ggplot_ld

Display SNP r2 correlations using points or diamonds with text.

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_ld function

<dl><dt>df_ld</dt>
<dd>Data frame with columns SNP_A, SNP_B, and R2.
As returned by the snprelate_ld function.</dd>
<dt>diamonds</dt>
<dd>Should the values be displayed as diamonds or points ?
Default is TRUE for less than 40 SNPs.</dd>
<dt>point_size</dt>
<dd>Size for geom_point. Ignored if diamonds is TRUE.</dd>
<dt>reverse</dt>
<dd>Reverse the display (horizontal symmetry)</dd>
<dt>reindex</dt>
<dd>If FALSE, SNPs are positionned following their IDs</dd></dl>

Arguments

Ggplot linkage disequilibrium — ggplot_ld

<dl>

<dt>df_ld</dt>
<dd>Data frame with columns SNP_A, SNP_B, and R2.
As returned by the snprelate_ld function.</dd>


<dt>diamonds</dt>
<dd>Should the values be displayed as diamonds or points ?
Default is TRUE for less than 40 SNPs.</dd>


<dt>point_size</dt>
<dd>Size for geom_point. Ignored if diamonds is TRUE.</dd>


<dt>reverse</dt>
<dd>Reverse the display (horizontal symmetry)</dd>


<dt>reindex</dt>
<dd>If FALSE, SNPs are positionned following their IDs</dd>

</dl>

ggplot_ld: Ggplot linkage disequilibrium

Description

Usage

Value

Arguments