cytopy.data.read_write¶

The read_write module contains tools for accessing *.fcs files and relies on the Python library FlowIO by Scott White. This is used by Experiment to population FileGroups.

Projects also house the subjects (represented by the Subject class; see cytopy.data.subject) of an analysis which can contain multiple meta-data.

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THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Classes:

FCSFile(filepath[, comp_matrix])

Utilising FlowIO to generate an object for representing an FCS file

Functions:

`chunks`(df_list, n)	Yield successive n-sized chunks from l.
`explore_channel_mappings`(fcs_dir[, …])	Given a directory, explore all fcs files and find all permutations of channel/marker mappings
`fcs_mappings`(path)	Fetch channel mappings from fcs file.
`filter_fcs_files`(fcs_dir[, exclude_comps, …])	Given a directory, return file paths for all fcs files in directory and subdirectories contained within
`get_fcs_file_paths`(fcs_dir, control_names, …)	Generate a standard dictionary object of fcs files in given directory :param fcs_dir: target directory for search :type fcs_dir: str :param control_names: names of expected control files (names must appear in filenames) :type control_names: list :param ctrl_id: global identifier for control file e.g.

class cytopy.data.read_write.FCSFile(filepath, comp_matrix=None)¶

Utilising FlowIO to generate an object for representing an FCS file

filepath¶

location of fcs file to parse

Type: str

comp_matrix¶

csv file containing compensation matrix (optional, not required if a spillover matrix is already linked to the file)

Type: str

Methods:

compensate()

Apply compensation to event data

compensate()¶

Apply compensation to event data

Returns
Return type: None

cytopy.data.read_write.chunks(df_list: list, n: int) → pandas.core.frame.DataFrame¶

Yield successive n-sized chunks from l. ref: https://stackoverflow.com/questions/312443/how-do-you-split-a-list-into-evenly-sized-chunks

Parameters

df_list (list) – list of DataFrames to generated ‘chunks’ from
n (int) – number of chunks to generate

Returns

Yields successive n-sized DataFrames

Return type

generator

cytopy.data.read_write.explore_channel_mappings(fcs_dir: str, exclude_comps: bool = True) → list¶

Given a directory, explore all fcs files and find all permutations of channel/marker mappings

Parameters

fcs_dir (str) – root directory to search
exclude_comps (bool, (default=True)) – exclude compentation files (must have ‘comp’ in filename)

Returns

list of all unique channel/marker mappings

Return type

List

cytopy.data.read_write.fcs_mappings(path: str) → list¶

Fetch channel mappings from fcs file.

Parameters: path (str) – path to fcs file
Returns: List of channel mappings. Will return None if file fails to load.
Return type: List or None

cytopy.data.read_write.filter_fcs_files(fcs_dir: str, exclude_comps: bool = True, exclude_dir: str = 'DUPLICATES') → list¶

Given a directory, return file paths for all fcs files in directory and subdirectories contained within

Parameters

fcs_dir (str) – path to directory for search
exclude_comps (bool) – if True, compensation files will be ignored (note: function searches for ‘comp’ in file name for exclusion)
exclude_dir (str (default = 'DUPLICATES')) – Will ignore any directories with this name

Returns

list of fcs file paths

Return type

List

cytopy.data.read_write.get_fcs_file_paths(fcs_dir: str, control_names: list, ctrl_id: str, ignore_comp: bool = True, exclude_dir: str = 'DUPLICATE') → dict¶

Generate a standard dictionary object of fcs files in given directory :param fcs_dir: target directory for search :type fcs_dir: str :param control_names: names of expected control files (names must appear in filenames) :type control_names: list :param ctrl_id: global identifier for control file e.g. ‘FMO’ (must appear in filenames) :type ctrl_id: str :param ignore_comp: If True, files with ‘compensation’ in their name will be ignored (default = True) :type ignore_comp: bool, (default=True) :param exclude_dir: Will ignore any directories with this name :type exclude_dir: str (default = ‘DUPLICATES’)

Returns: standard dictionary of fcs files contained in target directory
Return type: dict