cr_genes_gtrellis: Visualize CR genes in gtrellis layout

In jokergoo/epik: Integrative Analysis and Visualization of Epigenomic Sequencing Data

Description

Visualize CR genes in gtrellis layout

Usage

cr_genes_gtrellis(cr, txdb, expr)

Arguments

cr	correlated regions, should be returned by cr_enriched_heatmap
txdb	transcriptome annotation which was used in correlated_regions
expr	expression matrix which was used in correlated_regions

Details

CR genes in k-means group 1 and 4 (which correspond to negative correlated gene body and positive correlated gene body) are visualized in gtrellis layout. Cytobands which are significantly overlapped by CR genes are highlighted. In gtrellis layout, there are following tracks:

• rainfall plot for genes in k-means cluster 1. The y-axis corresponds to the minimal distance to neighbouring genes. The color of points corresponds to the epxression value (blue is low expression and red is high expression) and size of points corresponds to gene length.

• a one row heatmap showing how much each cytoband is covered by CR genes in cluster 1.

• rainfall plot for genes in k-means cluster 4

• a one row heatmap showing how much each cytoband is covered by CR genes in cluster 4.

• cytoband

Value

A list of two elements which shows how each cytoband is overlapped by CR genes

Author(s)

Zuguang Gu <[e-mail]>

Examples

# There is no example
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jokergoo/epik documentation built on Sept. 28, 2019, 9:20 a.m.