mcc_tree_plot: Plot the maximum clade credibility tree and showing HPD node...
In emvolz-phylodynamics/sarscov2Rutils: Scripts to support preparation and analysis of SARS CoV 2 analyses
Description
Usage
Arguments
Value
Description
You will need to combine your tree logs like this:
logcombiner -trees -burnin <integer corresponding to half of sample, eg 5000000> <treelog1> ... <treelog_n> <combined.trees>
You can use the *tree_combiner_helper* function. See ?tree_combiner_helper
NOTE make sure that tree logs included here only correspond to those beast runs that passed checks in *combine_logs_and_traj*
treeannotator2 -limit 0.5 -burnin 0 <combined>.trees <outputFileName>.nex
Usage
1
2
3
4
5
6
mcc_tree_plot(
nexfn,
mostRecentSampleDate,
regionDemes = c("Il", "Ih", "E"),
ofn = "mcc.png"
)
Arguments
nexfn
Path to nexus file containing annotated MCC tree (output of treeannotator2)
mostRecentSampleDate
A character string containign the date of the most recent sample in the form 2020-03-17
regionDemes
A character vector of deme names which will be coloured red
ofn
Output file name of figure
Value
A ggtree object which can be customized further
emvolz-phylodynamics/sarscov2Rutils documentation built on Nov. 17, 2020, 9:22 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.
Description Usage Arguments Value
Description
You will need to combine your tree logs like this: logcombiner -trees -burnin <integer corresponding to half of sample, eg 5000000> <treelog1> ... <treelog_n> <combined.trees> You can use the *tree_combiner_helper* function. See ?tree_combiner_helper NOTE make sure that tree logs included here only correspond to those beast runs that passed checks in *combine_logs_and_traj* treeannotator2 -limit 0.5 -burnin 0 <combined>.trees <outputFileName>.nex
Usage
1 2 3 4 5 6 | mcc_tree_plot(
nexfn,
mostRecentSampleDate,
regionDemes = c("Il", "Ih", "E"),
ofn = "mcc.png"
)
|
Arguments
nexfn |
Path to nexus file containing annotated MCC tree (output of treeannotator2) |
mostRecentSampleDate |
A character string containign the date of the most recent sample in the form 2020-03-17 |
regionDemes |
A character vector of deme names which will be coloured red |
ofn |
Output file name of figure |
Value
A ggtree object which can be customized further
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.