make_combined_plot: Generated a combined plot with two locuszoom plots and a...

In boxiangliu/locuscomparer: locuscomparer: Visualization of GWAS-QTL Colocalization Events

Generated a combined plot with two locuszoom plots and a locuscompare plot. Each locuszoom plot represent an association study.

Description

Generated a combined plot with two locuszoom plots and a locuscompare plot. Each locuszoom plot represent an association study.

Usage

make_combined_plot(merged, title1, title2, ld, chr, snp = NULL,
  combine = TRUE, legend = TRUE, legend_position = c("bottomright",
  "topright", "topleft"), lz_ylab_linebreak = FALSE)

Arguments

merged	(data.frame) An input data.frame which has the following columns: rsid, pval1 (p-value for study 1), logp1 (p-value for study 2), logp1 (log p-value for study 1), logp2 (log p-value for study 2), chr, pos. See the example for 'get_lead_snp()' on how to generate this data.frame.
title1	(string) The title for the x-axis.
title2	(string) The title for the y-axis.
ld	(data.frame) The output from 'retrieve_LD()'.
chr	(string) Chromosome name. e.g. '22'. Notice that the name should not contain 'chr'.
snp	(string, optional) SNP rsID. If NULL, the function will select the lead SNP. Default: NULL.
combine	(boolean, optional) Should the three plots be combined into one plot? If FALSE, a list of three plots will be returned. Default: TRUE.
legend	(boolean, optional) Should the legend be shown? Default: TRUE.
legend_position	(string, optional) Either 'bottomright','topright', or 'topleft'. Default: 'bottomright'.
lz_ylab_linebreak	(boolean, optional) Whether to break the line of y-axis of the locuszoom plot. If FALSE, the y-axis title and '-log10(p-value)'. will be on the same line. Default: FALSE.

Examples

# The data.frame `merged` comes from the example of `add_label()`.
# the data.frame `ld` comes from the example for `retrieve_LD()`.
make_combined_plot(merged, 'GWAS', 'eQTL', ld, chr)

boxiangliu/locuscomparer documentation built on Nov. 27, 2022, 7:26 a.m.