ggplot_associations

Get SNPs associations ggplot, either as points or as a linked area.
Optionally add labels to most associated points using ggrepel.

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_associations function

<dl><dt>df_snp</dt>
<dd>SNP annotation data frame with columns chromosome,
position, and as specified by parameters pvalue_colname
and optionally labels_colname.</dd>
<dt>pvalue_colname</dt>
<dd>Column name of df_snp with association values</dd>
<dt>labels_colname</dt>
<dd>Optional column name of df_snp with labels.
Set to NULL to remove.</dd>
<dt>n_labels</dt>
<dd>Number of labels of most associated points to display.</dd>
<dt>nudge</dt>
<dd>Nudge parameter passed to ggrepel::geom_label_repel.</dd>
<dt>linked_area</dt>
<dd>Add a linked area to associations points, default FALSE</dd>
<dt>byindex</dt>
<dd>Display by SNP index or chromosomic position (default)</dd>
<dt>colors</dt>
<dd>Colors of SNPs</dd></dl>

Arguments

Ggplot associations — ggplot_associations

<dl>

<dt>df_snp</dt>
<dd>SNP annotation data frame with columns chromosome,
position, and as specified by parameters pvalue_colname
and optionally labels_colname.</dd>


<dt>pvalue_colname</dt>
<dd>Column name of df_snp with association values</dd>


<dt>labels_colname</dt>
<dd>Optional column name of df_snp with labels.
Set to NULL to remove.</dd>


<dt>n_labels</dt>
<dd>Number of labels of most associated points to display.</dd>


<dt>nudge</dt>
<dd>Nudge parameter passed to ggrepel::geom_label_repel.</dd>


<dt>linked_area</dt>
<dd>Add a linked area to associations points, default FALSE</dd>


<dt>byindex</dt>
<dd>Display by SNP index or chromosomic position (default)</dd>


<dt>colors</dt>
<dd>Colors of SNPs</dd>

</dl>

ggplot_associations: Ggplot associations

Description

Usage

Value

Arguments