Hi,
I'm using py4cytoscape to automate some figure preparation, and I've come across a problem. My script successfully turns these dataframes into networks.
However, they always have some kind of rectangular layout, and I'm unable to change it, either from py4cytoscape or even within the Cytoscape app. Instead, what happens in both cases is that the view fits to the network, or the rectangular layout may change dimensions to be two columns instead of 12, or something like that. It depends on what layout I try.
Layouts both in py4cytoscape and in the Cytoscape app work just fine for other networks, like for Cytoscape's default tutorial network with yeast. I've tried both using Mu editor as well as using a Jupyter notebook, with no differences. So I'm thinking there's something different about a network I've made myself - maybe I need to include some attribute in the node file.
My next step is to retrieve edges from String's protein query, at which point it's possible the additional information will rectify the problem...? I don't know how to do that yet though, or if it's available in py4cytoscape.
Here's my code:
Thanks in advance for any insight!
`import csv import pandas as pd import py4cytoscape as py4
load files
ourdatawb = 'HB filtered 01162023 mTOR phos round 2 summary.xlsx' wgfile = 'enrichment_results_wg_result1675954646.txt'
parameters
ourdatasheet = '4 Filtered' ourdata_idcol = 'Uniprot' wg_idcol = 'id'
turn csv into list with a dataframe for each pathway found
def unpack(filename): with open(filename) as csvfile: reader = csv.reader(csvfile,delimiter=' ') list1 = [[pd.DataFrame(data={wg_idcol:i[-1].split(';'),'pathway':i[1]},columns=['id','pathway'])] for i in reader] return list1
pathways = unpack(wgfile)[1:]
ourdf = pd.read_excel(ourdatawb, sheet_name=ourdatasheet)
import data to each pathway dataframe, and make a newtwork from each
for i in pathways: df1 = pd.merge(i[0],ourdf,left_on=wg_idcol, right_on=ourdata_idcol) py4.create_network_from_data_frames(df1, title=str(df1.loc[0,'pathway'])) py4.layout_network('attribute-circle')`
