds) {
return `${SITE_DEFAULTS.API_PATH}services/collationplots/?datasetIds=${datasetIds}&id=${id}`
return `${SITE_DEFAULTS.API_PATH}services/collationplots/?datasetIds=${datasetIds}&filters=${id}`
}

// the targets are resolved by `bycon` (bycon/services/ids.py)
Expand Down

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