legoplot3d: A wrapper function to create a sequence context "legoplot"

In barplot3d: Create 3D Barplots

Description

A wrapper function to create a sequence context "legoplot"

Usage

legoplot3d(contextdata, alpha = 1, scalexy = 1, gap = 0.2,
  sixcolors = "broad", theta = 50, phi = 40, gridlines = TRUE,
  labels = FALSE, zlabels = TRUE, zsub = FALSE)

Arguments

contextdata	A numeric vector of counts or frequencies of the 96 possible somatic mutations and trinucleotide contexts. These MUST be in the same order as in the example (see example and/or vignette).
alpha	The alpha channel (transparency) of the sides of 3D bars. Range 0-1.
scalexy	Scaling factor for x and y coordinates; this constant can be used to make the plot "skinnier" or "fatter".
gap	Gap between 3D bars.
sixcolors	The color scheme. "broad" for Broad Institute colors, "sanger" for Sanger Institute colors or a vector of six hexadecimal RGB colors.
theta	Polar coordinate for viewing the 3D barplot; range 0 to 360 (rotates the plot).
phi	Polar coordinate for viewing the 3D barplot; range -90 to 90 (-90 is directly below, 90 directly above).
gridlines	Draw gridlines on the plot (TRUE or FALSE).
labels	Include the default axis labels (TRUE or FALSE).
zlabels	Labels for the z axis; add numeric scale to the vertical dimension of the plot (TRUE or FALSE).
zsub	Descriptive label for the z axis.

Value

Nothing is returned (invisibly returns NULL).

Examples

# Read in COSMIC signature probabilities
x=system.file("extdata", "signature_probabilities.txt", package = "barplot3d")
sigdata=read.table(x,header=TRUE,stringsAsFactors = FALSE)
# Plot signature 2 with Sanger colors and some transparency so we can see all bars
legoplot3d(contextdata=sigdata$Signature_2,labels=TRUE,scalexy=0.05,sixcolors="sanger",
alpha=0.4,zsub="Probability")

barplot3d documentation built on Nov. 6, 2019, 5:08 p.m.