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Radar plot for L2G partial scores from studiesAndLeadVariantsForGeneByL2G()

Source: R/plot_l2g.R
plot_l2g.Rd

This function returns a radar plot to compare the partial scores, important for prioritising the causal genes that are obtained from the studiesAndLeadVariantsForGeneByL2G() function. The user can decide to plot only for a specific disease by specifying an EFO ID for the disease argument, otherwise the returned plot will will facet based on existing traits/diseases in the outputs from studiesAndLeadVariantsForGeneByL2G().

Usage

plot_l2g(data, disease_efo = NULL, l2g_cutoff = 0.5, top_n_disease = 1)

Arguments

data

Data frame: result of studiesAndLeadVariantsForGeneByL2G function.

disease_efo

Character: Input EFO id to filter the L2G data for a particular disease.

l2g_cutoff

Numeric: Sets the minimum L2G score threshold for diseases to be considered in the plot.

top_n_disease

Numeric: Determines the number of top diseases to plot for each gene, ranked by L2G score.

Value

A radar plot for the input disease and the genes associated with that disease. The variables shown include L2G score, chromatin interaction, variant pathogenicity and distance.

Examples

if (FALSE) { # \dontrun{
p <- studiesAndLeadVariantsForGeneByL2G(list("ENSG00000167207","ENSG00000096968",
  "ENSG00000138821", "ENSG00000125255")) %>% plot_l2g(disease = "EFO_0003767")
p
} # }