CircosTargets: Circos plot for the Transcription Factors/genes targets.

In cbiagii/CeTF: Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

Circos plot for the Transcription Factors/genes targets.

Description

Generate an plot for Transcription Targets (TFs) or any gene targets. This plot consists of sorting all the chromosomes of any specie based in GTF annotation file and showing how the selected TF(s)/gene(s) targets are distributed. If a target is connected to the same chromosome as the selected one so the connection is defined as cis, otherwise it is a trans connection.

Usage

CircosTargets(object, file, nomenclature, selection, cond)

Arguments

object	CeTF class object resulted from runAnalysis function.
file	GTF file or path.
nomenclature	Gene nomenclature: SYMBOL or ENSEMBL.
selection	Specify a single or up to 4 TF/gene to be visualized for.
cond	The options are condition1 or condition2 based on the conditions previously defined in runAnalysis function.

Details

The black links are between different chromosomes while the red links are between the same chromosome.

Value

Returns an plot with a specific(s) TF/gene and its targets in order to visualize the chromosome location of each one.

Examples

## Not run: 
CircosTargets(object = out, 
file = '/path/to/gtf/specie.gtf', 
nomenclature = 'SYMBOL', 
selection = 'TCF4', 
cond = 'condition1')

## End(Not run)

cbiagii/CeTF documentation built on Feb. 1, 2023, 3:19 p.m.