make_miami_labels: Make label data.frame for miami plot

In juliedwhite/miamiplot: Create a ggplot2 miami plot

Make label data.frame for miami plot

Description

Make label data.frame for miami plot

Usage

make_miami_labels(
  data,
  hits_label_col,
  hits_label = NULL,
  top_n_hits = 5,
  logged_p = "logged_p",
  rel_pos = "rel_pos"
)

Arguments

data	A data.frame object. Required.
hits_label_col	Either the name of the column(s), max = 2, to use for automatically labeling n hits, determined using top_n_hits, or the column where the values you provide in hits_label can be found. Required.
hits_label	A user-specified character vector of probes/genes/SNPs to label. Defaults to NULL.
top_n_hits	How many of the top hits do you want to label? Defaults to 5. Set to NULL to turn off this filtering, but this is not recommended because the plot can get cluttered easily.
logged_p	The name of the column containing your logged p-value information. Defaults to "logged_p," assuming data preparation with prep_miami_data
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 prep_miami_data.

Value

A data.frame with three columns: relative position, logged p-value, and the label to add to the miami plot. Designed to be used with ggrepel.

Author(s)

Julie White

References

https://github.com/juliedwhite/miamiplot

Examples

 ## Not run: 
 # If you have already run prep_miami_data and want to label the top 5 hits
 # with SNP and gene name:
   upper_top5_labels <- make_miami_labels(data = plot_data$upper,
                                          hits_label_col = c("SNP", "Gene"))

 # If you have already run prep_miami_data and want to label the top 10 hits
 # from the AHRR, TBX15, and RARA genes:
   upper_top10_labels <- make_miami_labels(data = plot_data$upper,
                                           hits_label_col = "Gene",
                                           hits_label =
                                                  c("AHRR", "TBX15", "RARA"),
                                           top_n_hits = 10)

 # When labeling, the items in hits_label must all come from a single column.
 # Specifying multiple columns will return an error.
 ggmiami(data = gwas_results, split_by = "study", split_at = "A",
         hits_label_col = c("chr", Gene"),
         hits_label = c("1", AHRR", "2", "TBX15", "RARA"), top_n_hits = 10)

 # If you have not run prep_miami_data:
   labels <- make_miami_labels(datat = df, hits_label_col = c("SNP", "pos"),
                               logged_p = "logp",
                               rel_pos = "relative_SNP_position")
 
## End(Not run)

juliedwhite/miamiplot documentation built on Aug. 16, 2022, 12:05 a.m.