Output Formats

Several output schemes are available.

Single-cell pseudo-time

This is the inferred pseudo-time for the cells.

Rotation matrix

This the matrix for transforming the pseudo-times to an “ideal cycling cell”.

Corrected expression matrix

This is provided for convenience. Because the corrected expression matrix is calculated by the original input matrix, single-cell pseudo-time and rotation matrix, it would be more space-efficient if not storing it.

To store the corrected expression matrix, there are two ways – csv and binary file. Although csv file is human readable, importing csv in R is significantly slow, due to overhead of parsing the file. Binary file is much smaller and faster, but not human readable.

Csv file

Storing matrix or data frame into csv file can be done using the numpy and pandas packages directly.

Binary file

We provide cyclum.writer.write_matrix_to_binary() and cyclum.writer.write_df_to_binary() function to store matrix and data frames. For more details about the binary format, please refer to the module cyclum.writer.