Function that draws the chromosomes and the position of the desired regions in a circular plot It draws each regions set provided as input in separate circles, so you can input chromosome sizes for different assemblies. It also allows to connect "paired" regions across each provided regions set and circle. It allows to color regions by "region", "strand" or "extra", which is provided through extra_info.
circleRegions(
chromsizes_sets,
regions_sets,
chr_exclude = c("Un", "Random", "JH", "GL", "\\."),
chr_order = c(seq(from = 1, to = 23, by = 1), "X", "Y", "M", "MT", paste("chr",
c(seq(from = 1, to = 23, by = 1), "X", "Y", "M", "MT"), sep = "")),
chr_label = "Black",
chr_line = FALSE,
sets_names = names(regions_sets),
colors = c("Black", "Red", "Blue"),
color_by = "region",
title = NULL,
subtitle = NULL,
caption = NULL,
legend = "bottom",
draw_points = TRUE,
paired = FALSE,
paired_color = "blue",
extra_info = NULL
)(Named) List of character vectors or dataframes. List with paths to chrom.sizes file or list of data frames with the names of the chromosomes and their sizes. The file must not contain column names. Length and order must be the same as 'regions_sets'.
(Named) List of character vectors or dataframes. List with paths to BED/TSV files or dataframes with chromosome names, start, end, region id, length and strand. Strand must be "+", "-" or ".". Length and order must be the same as 'chromsizes_sets'.
Character. Regular expressions to match the chromosomes names to exclude . Default: c("Un", "Random", "JH", "GL", "\.").
Character. Chromosome names written in the order to be plotted. The names must matchthe chromosome names in chrom_sizes and regions. Default: c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,"X","Y","M","MT")
Character of length 1. Color of the chromosome labels. If all the elements in chromsizes_sets are equal, only prints the labels once. Default: "Black"
Logical of length 1. If TRUE, it draws a dashed line that separates a the chromosomes. This line is done only for the first chromsizes set.
Character of length equal to 'chromsizes_sets' and 'regions_sets'. Names of the input regions in the correct order. They are used to name the regions_sets, the chromsizes_sets and the extra_info lists. Default: names(regions_sets).
Character. Colors of the input regions. Depends on 'color_by': if it is 'region', the length must be equal or greater to the lenght of 'regions_sets'; if it is 'strand' the lenght must be 2 or more; if it is 'extra', the length must be equal or greater to the groups provided in extra_info.
Character of length 1. One of 'region', 'strand' or 'extra'. If 'region', colors by the regions in 'regions_sets'. If 'strand', colors by strand. If 'extra' colors by the grouping provided in 'extra_info' (if provided).
Character of length 1 or NULL. Title of the plot. Default: NULL
Charachter of length 1 or NULL. Subtitle of the plot. Default: NULL.
Character of length 1, TRUE or NULL. Caption to be written in the bottom-right corner. If TRUE, it will write the number of regions in the input; if charachter, it will write the written caption. Default: NULL.
Character of length 1. Position of the legend, passed through ggpubr::theme_pubr(). One of c("top", "bottom", "left", "right", "none"). Default: "bottom".
Logical of lenght 1. If TRUE, draws points in each of the drawn regions. Default: TRUE.
Logical of lenght 1. If TRUE, draws a line between the paired regions in each set/circle. Default: FALSE.
NULL or (named) list of length equal to 'chromsizes_sets' and 'regions_sets', and with the same order. List of path to files or list of data.frames with two columns containing the id column of the regions contained in each set of 'regions_sets' and a column with extra (discrete) information. Default: NULL.
Character of length 1. Color of the lines that connect the paired regions.