plot_gwas | R Documentation |
Plot annotated manhattan plot
plot_gwas( gwas_table, title = "No Title", subtitle = NULL, p_filter = 2, mac_filter = 0, nlabels = 5, annotated = TRUE, labeltype = "GeneId", match_nearest = FALSE )
gwas_table |
Object returned from |
title |
Specify plot title |
subtitle |
Specify plot subtitle |
p_filter |
everything with a log10(p) below this value will not be included in the plot (default: 2) |
mac_filter |
everything with a mac (minor allele count) below this will not be plotted. (default: 0) |
nlabels |
How many labels should be plotted (default: 5) |
annotated |
Should the plot contain annotations for some peaks (controls see below)? Default is TRUE |
labeltype |
Which entry from the lookup should be displayed (character, defaults to "GeneId"). Options: SNP_rank, chrom, pos, Significant, log10_p, mac, GeneId, max_distance, description, transcript_biotype, start_position, end_position. |
match_nearest |
Defaults to FALSE; if TRUE will use find_nearest_genes instead of find_overlapping_genes for annotations |
Based on a GWAS table, generates a manhatten plot, with gene annotations. Number of annotations can be toggled by changing nlabels. By default only plots annotations for SNPs that are within a gene annotation. For performance reasons, everything with a log10(p) smaller than p_filter is filtered out.
format_gwas
plot_gwas
get_nearest_genes
get_overlapping_genes
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