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 = "pretty"
)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::h5createDatasetfor 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; the default is
pretty