Write .fcs files for flow cytometry
Adapted from https://github.com/ZELLMECHANIK-DRESDEN/fcswrite
- cytoflow.utility.fcswrite.write_fcs(filename, chn_names, chn_ranges, data, compat_chn_names=True, compat_percent=True, compat_negative=True, compat_copy=True, verbose=0, **kws)¶
Write numpy data to an .fcs file (FCS3.0 file format)
filename (str) – Path to the output .fcs file
chn_names (list of str, length C) – Names of the output channels
chn_ranges (dictionary) – Keys: channel names. Values: ranges
data (2d ndarray of shape (N,C)) – The numpy array data to store as .fcs file format.
compat_chn_names (bool) – Compatibility mode for 3rd party flow analysis software: The characters ” “, “?”, and “_” are removed in the output channel names.
compat_percent (bool) – Compatibliity mode for 3rd party flow analysis software: If a column in
datacontains values only between 0 and 1, they are multiplied by 100.
compat_negative (bool) – Compatibliity mode for 3rd party flow analysis software: Flip the sign of
dataif its mean is smaller than zero.
compat_copy (bool) – Do not override the input array
datawhen modified in compatibility mode.
kwargs (Str) – Additional keyword arguments are written as keyword/value pairs in the TEXT segment of the FCS file.
These commonly used unicode characters are replaced: “µ”, “²”