9. Understanding the file formats
Saved networks
When a network is saved as a text file, the file will have the following format:
| N | ||
| gene_1 | x | y |
| gene_2 | x | y |
| ... | ||
| M | ||
| gene_1 | gene_2 | pcor |
| gene_3 | gene_4 | pcor |
| ... |
Where N denotes the number of genes in the network. Following N is N number of lines with a gene name and its x and y coordinates in the network (ranging [0,1]). M denotes the number of correlations. Following M is M number of lines with two cells that correlate and their partial correlation. A gene may be correlated to multiple other genes, and the order of the gene names before a partial correlation does not matter, e.g jun fos 1 means the exact same as fos jun 1.