image.phyloLayout: image
In ArtPoon/ggfree: ggplot2-style plots with base R graphics
image.phyloLayout R Documentation
image
Description
Generic function for drawing a grid of coloured or grey-scale
rectangles corresponding to values in a matrix 'z'. Rows in
the matrix are assumed to correspond to tips of the tree.
Usage
## S3 method for class 'phyloLayout'
image(obj, z, xlim = NA, col = NA, border = "white", xaxt = "y", ...)
Arguments
obj:
an S3 object of class 'phyloLayout'
z:
matrix, data to annotate tips in order of *nodes*; this will be
recast as a factor, and then an integer vector. If your input
'z' is a numeric (continuous-valued) vector, then you should run
'cut(z)' to discretize the distribution.
xlim:
limits (x1, x2) of grid relative to current plot device.
For a radial tree layout, these correspond to the inner and
outer radii. You may need to use trial-and-error to find
a good set of boundaries. Note this function will call
'xpd=NA' to permit drawing in margins.
Defaults to 'max(x)+0.01*range(x)' to 'max(x)+0.06*range(x)'
col:
a vector of colours that maps to factor levels in 'z'
border:
colour for border of rectangles in grid
xaxt:
if 'n', suppress drawing of axis and labels
ArtPoon/ggfree documentation built on July 11, 2024, 11:15 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
| image.phyloLayout | R Documentation |
image
Description
Generic function for drawing a grid of coloured or grey-scale rectangles corresponding to values in a matrix 'z'. Rows in the matrix are assumed to correspond to tips of the tree.
Usage
## S3 method for class 'phyloLayout'
image(obj, z, xlim = NA, col = NA, border = "white", xaxt = "y", ...)
Arguments
obj: |
an S3 object of class 'phyloLayout' |
z: |
matrix, data to annotate tips in order of *nodes*; this will be recast as a factor, and then an integer vector. If your input 'z' is a numeric (continuous-valued) vector, then you should run 'cut(z)' to discretize the distribution. |
xlim: |
limits (x1, x2) of grid relative to current plot device. For a radial tree layout, these correspond to the inner and outer radii. You may need to use trial-and-error to find a good set of boundaries. Note this function will call 'xpd=NA' to permit drawing in margins. Defaults to 'max(x)+0.01*range(x)' to 'max(x)+0.06*range(x)' |
col: |
a vector of colours that maps to factor levels in 'z' |
border: |
colour for border of rectangles in grid |
xaxt: |
if 'n', suppress drawing of axis and labels |
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.