makeCoOccTablesCondensed.RdMake 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
makeCoOccTablesCondensed(
DB,
variantFile,
startDate = NULL,
endDate = NULL,
archiveDBFile = NULL,
saveTable = FALSE,
saveFolder = NULL,
height = NULL,
width = NULL,
colWidth1 = NULL,
colWidth2 = NULL,
colWidth3 = NULL,
colWidth4 = NULL,
colWidth5 = NULL
)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()
csv file containing "Displayed_Lineage_Order" column for ordering row names/row groups in the GT table
start date for subset DB, if NULL then the .1 percent analysis won't be run
start date for subset DB, if NULL then the .1 percent analysis won't be run
File path to archive db (used to retrieve older subset of data for comparison; older subset uses same length of time as input subset db, e.g. start_date is "2022-5" and end_date is "2022-07", then older subset start date is "2022-02 and "2022-04)
logical value indicating whether to save the tables to the specified saveFolder
file path containing folder the finished tables will be saved in
desired height of table .png images
desired width of table .png images; if the width is not large enough, text will wrap or table will be cut off
width of "Pangolin Lineage" column in px; if NULL, widths are automatically assigned to try to fit all text
width of "5" column in px; if NULL, widths are automatically assigned to try to fit all text
width of ">=6" column in px; if NULL, widths are automatically assigned to try to fit all text
width of "Sequences by Lineage" column in px; if NULL, widths are automatically assigned to try to fit all text
width of all other columns in px; if NULL, widths are automatically assigned to try to fit all text