Function that draws the chromosomes and the position of the desired regions.
chromRegions(
chrom_sizes,
regions_list,
regions_names = names(regions_list),
regions_order = names(regions_list),
colors = c("Black", "Red", "Blue"),
color_by = "region",
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 = "")),
title = NULL,
subtitle = NULL,
caption = NULL,
ylab = "",
xlab = "Chromosome",
legend = "bottom",
draw_points = TRUE,
coord_flip = FALSE,
extra_info = NULL,
cyto_bands = NULL,
y_text_size = NULL
)Character of lenght 1 or dataframe. Path to the chrom.sizes file or data frame with the names of the chromosomes and their sizes. The file must not contain column names.
(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 ".".
Character of length equal to regions_list. Names of the input regions. Default: names(regions_list).
Character of length equal to regions_list. Names of the input regions in the desired order. Default: names(regions_list).
Character of length 2 or of length equal to regions_list. Colors of the input regions. If col_by_strand is FALSE, the length must be equal to the input regions, if col_by_strand is TRUE, the length must be 2. Default: sample(x = colors(), size = length(regions_list), replace = F).
Character of length 1. One of 'region', 'strand' or 'extra'. If 'region', colours by the regions in 'regions_list'. If 'strand', colours by strand. If 'extra' colours by the grouping provided field in 'extra_info' (if provided).
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 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. Title of the X axis. Default: ""
Character of lenght 1. Title of the Y axis. Default: "Chromosome".
Character of length 1. Position of the legend, passed through ggpubr::theme_pubr(). One of c("top", "bottom", "left", "right", "none"). Default: "right".
Logical of lenght 1. If TRUE, draws points in each of the drawn regions. Default: TRUE
Logical of lenght 1. If TRUE, change the position of the axes (Y axis is position and X is chromosome). Default: FALSE
NULL or (named) list of length equal to 'regions_list', 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_list' and a column with extra (discrete) information. Default: NULL.
NULL, data.frame or character. Path to the file (character) or imported file (dataframe) of the positions of the cytogenetic bands. Default: NULL
NULL or numeric of length 1. If NULL, do not draw the text on the Y axis (position in bp). If numeric, the size of the text in the Y axis. Default: NULL