Plot ADN, CDN, priority, frameshift, and fusion derived nmers for class I and class II MHC by sample_id.

garnish_plot(input, ext = "pdf")

Arguments

input

Output from garnish_affinity to graph. input may be a data table object, list of data tables, or file path to a rio::import-compatible file type. If a list of data tables is provided, unique plots will be generated for each data table.

ext

File extension passed to ggplot2::ggsave, default is "pdf".

Value

NULL

As a side effect: saves graph illustrating the number of neoantigens in each sample to the working directory. The threshold for inclusion of neoantigens is \(IC_{50}\) < 500nM.

See also

Examples

if (FALSE) { library(magrittr) library(data.table) library(antigen.garnish) # load example output dir <- system.file(package = "antigen.garnish") %>% file.path(., "extdata/testdata") "antigen.garnish_PureCN_example_output.txt" %>% file.path(dir, .) %>% # create plot garnish_plot }