genome_loadings: Plot Component Loadings by Genomic Location

In marchinilab/SDAtools: SDAtools: A toolkit for SDA

Description

genome_loadings Plot Component Loadings by Genomic Location

Usage

genome_loadings(component = NULL, max.items = 20, label.size = 3,
  label.repel = 1, label_both = TRUE, label_X = FALSE,
  min_loading = 0.01, gene_locations = NULL,
  chromosome_lengths = NULL, hide_unknown = FALSE,
  highlight_genes = NULL, label_genes = NULL)

Arguments

component	numeric; A named numeric vector containing the gene loadings and their names as the attribute "names"
max.items	integer; Number of genes to label each side of 0. I.e. if label_both is TRUE then the total number of labels will be twice max.items.
label.size	numeric; size of point labels
label.repel	numeric; force of label repulsion
label_both	logical; If TRUE the top N genes by absolute loadings will be labeled. If FALSE only genes with either positive OR negative loadings will be labeled, depending on which side has the largest loading.
label_X	logical; if TRUE forces labelling of the X chromosome
min_loading	numeric; threshold on loading for labeling points;
gene_locations	data.table; The output of load_gene_locations() containing the gene chromosome location coordinates, if not given load_gene_locations() will be called internally.
chromosome_lengths	data.table; The ouput of load_chromosome_lengths(), if not given load_chromosome_lengths() will be called internally.
hide_unknown	logical; if TRUE genes wihtout a chromosome (e.g. placed in scaffolds) are not plotted
highlight_genes	charachter vector of gene names; if provided, these genes will be coloured red
label_genes	charachter vector of gene names; if provided these genes will be labeled in addition to the others

Value

A data table of statistics and their values

Examples

data(results)
genome_loadings(results$loadings[[1]][8,])

marchinilab/SDAtools documentation built on Jan. 31, 2020, 3:51 a.m.