MappgeneSummary

Installation from Github

install_github("LLNL/MappgeneSummary")

Additionally, there are a few functions and color palettes from the jakR package. Install from github...

install_github("jeffkimbrel/jakR")

Examples

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"))

Summary.Rmd File

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")

Customizing

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: If TRUE, 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 to TRUE to run all code blocks, or to FALSE to use saved Rds files.
• api_top_count: Number of Outbreak API SNVs to generate plots for.

Citation

If you use mappgeneSummary in your work, please cite:

Viruses 2022, 14(12), 2775; https://doi.org/10.3390/v14122775