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
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 = "pretty"
)The output of the ClustAssess automatic pipeline
The expression matrix
The metadata
The folder where the files will be written
The compression level for the h5 files (See `rhdf5::h5createFile`` for more details)
The chunk size for the rank matrix (See rhdf5::h5createDataset for more details)
The threshold for the gene variance; genes with variance below this threshold will be removed
The function used for summarizing the stability values; the default is median
The colorspace used for generating the colors; the default is pretty
NULL (the files are written in the project_folder)