ggideogram: Plot ideogram and annotations on chromosome

In liuyujie0136/tinyfuncr: tiny R functions

Plot ideogram and annotations on chromosome

Description

Plot ideogram and annotations on chromosome. Annotations can be text (with different color/size), point (with different shape/size), or lines (i.e. values for each position).

Usage

ggideogram(
  karyotype_info,
  gff_file = NULL,
  slide_window = 1e+05,
  plot_direction = c("vertical", "horizontal"),
  chrom_display = c("gene_density", "border_only"),
  density_color = c("skyblue", "red"),
  circ_ratio = NULL,
  ann_type = c("none", "text", "shape", "textshape", "line", "multiline", "textline",
    "shapeline", "textshapeline"),
  ann_data = NULL,
  ggfanplot_args = list(htext_direction = c("right", "left"), replusive = 1e+06,
    text_size = 1, text_color = "black", shape_size = 1, shape_color = "skyblue",
    shape_repel = 0.25),
  ann_line_args = list(size = 0.4, color = "black", linetype = "solid")
)

Arguments

karyotype_info	tab-separated file (or a data frame) containing karyotype information, with first column being "Chr", second being "Start", third being "End". File should NOT have header.
gff_file	GFF file, used only when chrom_display = "gene_density"
slide_window	length of each slide window, defaut 100kb
plot_direction	direction of chromosome, one of "vertical" and "horizontal"
chrom_display	method to display chromosome, one of "gene_density" and "border_only"
density_color	when chrom_display = "gene_density", set "low" and "high" color to display gene density (1st: "low", 2nd: "high"), used in scale_fill_gradient
circ_ratio	ratio to make chromosome endtip round, where x and y scale are not the same, change according to plot size
ann_type	type of annotation added to chromosome plot, one of "none", "text", "shape", "textshape", "line", "multiline", "textline", "shapeline", and "textshapeline"
ann_data	a data frame containing annotation information, colnames should be set as following: For text type (in ann_type), first column is "Chr", second is "Pos", third is "Text", fouth is "TextSize", fifth is "TextColor", where fouth and fifth column is optional. When "TextSize" and "TextColor" are not given to each annotation, use global options from text_size and text_color in ggfanplot_args. For shape type, first column is "Chr", second is "Pos", third is "Shape", fouth is "ShapeSize", fifth is "ShapeColor", where fouth and fifth column is optional. When "ShapeSize" and "ShapeColor" are not given to each shape, use global options from shape_size and shape_color in ggfanplot_args. For textshape type, first column is "Chr", second is "Pos", third is "Text", fouth is "Shape", fifth is "TextSize", sixth is "TextColor", seventh is "ShapeSize", eighth is "ShapeColor", where 5-8 columns are optional. For line type, first column is "Chr", second is "Pos", third is "Value" For multiline type, first column is "Chr", second is "Pos", the rest columns are "Value"s, where "Value"s' name can be changed to any string to match its meaning For textline type, first column is "Chr", second is "Pos", third is "Value", fouth is "Text", fifth is "TextSize", sixth is "TextColor", where 5-6 columns are optional. For shapeline type, first column is "Chr", second is "Pos", third is "Value", fouth is "Shape", fifth is "ShapeSize", sixth is "ShapeColor", where 5-6 columns are optional. For textshapeline type, first column is "Chr", second is "Pos", third is "Value", fouth is "Text", fifth is "Shape", sixth is "TextSize", seventh is "TextColor", eighth is "ShapeSize", nineth is "ShapeColor", where 6-9 columns are optional.
ggfanplot_args	args used in ggfanplot, see ggfanplot()
ann_line_args	args used in geom_path, see ggplot2::geom_path()

Author(s)

Yujie Liu

liuyujie0136/tinyfuncr documentation built on Dec. 13, 2024, 8:49 a.m.