ggplot_snp_pos

Get SNPs position ggplot with mappings to combine with other ggplots.
Optionally add labels and an upper subset.

Linkage disequilibrium visualizations of up to several hundreds of single nucleotide polymorphisms (SNPs), annotated with chromosomic positions and gene names. Two types of plots are available for small numbers of SNPs (<40) and for large numbers (tested up to 500). Both can be extended by combining other ggplots, e.g. association studies results, and functions enable to directly visualize the effect of SNP selection methods, as minor allele frequency filtering and TagSNP selection, with a second correlation heatmap. The SNPs correlations are computed on Genotype Data objects from the 'GWASTools' package using the 'SNPRelate' package, and the plots are customizable 'ggplot2' and 'gtable' objects and are annotated using the 'biomaRt' package. Usage is detailed in the vignette with example data and results from up to 500 SNPs of 1,200 scans are in Charlon T. (2019) <doi:10.13097/archive-ouverte/unige:161795>.

Thomas Charlon

snplinkage

Single Nucleotide Polymorphisms Linkage Disequilibrium
Visualizations

Karl Forner

Alessandro Di Cara

Jérôme Wojcik

ggplot_snp_pos function

<dl><dt>df_snp</dt>
<dd>SNP annotation data frame with a column named position
and, if specified, one named as the labels_colname
parameter.</dd>
<dt>upper_subset</dt>
<dd>Subset of df_snp for the positions on the upper side</dd>
<dt>labels_colname</dt>
<dd>Optional column name of df_snp to use as SNP labels.</dd>
<dt>colors</dt>
<dd>Colors for each SNP</dd></dl>

Arguments

Ggplot SNPs position — ggplot_snp_pos

<dl>

<dt>df_snp</dt>
<dd>SNP annotation data frame with a column named position
and, if specified, one named as the labels_colname
parameter.</dd>


<dt>upper_subset</dt>
<dd>Subset of df_snp for the positions on the upper side</dd>


<dt>labels_colname</dt>
<dd>Optional column name of df_snp to use as SNP labels.</dd>


<dt>colors</dt>
<dd>Colors for each SNP</dd>

</dl>

ggplot_snp_pos: Ggplot SNPs position

Description

Usage

Value

Arguments