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digraph {
label="A roadmap to make the network"
buildRmatrix -> slice_TPM_to_JSON[label="TPM.txt"];
buildRmatrix -> create_edges4[label="TPM.txt"];
buildCmatrix -> create_edges4[label="binding.txt"];
make_parameter_bw -> get_binding[label="parameter_for_buildCmatrix.txt"];
make_parameter_dapseq2 -> get_binding[label="parameter_for_buildCmatrix.txt"];
common_peak -> make_parameter_dapseq3[label="*.merged.narrowPeak"];
make_parameter_dapseq3 -> get_binding2[label="parameter_for_buildCmatrix.txt"];
get_binding -> buildCmatrix[label="binding files"];
get_binding2 -> buildCmatrix[label="binding files"];
prepare_gene_file -> buildCmatrix[label="gene_file.txt"];
slice_TPM_to_JSON -> html_network[label="json/"];
buildCmatrix -> slice_binding_to_JSON[label="binding.txt"];
parameter_for_net -> slice_binding_to_JSON[label="parameter_for_net.txt"];
slice_binding_to_JSON -> html_network[label="json2/"];
download_ena_records -> parse_ena_xml[label="ena_*.xml"];
parse_ena_xml -> html_network[label="rnaseq_info_database.txt"];
parse_ena_xml -> download_and_map[label="rnaseq_info_database.txt"];
slice_TPM_to_JSON -> start_webapp[label="json/"];
download_and_map -> make_parameter_rnaseq[label="ERR#_quant.txt"];
make_parameter_rnaseq -> buildRmatrix[label="parameter_for_buildRmatrix.txt"];
create_edges4 -> html_network[label="edges.txt"];
create_edges4 -> draw_network;
html_network -> update_network[label="summary.html"];
html_network -> start_webapp[label="summary/*.*"];
c3 -> html_network[label="scatterplot.js\nc3.min.js\nd3.min.js\nc3.min.css"];
parameter_for_net -> create_edges4[label="parameter_for_net.txt"];
c3[label="Edit and download"]
parameter_for_net[label="Edit"]
create_edges4[label="create_edges4 \n {TPM2JSON.py, make_target_tf.py}" style="filled" fillcolor="yellow"]
buildRmatrix[style="filled" fillcolor="yellow"]
buildCmatrix[style="filled" fillcolor="yellow"]
update_network[style="filled" fillcolor="yellow"]
download_and_map[label="download_and_map \n {get_TPM_by_salmon.py}"]
}
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