Make Tables for Co-occurring mutations — makeCoOccTables • CoMIT

Make 2 tables (one version with all mutated sequences and one version with sequences with high-risk mutations) showing mutated sequence counts categorized by number of assays affected on top and by variant on the left

makeCoOccTables(
  DB,
  variantFile,
  saveTable = FALSE,
  saveFolder = NULL,
  height = NULL,
  width = NULL,
  colWidth1 = NULL,
  colWidth2 = NULL
)

Arguments

DB: File path to subset database file. In the case of making summary tables, we use the 3M version from CoMIT, returned from pull_subset_DB()
variantFile: csv file containing "Displayed_Lineage_Order" column for ordering row names/row groups in the GT table
saveTable: logical value indicating whether to save the tables to the specified saveFolder
saveFolder: file path containing folder the finished tables will be saved in
height: desired height of table .png images
width: desired width of table .png images
colWidth1: width of "Pangolin Lineage" and "WHO Label" columns in px; if NULL, widths are automatically assigned to try to fit all text
colWidth2: width of all other columns in px; if NULL, widths are automatically assigned to try to fit all text