Write the objects for the ClustAssess ShinyApp — write

Given the output of the ClustAssess pipeline, the expression matrix and the metadata, this function creates the files needed for the ClustAssess ShinyApp. The files are written in the project_folder and are the following:

metadata.rds: the metadata file
stability.h5: contains the stability results
expression.h5: contains the expression matrix and the rank matrix

Usage

write_objects(
  clustassess_object,
  expression_matrix,
  metadata,
  project_folder = ".",
  compression_level = 6,
  chunk_size = 100,
  gene_variance_threshold = 0,
  summary_function = stats::median,
  qualpalr_colorspace = list(h = c(0, 360), s = c(0.1, 0.5), l = c(0.6, 0.85))
)

Arguments

clustassess_object: The output of the ClustAssess automatic pipeline
expression_matrix: The expression matrix
metadata: The metadata
project_folder: The folder where the files will be written
compression_level: The compression level for the h5 files (See `rhdf5::h5createFile“ for more details)
chunk_size: The chunk size for the rank matrix (See rhdf5::h5createDataset for more details)
gene_variance_threshold: The threshold for the gene variance; genes with variance below this threshold will be removed
summary_function: The function used for summarizing the stability values; the default is median
qualpalr_colorspace: The colorspace used for generating the colors; we use the default as defined in the qualpalr package

Value

NULL (the files are written in the project_folder)