write_circos_karyotype: write_circos_karyotype

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 writes a "karyotype" file for Circos plotting

Usage

write_circos_karyotype(df, chromosome_grouping = FALSE,
  band_grouping = FALSE, start_position, end_position,
  file_name = "karyotype.txt", file_path = NULL)

Arguments

df	A database to draw Circos data from
chromosome_grouping	A column defining the circos chromosomes. Passed as column index or "column name"
band_grouping	A column defining the circos bands. Passed as column index or "column name"
start_position	A column defining the lineage start positions. Passed as column index or "column name"
end_position	A column defining the lineage start positions. Passed as column index or "column name"
file_name	The desired file name. Defaults to karyotype.txt in the current working directory
file_path	The desired file path destination folder. Defaults to NULL

Value

Writes a Circos-compatible karyotype file to the desired directory

Author(s)

Matthew Woodruff, Emory University

Examples

df <- data.frame(chrom = c(1, 1, 2, 2), band = c(1, 2, 1, 2), start = c(1, 5, 1, 8),
end = c(5, 10, 8, 13), n = c(5, 5, 8, 5))

write_circos_karyotype(df = df, chromosome_grouping = "chrom", band_grouping = "band",
start_position = "start", end_position = "end",
file_name = "karyotype.txt", file_path = tempdir())

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