scimap.pp.mcmicro_to_scimap

Short description

The function helps to convert mcmicro output to AnnData object.

Parameters

image_path : list
List of path to the image or images. Each Image should have a unique path supplied.

remove_dna : bool, optional (The default is True)
Remove the DNA channels from the final output. Looks for channels with the string 'DNA' in it.

remove_string_from_name : string, optional (The default is None)
Used to celan up channel names. If a string is given, that particular string will be removed from all marker names.
If multiple images are passed, just use the string that appears in the first image.

log : bool, optional (The default is True)
Log the data (log1p transformation will be applied).

drop_markers : list, optional (The default is None)
List of markers to drop from the analysis. e.g. ["CD3D", "CD20"].

random_sample : int, optional (The default is None)
Randomly sub-sample the data with the desired number of cells.

CellId : string, optional (The default is CellID)
Name of the column that contains the cell ID.

unique_CellId: bool, optional (The default is True)
By default, the function creates a unique name for each cell/row by combining the CellId and imageid. If you wish not to perform this operation please pass False. The function will use whatever is under CellId. In which case, please be careful to pass unique CellId especially when loading multiple datasets togeather.

split : string, optional (The default is 'X_centroid')
To split the CSV into counts table and meta data, pass in the name of the column
that immediately follows the marker quantification.

custom_imageid: string, optional (The default is the name of the CSV file)
Pass a user defined Image ID.

min_cells: int, optional (The default is None)
If these many cells are not in the image, the image will be dropped.
Particularly useful when importing multiple images.

Returns

AnnData object.

Example

image_path = ['/Users/aj/desktop/PTCL1_450.csv',
             '/Users/aj/desktop/PTCL2_552.csv']

adata = sm.pp.mcmicro_to_scimap (image_path, drop_markers= ['CD21', 'ACTIN'], random_sample=5000)