SanzCircos (version 0.1.0)

make_circos_links: make_circos_links

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.

Examples

# NOT RUN {
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)
# }