2.0
Sam Ng and Joshua M. Stuart
- Install dependencies
- Download the pathmark-scripts repository to the desired location
- Run "make" in pathmark-scripts/ to generate source files; may also require downloading the paradigm-scripts repository (see https://github.com/ucscCancer/paradigm-scripts)
- Source init files for pathmark-scripts and paradigm-scripts (init.sh for bash and init.csh for csh)
- Run code on example data in examples/ with "make"
galaxyPATHMARK.py [options] data_matrix phenotype_matrix pathway_file
data_matrix - sample by feature data file
phenotype_matrix - phenotype by sample dichotomy file
pathway_file - PARADIGM pathway interactions file
-b bootstrap_size - number of bootstrap sample to be generated for robustness estimation
-n null_size - number of null samples to be generated for significance estimation
-p null_permute - permutation method for null model
-m signature_method - differential method for computing signatures
-f filter_parameters - filter threshold coefficients
-t diffusion_time - heat diffusion time for signature scores across the network
-u - apply hub filter that includes hubs with high representation of its children
-z random_seed - fix random seed
circlePlot.py [options] output_directory input_matrix [input_matrix ...]
output_directory - path to directory to output plots
input_matrix - sample by feature data matrix for plots, rings created from inner to outer
-s sample_file - one column file of samples to plot
-f feature_file - one column file of features to plot
-o order_parameters - feature:file[,file ...] hierarchical sort on feature and data files
-c center_file - two column file of feature scores for center circle colors
-m color_map - color parameters file
-e file_extension - output file extension (default: png)
-l - output feature names for each plot
- bin : executables
- cytoscape : CytoscapeWeb and Cytoscape visualization files
- examples : BCCL inputs for demonstration purposes
Feature requests, comments and requests for clarification should all be sent to the author at [email protected]. I will try to respond quickly to all requests, so feel free to email me!