AMatReader Cytoscape App

AMatReader is a general adjacency matrix importer plugin for Cytoscape.
Download the app on the Cytoscape app store

REQUIRES Cytoscape 3.6+

Sample adjacency matrix formats can be found in the samples directory.

Below is a sample format for a matrix file:

#Simple tab-delimited adjacency matrix
	Node1	Node2	Node3	Node4
Node1		1	4	
Node2	1		3	3
Node3	4	3		1
Node4		3	1		

More sample adjacency matrix files are available in the samples directory in the parent folder of this repo

Note that lines starting with # are considered comments and are ignored

Using the app in Cytoscape

From File>Import or Drag'n'Drop

NOTE: Files imported in either manner MUST use the .adj or .mat suffix to be recognizes as matrix files. To import other filetypes (.csv, .txt, etc.) use the Apps Menu method below

Go to File>Import>Network>File... and select the individual file for import.

OR

Drag multiple .mat/.adj files into the network panel.

From the Apps Menu

Go to Apps> AMatReader> Import Matrix Files. Select the file(s) you want import and hit Import

AMatReader will peek at each file and predict the parameters for import.

The settings in this dialog (also available through CyREST) are described below.

Name	Description
files	list of files to be imported
delimiter	separator used between values in the matrix (tab, comma, pipe
ignoreZeros	whether or not to create edges for zero values in the matrix
interactionType	value given to the interaction column in the Cytoscape Edge table
rowNames	True if the first column of the matrix specifies node names, False otherwise
columnNames	True if the first row of the matrix specifies nodes names, False otherwise
undirected	directed-ness of the resulting graph. If True, only the top triangle of the matrix is used
removeColumnPrefix	Useful for Matlab/R imports, where column names are prefixed by some description.

The New column name field in the dialog defines the edge column to be created. In CyREST, the file basename is used as the new column name

pyCyAMatReader Pypi package

A python interface was created to allow importing adjacency matrices into Cytoscape in a RESTful manner. This package uses the CyREST endpoints of AMatReader to import files, pandas DataFrames, and numpy arrays that represent adjacency matrices.

To use the pyCyAMatReader package, follow these steps:

1. Install the pypi package with

pip install pycyamatreader

Start Cytoscape and make sure the AMatReader app is installed. PyCyAMatReader makes use of the CyREST interface for AMatReader and will only work with Cytoscape 3.6+.

2. Create an AMatReader object

from pyCyAMatReader import AMatReader
_amatreader = AMatReader()  # assumes Cytoscape answers at http://localhost:1234

3. Specify import parameters in python dictionary

data = {
  "files": [file1, file2],
  "delimiter": "TAB",
  "ignoreZeros": True,
  "undirected": False,
  "interactionName": "interacts with",
  "rowNames": True,
  "columnNames": True,
  "removeColumnPrefix": False
}

4a. Import some matrix file(s) into Cytoscape

To import a file as a new Cytoscape network

data['files'] = ['sample.mat']
result = _amatreader.import_matrix(data)

Or extend an existing network

data['files'] = ['sample2.mat']
# use the resulting network from the import above
suid = result['suid'] 
_amatreader.import_matrix(data, suid=suid)

4b. Import some pandas/numpy matrices into Cytoscape

You can also now import pandas DataFrames and numpy arrays using aMatReader

NOTE: python dataframes are saved to a temporary file for import. This is not advised for large files. If you have a large file, use the util_numpy helper in py2Cytoscape

To import a numpy matrix that represents an adjacency matrix

mat = np.random.random([5, 5]) # sample 5x5 numpy matrix

# numpy saves matrices without row/column names by default
data = data.update({'columnNames': False,
                    'rowNames': False,
                    'undirected': 'true'})
result = _amatreader.import_numpy(mat, data, names=['A', 'B', 'C', 'D', 'E'])

To import a pandas DataFrame that represents an adjacency matrix

# pandas does not save with row names by default
data['rowNames'] = False 
df = pd.DataFrame(np.random.randint(low=0, high=10, size=(5, 5)),
            columns=['A', 'B', 'C', 'D', 'E'])
result = _amatreader.import_pandas(df, data)