View source: R/highlight_miami.R
highlight_miami | R Documentation |
Make highlight data.frame for miami plot
highlight_miami(
data,
highlight,
highlight_col,
highlight_color = "green",
logged_p = "logged_p",
rel_pos = "rel_pos"
)
data |
A data.frame object. Required. |
highlight |
A vector of SNPs or gene names you would like to highlight. Defaults to NULL. If you specify this, you must also specify highlight_col so that we know where to find the items. |
highlight_col |
The column where the values you provide in
|
highlight_color |
The color that you would like the highlighted SNPs or genes to be. Defaults to "green." |
logged_p |
The name of the column containing your logged p-value
information. Defaults to "logged_p," assuming data preparation with
|
rel_pos |
The name of the column containing the positon of each
SNP/probe relative to all other SNPs/probes in the genome. Defaults to
"rel_pos," assuming data preparation with |
A data.frame with three columns: relative position, logged p-value, and highlight color.
Julie White
https://github.com/juliedwhite/miamiplot
## Not run:
# You can provide a list of SNP / gene names
upper_highlight <- highlight_miami(data = plot_data$upper,
highlight = c(rs1, rs2, rs3, ..., rsN),
highlight_col = "rsid")
# Or an object containing those names.
upper_highlight <- highlight_miami(data = plot_data$upper,
highlight = snps_of_interest,
highlight_col = "rsid")
# When highlighting, the items in 'highlight' must all come from a single
# column. Specifying multiple columns in highlight_col will return an error.
highlight_miami(data = df, split_by = "study", split_at = "A",
highlight = snps_of_interest,
highlight_col = c("rsid", "gene"))
## End(Not run)
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