Plots & Data Visualizations

Image Formats

The standard format for (plot-)images generated on Progenetix is Scalable Vector Graphics (SVG). As the name implies, SVG is scalable, i.e. images can be scaled up without loosing quality or expanding in storage size. However, some of teh generated images use also embedded rastered components which will deteriorate during scaling - this is e.g. the case for array probe plots.

Wikipedia

All major modern web browsers—including Mozilla Firefox, Internet Explorer, Google Chrome, Opera, Safari, and Microsoft Edge—have SVG rendering support.

On most pages where plots are being displayed there is a download option for the images - (please alert us where those are missing). Browsers also have the option to export SVGs themselves e.g. as PDF.

The bycon plotting library

• read and write e.g. Progentix .pgxseg segment files
• render plots of sample-specific and aggregate CNV data, such as histograms clustered CNV sample strips

Links

• bycon plot documentation with all plot parameters

Plot Types

CNV Histogram Plots

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
   • progenetix.org/services/collationPlots/?datasetIds=progenetix&id=NCIT:C4443
2. a Beacon API query with the added option &output=histoplot
   • progenetix.org/beacon/biosamples/?limit=200&datasetIds=progenetix&referenceName=refseq:NC_000009.12&variantType=EFO:0030067&start=21500000,21975098&end=21967753,22500000&filters=NCIT:C3058&output=histoplot

Please use option 1 if accessing complete entities (i.e. only using a single filters value) - this option is not limited through large sample numbers.

Examples

• customized plot for glioblastoma CNV frequencies, limited to chromosomes 7, 9 and 10
  • progenetix.org/services/collationPlots/?id=NCIT:C3058&chr2plot=7,9,10&colorschema=redgreen&size_plotimage_w_px=640

Additional plot parameters

Plot parameters can be added to the request using a standard &__parameter__=__value__ syntax.

• chr2plot
  • comma-concatenated list of chromosomes to plot
  • default is 1 -> 22 since X & Y are not always correctly normalized for CNV frequencies
    • chr2plot=1,2,3,44,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y
    • chr2plot=9
• size_plotimage_w_px
  • modifies the width of the plot image in px (default 800)
  • progenetix.org/services/collationPlots/?id=PMID:22824167&size_plotimage_w_px=1084
• size_plotarea_h_px
  • height of the plot area (excluding labels etc.) in px (default 100)
  • progenetix.org/services/collationPlots/?id=NCIT:C7376&size_plotarea_h_px=300
• size_text_title_px
  • size in px of the title text (default 14)
• value_plot_y_max
  • modifies the histogram's maximum value in percent (default 100)
  • progenetix.org/services/collationPlots/?id=pgx:cohort-TCGAcancers&value_plot_y_max=50
• labels
  • arbitrary labels (e.g. for genes or other regions of interest)
  • format is chro : start - end : some text
  • multiple labels can be concatenated by ,
  • colors are randomized from a "decent" palette
  • progenetix.org/services/collationPlots/?id=pgx:icdom-80123&value_plot_y_max=80&chr2plot=5,8&labels=5:0-48000000:Frequent+5p+gain,8:127735434-127742951:MYC&marker_text_px=12
• marker_text_px
  • text size for the labels (default 10)

• marker_opacity

  • opacity of the region overlay on the plot (default 0.2)

• colorschema

  • change of colors used for gains and losses

  • options

    • orangeblue (default)
    • redgreen
    • greenred
    • bluered

  • progenetix.org/services/collationPlots/?id=NCIT:C7376&size_plotarea_h_px=40&value_plot_y_max=50&colorschema=bluered&chr2plot=1,3,9,17,22

The PGX plotting library

Plots on Progenetix are generated using the PGX package, a set of Perl libraries for processing and graphical representation of CNV data. The package contains tools to

• ~~read and write e.g. Progentix segment files
• generate binned status maps
• render plots of sample-specific and aggregate CNV data, such as histograms and CNV frequency heatmaps