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2D genomic heatmaps #136

Merged
merged 28 commits into from
Feb 23, 2019
Merged

2D genomic heatmaps #136

merged 28 commits into from
Feb 23, 2019

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eweitz
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@eweitz eweitz commented Feb 23, 2019

This adds a new annotation layout for 2D genomic heatmaps.

Such 2D heatmaps are great for visualizing large data tables. The motivating example for 2D heatmaps is depicting an expression matrix of how much each gene is expressed in each cell -- for all genes across all cells in a sample set. (Expression matrices are commonly output from single-cell RNA-seq.) The rich granular views from 2D heatmaps complement the glanceable summaries provided by 1D heatmaps.

The 2D heatmap requires a TSV expression matrix file, and can only be displayed vertically on a single human chromosome at a given time. Support for more organisms and more efficient matrix file formats is planned.

This brain cancer example shows how 2D heatmaps enable inspection of genome-wide summaries:

ideogram_2d_genomic_heatmap

eweitz added 28 commits January 22, 2019 23:15
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Coverage Status

Coverage decreased (-0.2%) to 91.605% when pulling 6bdccd7 on 2d-genomic-heatmaps into 770ce1f on master.

@eweitz eweitz merged commit 3506ee6 into master Feb 23, 2019
@eweitz eweitz deleted the 2d-genomic-heatmaps branch April 24, 2019 13:49
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