install_github("LLNL/MappgeneSummary")
Additionally, there are a few functions and color palettes from the jakR
package. Install from github...
install_github("jeffkimbrel/jakR")
get_state_outbreak_info(states = c("ca", "OR"), SNVs = c("S:y1155H", "S:P681H"))
get_country_outbreak_info(countries = c("usa", "can"), SNVs = c("S:y1155H", "S:P681H"))
get_global_outbreak_info(SNVs = c("S:y1155H", "S:P681H"))
To make a copy of the .Rmd
file and the required styles.css
file, type the following giving a path and file name. By default, the html and file outputs will be written to the same path
.
MappgeneSummary::copy_summary_template(path = "~/Desktop/", name = "test.Rmd")
There are several parameters that you can change in the .Rmd yaml header.
params:
echo_type: FALSE
mappgene_file_path: test
summary_output_file_path: "."
overwrite_Rds_files: TRUE
api_top_count: 10
echo_type
: IfTRUE
, will show the code blocks in the html file.mappgene_file_path
: If set to 'test' it will use the test files included in the package. Otherwise, change this to the path where your mappgene output is located.summary_output_file_path
: The path location of the output files.overwrite_Rds_files
: Some code blocks take time to run. Set toTRUE
to run all code blocks, or toFALSE
to use saved Rds files.api_top_count
: Number of Outbreak API SNVs to generate plots for.
If you use mappgeneSummary
in your work, please cite:
Viruses 2022, 14(12), 2775; https://doi.org/10.3390/v14122775