Functions overview

The GAMBLR.viz package proveds a set of function families to visualize and plot a wide range of different types of genomic data and their combinations. Below is the summary overview of the functions available with GAMBLR.viz:

pretty functions

  • prettyChromoplot Chromosome plot displaying the frequency of CNVs across genome using GISTIC2.0 scores output.
  • prettyOncoplot Oncoplot displaying frequency and type of coding mutations.
  • prettyCoOncoplot Side-by-side oncoplots for two comparisons groups. This function is a convenient wrapper around the prettyOncoplot function.
  • prettyForestPlot Compare frequrncy of mutations between two different groups ans generate summary forest plot.
  • prettyGeneCloud Gene cloud plot.
  • prettyRainfallPlot Visualize intermutational distance between individual mutations and compare it to the position of structural variants.
  • pretty_lollipop_plot Lollipop Plot (generates HTML output).

fancy functions

  • fancy_alignment_plot Plot Alignment Metrics
  • fancy_circos_plot SSM and SV Circos Plot.
  • fancy_cnbar Copy Number states barplot.
  • fancy_ideogram Genome-wide ideogram annotated with SSM and CN information.
  • fancy_multisamp_ideogram Genome-wide ideogram (CN segments) for multiple samples.
  • fancy_propcov_plot Proportional Coverage Plot.
  • fancy_proportions_plot Proportional Metrics Plot.
  • fancy_qc_plot Plot Quality Control Metrics.
  • fancy_snv_chrdistplot n SNVs per chromosome plot.
  • fancy_sv_sizedens Structural Variants Size Plot.
  • fancy_v_chrcount Number of variants per chromosome plot.
  • fancy_v_count Total number of variants count plot.
  • fancy_v_sizedis Variant size distribution plot.

Other functions

  • ashm_multi_rainbow_plot Multi-panel Rainbow Plot to display aSHM across several regions.
  • ashm_rainbow_plot Rainbow Plot to display aSHM across one region of interest.
  • comp_report Sample-level SV/SSM/CN reports in PDF
  • copy_number_vaf_plot Copy Number VAF Plot.
  • focal_cn_plot Copy Number Segments Plot.
  • heatmap_mutation_frequency_bin Heatmap of mutation counts across sliding windows for multiple regions.
  • map_metadata_to_colours Assign a colour palette to metadata columns automatically and consistently.
  • plot_sample_circos Sample-level Circos Plot.
  • splendidHeatmap Heatmap of features to visualize NMF and random forest classifiers.
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