Description Usage Arguments Value Examples
View source: R/brownian_motion_package.r
This function plots the densities of log fold change in each species relative to a single species. Expression differences may be normalized, to assess the fit of the phylogentic model
1 2 3 |
dat |
a matrix of comparative data, in which rows correspond to species and columns correspond to traits |
groups |
a list of gene groups, in the same format as the output of read.groups |
group_name |
the name of the gene group for which to plot density. Leave as default to use all genes |
normalize |
a vector of normalizations, corresponding to the order of speices in dat |
remove.row |
a species of the data matrix to remove. Use this option to ensure that the normalizing species is not plotted |
color |
a vector of colors in which to plot densities |
main |
the title of the plot. Default is group name. |
names.arg |
the name to assign to each density. Default is species name. |
plot.legend |
a logical indicating whether to plot a legend |
lwd |
the line width for each density |
Nothing
1 2 3 4 5 6 | data(yeast)
sqrt.dist = compute.sqrt.dist(yeast.tree)
par(mfrow=c(1,2))
test_group = "GO:0007346|regulation of mitotic cell cycle"
plot_logfoldchange(yeast.homozygote,GO.groups,test_group)
plot_logfoldchange(yeast.homozygote,GO.groups,test_group,normalize=sqrt.dist)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.