We have a number of Jupyter Notebooks that provide detailed examples of how to use CytoPy. Broken down into the common tasks these are:
General note on utilities¶
CytoPy offers a number of utility modules useful for studying cytometry data. For the most part, the user can access the general class structures of CytoPy and not have to touch these individual utility modules. However, you will be passing arguments that call on these utilities, so it is useful to understand what is going on under the hood.
The cytopy.flow.transform module houses functionality for common data transforms applied to cytometry data:
Data transformation is handled by the Transformer class with a child class for each of the logicle, hyperlog, log, and inverse hyperbolic sine transformations. A Transformer is initialised with the parameters of the transformation function to be applied and then exposes data to two functions:
scale - takes a DataFrame and list of columns to transform and returns the transformed DataFrame
inverse_scale - takes a DataFrame of previously transformed data and a list of columns to inverse this transformation for, and returns the DataFrame with data of the original scale
There are a couple of convenient functions in this module that construct the Transformer class and return the transformed data and the Transformer, which can then be used to inverse the transformation at a later point. These functions are:
apply_transform - takes the data, transform method as a string, and the features (columns) to transform, applying the same transformation to each column.
apply_transform_map - same as above except it takes a dictionary where the key is the name of the feature (column) to transform and the value is the transform method to be applied; this enables different transforms to be applied to different features.
Finally, the transform module also provides the Scaler class, a convenient wrapper for Scikit-Learn’s scaling functions. The user constructs this class by specifying a method which then will apply a scaling function:
“standard” - sklearn.preprocessing.StandardScaler
“minmax” - sklearn.preprocessing.MinMaxScaler
“robust” - sklearn.preprocessing.RobustScaler
“maxabs” - sklearn.preprocessing.MaxAbsScaler
“quantile” - sklearn.preprocessing.QuantileTransformer
“yeo_johnson” - sklearn.preprocessing.PowerTransformer
“box_cox” - sklearn.preprocessing.PowerTransformer
Making a call to this function with a DataFrame and a list of features (columns) will apply scaling to the DataFrame. Additionally, where supported, the user can call inverse on the same DataFrame and inverse the scaling performed.
Throughout CytoPy when we want to take a sample of our data, often to make our operations computationally viable, we will specify a sampling method and we will be offered the option to pass additional keyword arguments for this sampling method. When this action occurs, we are making a call to one of the functions in the cytopy.flow.sampling module. The functions within this module are:
uniform_downsampling (‘uniform’) - wraps the Pandas DataFrame sampling method with some additional error handling. Will downsample the given dataframe with a uniform weight given to each row.
faithful_downsampling (‘faithful’) - an implementation of faithful downsampling as described in: Zare H, Shooshtari P, Gupta A, Brinkman R. Data reduction for spectral clustering to analyze high throughput flow cytometry data. BMC Bioinformatics 2010;11:403
density_dependent_downsampling (‘density’) - density dependent down-sampling to remove risk of under-sampling rare populations. Originally described in SPADE, this algorithm constructs a nearest neighbour tree to estimate local density and assigns a higher probability for sampling events in low density regions whilst also ignore outliers.
For more information regarding the parameters to control each of these methods, please see their individual API docs.
Dimension reduction is a popular method for visualising cytometry data and is useful for data exploration. CytoPy has a common function for performing dimension reduction: cytopy.flow.dim_reduction.dimensionality_reduction.
This function takes the target DataFrame and a list of features (columns) to be used when generating the desired embedding. We specify the method to use as a string; supported methods should be familiar to those in the bioinformatics domains and are: ‘UMAP’, ‘PCA’, ‘KernelPCA’, ‘PHATE’, and ‘tSNE’, with the objective to expand supported methods in future versions.
By default, the DataFrame is returned with the generated embeddings as appended columns. The column names will carry the name of the method followed by the index of the embedding starting from 1; e.g. if we use UMAP and set n_components to 4, then these columns will be “UMAP1”, “UMAP2”, “UMAP3” and “UMAP4”.
UMAP and PHATE are computed using the UMAP and PHATE objects from the umap and phate libraries respectively. Other methods are provided by Scikit-Learn. The additional parameters we might want to pass to these methods are passed as additional keyword arguments to dimension_reduction. We can also specify to return the reducer object and also specify to just return the embeddings and not the whole DataFrame.