make_circos_links: make_circos_links

In SanzCircos: Functions for Creating 'Circos' Files

Description

A function that takes a data frame in the format of those returned by the 'make_circos_df_*' functions, and returns a data frame containing all possible lineage links, and some additional metadata about each link for filtering purposes.

***NOTE: This function is optimized for parallelized computing. Setting the "status" argument to true will eliminate this feature, and instead provide a status bar to track progress.

Usage

make_circos_links(df, chromosome_grouping, band_grouping, link_grouping,
  start_position, end_position, status = FALSE)

Arguments

df	A data frame in the format of those returned by the 'make_circos_df_*' functions
chromosome_grouping	A column defining the circos chromosomes. Passed as column index or "column name".
band_grouping	A column defining the circos chromosome bands. Passed as column index or "column name".
link_grouping	A column defining the circos linkage IDs. Passed as column index or "column name".
start_position	A column defining the start positions of the linkage ID.
end_position	A column defining the end positions of the linkage ID.
status	Defaults to FALSE. Removes parallelized computing, and provides a status bar to track progress.

Value

Returns a links data frame suitable for filtering and exporting using the 'write_circos_links()' function.

Author(s)

Matthew Woodruff, Emory University

Examples

links_df <- data.frame(chrom = c(rep("chr1", 5), rep("chr2", 5)),
band = c(rep("band1", 3), rep("band2", 2), "band1", rep("band2", 4)),
link = c(1, 2, 3, 1, 2, 1, 1, 3, 4, 5),
start = c(1, 3, 5, 10, 35, 1, 5, 8, 13, 15),
end = c(3, 5, 10, 35, 39, 5, 8, 13, 15, 21))

links <- make_circos_links(links_df, "chrom", "band", "link", "start", "end", status = TRUE)

print(links)

SanzCircos documentation built on May 1, 2019, 7:55 p.m.