make_combined_plot | R Documentation |
Generated a combined plot with two locuszoom plots and a locuscompare plot. Each locuszoom plot represent an association study.
make_combined_plot(merged, title1, title2, ld, chr, snp = NULL, combine = TRUE, legend = TRUE, legend_position = c("bottomright", "topright", "topleft"), lz_ylab_linebreak = FALSE)
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. |
# 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)
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