Contents

Real-case gallery
Technical examples

Real-case gallery ¶

General-purpose real-case examples for circhic.

Caulobacter crescentus¶

Data from Le et al. (2013) Science, 342(6159), 731–734

Circular Hi-C and genomic data — Circular Hi-C and genomic data¶

Zooming in chromosomal interaction domains — Zooming in chromosomal interaction domains¶

Secondary diagonal from 'distant' mode — Secondary diagonal from ‘distant’ mode¶

Raw data — Raw data¶

Escherichia coli¶

Data from Lioy et al. (2018) Cell, 172(4), 771–783

Macrodomain phenomenology — Macrodomain phenomenology¶

Human - KBM7¶

Data from Rao et al. (2014) Cell, 162(3), 687-688

A human chromosome: KBM7's chr11 — A human chromosome: KBM7’s chr11¶

Technical examples ¶

Introductory examples for circhic.

Simple plots ¶

The basic units of a circhic plot to display genomic data.

Plotting bands — Plotting bands¶

Plotting bars — Plotting bars¶

Plotting lines — Plotting lines¶

Exploring options of the circular heatmaps ¶

Square versus circular displays — Square versus circular displays¶

Using a different color map — Using a different color map¶

Radius — Radius¶

Colorbars — Colorbars¶

Plotting linear chromosomes ¶

KBM-7 cell line, chromosome XI — KBM-7 cell line, chromosome XI¶

Schemas & misc ¶

Understanding Hi-C contact maps — Understanding Hi-C contact maps¶

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