plot_ideogram: Ideogram of SConES results.
In hclimente/martini: GWAS Incorporating Networks
plot_ideogram R Documentation
Ideogram of SConES results.
Description
Create a circular ideogram of the a network results using the
circlize package (Gu et al., 2014).
Usage
plot_ideogram(gwas, net, covars = data.frame(), genome = "hg19")
Arguments
gwas
A SnpMatrix object with the GWAS information.
net
An igraph network that connects the SNPs.
covars
A data frame with the covariates. It must contain a column
'sample' containing the sample IDs, and an additional columns for each
covariate.
genome
Abbreviations of the genome to use: hg19 for human (default),
mm10 for mouse, etc.
Value
A circular ideogram, including the manhattan plot, and the
interactions between the selected SNPs.
References
Gu, Z., Gu, L., Eils, R., Schlesner, M., & Brors, B. (2014).
circlize Implements and enhances circular visualization in R. Bioinformatics
(Oxford, England), 30(19), 2811-2.
https://doi.org/10.1093/bioinformatics/btu393
hclimente/martini documentation built on Feb. 26, 2024, 6:23 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
| plot_ideogram | R Documentation |
Ideogram of SConES results.
Description
Create a circular ideogram of the a network results using the circlize package (Gu et al., 2014).
Usage
plot_ideogram(gwas, net, covars = data.frame(), genome = "hg19")
Arguments
gwas |
A SnpMatrix object with the GWAS information. |
net |
An igraph network that connects the SNPs. |
covars |
A data frame with the covariates. It must contain a column 'sample' containing the sample IDs, and an additional columns for each covariate. |
genome |
Abbreviations of the genome to use: hg19 for human (default), mm10 for mouse, etc. |
Value
A circular ideogram, including the manhattan plot, and the interactions between the selected SNPs.
References
Gu, Z., Gu, L., Eils, R., Schlesner, M., & Brors, B. (2014). circlize Implements and enhances circular visualization in R. Bioinformatics (Oxford, England), 30(19), 2811-2. https://doi.org/10.1093/bioinformatics/btu393
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.