gmovizPlot: Generate an entire circular plot

In gmoviz: Seamless visualization of complex genomic variations in GMOs and edited cell lines

Description

Saves code supplied to plotting_functions a plot (with optional title and legends) as either .png, .svg or .ps.

Usage

gmovizPlot(file_name, file_type = "png", plotting_functions,
  legends = NULL, title = NULL, width = 338.7, height = 238.7,
  units = "mm", res = 300, background_colour = "transparent",
  title_x_position = 0.5, title_y_position = 0.9,
  title_font_face = "bold", title_size = 1.1, title_colour = "black",
  point_size = 11)

Arguments

file_name	The name of the file to be saved.
file_type	The type of image file to produce: either 'png', 'svg' or 'ps'.
plotting_functions	The functions you want to plot (e.g. insertionDiagram or gmovizInitialise).
legends	A legend object to plot, generated by makeLegends.
title	Text for the title, leave as NULL for no title.
width	Width of the image.
height	Height of the image.
units	Units for the width and height of the image. One of 'mm', 'cm' or 'in' (inches).
res	Resolution of the image (only needed for .png files).
background_colour	Colour of the image background.
title_x_position, title_y_position	X and Y positions of the title on the image.
title_font_face	Font face of the title: bold, italic or bold-italic.
title_size	Size of the title.
title_colour	Colour of the title.
point_size	Pointsize (for postscript output only).

Value

Saves a plot to disk in the specified format.

See Also

makeLegends for a function that generates the legend objects.

Examples

## make some example data
small_ideogram <- data.frame(chr=c('region 1', 'region 2', 'region 3'),
start=c(0, 0, 0), end=c(10000, 12000, 10000))
small_plot_data <- data.frame(
chr=sample(c('region 1', 'region 2', 'region 3'), size=40, replace=TRUE),
start=sample(0:10000, 40), end=sample(0:10000, 40),
val=rnorm(40, 2, 0.5))

## plot it
## Not run: 
gmovizPlot('test.png', {
gmovizInitialise(small_ideogram, custom_sector_width=c(0.3, 0.3, 0.3))
drawScatterplotTrack(small_plot_data)}, title='scatterplot')
## End(Not run)

gmoviz documentation built on Nov. 8, 2020, 5:41 p.m.