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#' Save coverage statistics to multi-worksheet Excel file.
#'
#' @param project.directory Path to project directory
#' @param file.name Name of output file
#' @param overwrite Logical indicating whether to overwrite existing file if it exists.
#'
#' @return None
#'
#'
save.coverage.excel <- function(project.directory, file.name, overwrite = TRUE) {
### INPUT TESTS ###########################################################
assertthat::assert_that( is.character(project.directory) );
assertthat::assert_that( 1 == length(project.directory) );
assertthat::assert_that( dir.exists(project.directory) );
### MAIN ##################################################################
# get data
coverage.sample <- get.coverage.by.sample.statistics(project.directory);
coverage.amplicon <- get.coverage.by.amplicon(project.directory);
# define header style for bolding
header.style <- openxlsx::createStyle(textDecoration = 'Bold');
workbook <- openxlsx::createWorkbook();
# add coverage by sample
sheet.name <- 'Coverage by sample';
openxlsx::addWorksheet(workbook, sheetName = sheet.name);
openxlsx::setColWidths(
workbook,
sheet = sheet.name,
cols = 1:ncol(coverage.sample),
widths = pmax(10, nchar(names(coverage.sample)) + 1)
);
openxlsx::writeData(
workbook,
sheet = sheet.name,
coverage.sample,
headerStyle = header.style
);
# add coverage by amplicon
sheet.name <- 'Coverage by amplicon';
openxlsx::addWorksheet(workbook, sheetName = sheet.name);
openxlsx::setColWidths(
workbook,
sheet = sheet.name,
cols = 1:ncol(coverage.amplicon),
widths = pmax(10, nchar(names(coverage.amplicon)) + 1)
);
openxlsx::writeData(
workbook,
sheet = sheet.name,
coverage.amplicon,
headerStyle = header.style
);
### SAVE TO FILE
openxlsx::saveWorkbook(
workbook,
file.name,
overwrite = overwrite
);
}
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