NetCrafter Tutorial

1. Launching NetCrafter

1.1 Installing NetCrafter on Windows and MacOS

• To launch NetCrafter:
•    1)  Download the package from NetCrafter website.
•    2)  Before installing the new version, make sure to delete the existing folder and icon.
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2. Main Functions of NetCrafter

This program is mainly draw network automatically based on Tanimoto coefficients using Gene, GO and HPO inputs.
The results can be saved as a file of PDF, JPG, and PNG format.

2.1 Running NetCrafter

• When NetCrafter starts, the main windows will appear that looks like this (captured on Window):
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2.2 Loading Data

• To obtain the sample loading data, you can download the file from the main page of NetCrafter.
•    1)  Select the data type; Gene or GOBP or HPO.
•    2)  Click the [Import data] button.
•    3)  Select your input file as csv format.
• When the data file is opened successfully, the matrix data will be visualized in the main panel:
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2.3 Selecting Data

• You can deselect genes or functions that you don't want to display in the network. Here’s how:
•    1)  You can sort the data by clicking on the column names, [Gene symbol] and [# Total functions].
•    2)  If there are only a few items you want to exclude, you can remove them manually.
        • Simply click the checkbox next to each gene or function to remove it from the network.
•    3)  For a larger number of items, use a filter or batch selection for quicker management:
        • Hold down the Shift or Ctrl key to select multiple items.
        • Click the [Selected] button to confirm your choices.
•    4)  The number of selected items will be automatically updated and displayed at the bottom of window.
• The following window will be displayed:
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2.4 Initial Settings (Gene Network)

• You can customize two criteria for the Gene Network:
•    1)  Criterion for Tanimoto calculation : [ GOBP / HPO ]
•    2)  Criterion for node size : [ Sum of -logP / # Ontology / Node data ]
        • Sum of -logP : Scale each node based on the total ontology weight (sum of -logP values) of its associated gene.
        • # Ontology : Set node sizes based on the number of ontologies linked to each gene.
        • Node data : Customize node sizes using values provided in your input file.
•    3)  Use consensus calculation : [Yes / No]
        • If enabled, combine p-values across gene sets using chi-square. If disabled, calculate weights per gene set.
        • It will be displayed only if the data more than two node shapes.
• You can select these options here:
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2.5 Visualizing Network

• Now that you have loaded your data, you are ready to visualize the network.
•    1)  By clicking the [Network] button, a new window will pop up, displaying the network.
•    2)  You can view names of each node by hovering your mouse over it.
•    3)  The number of nodes displayed in the network is shown in the upper right corner.
•    4)  You can customize network by manipulating control panel, under the number of nodes.
          We’ll explore the methods of controlling the network in Chapters 3 and 4.
•    5)  At the bottom, the functions representing the groups will be displayed.
• The following new window will be displayed:
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2.6 Saving Data

•    1)  Click the [Save Plot] button at the bottom of the control panel on the right.
•         You can save your data file as PDF, JPG, and PNG format.

• Format	Description
  PDF	Portable Document Format, ideal for sharing and printing
  JPG	Image file of high-quality resolution
  PNG	Image file with lossless compression

•    2)  Enter a name to saved file and click Save button.

3. Customizing Network

This application offers four options for editing the visualization. You can easily optimize the network by adjusting the options in the panel on the right, no graphic-editing skills required.

In this chapter, the options will be covered step by step, following the layout from top to bottom.

3.1 Control Panel

• 1) Network connection threshold
• You can adjust the Tanimoto cutoff using the scaling slider. Only nodes connected by edges with a Tanimoto score higher than the cutoff value will be displayed in the network.
  After modifying the cutoff value, click the [NETWORK] button to regenerate the network. The nodes and edges will be distributed based on the input values.
• 2) Two options for node:
•    • Node labeling - Enable node labels in the network by clicking the checkbox.
     • Node size - Adjust the scale to increase or decrease the size of the nodes.
• Once you’ve adjusted the settings, click the [UPDATE] button to apply your changes.
• 3) Two options for edge
•    • Edge thickness - Adjust the scale to make edges thicker or thinner.
     • Edge length - Increase the scale to spread clusters further apart in the network.
• After adjusting the settings, click the [UPDATE] button to confirm your changes.
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3.2 Cluster Selection

• The NetCrafter software automatically calculates similarity using Tanimoto coefficients to form clusters.
• The final option for customizing network is cluster selection. The representative functions of the groups, identified by their connected nodes, are displayed in the bottom section of the interface.
•    1)  Deselect the clusters which you don't want to display on the network.
•    2)  Click the [Display Selected Cluster] button to apply the changes.
• The updated network will reflect your selections.
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4. View Cluster Details

4.1 Detailed Cluster List

• For both gene and ontology networks, you can view a list of ontologies included in the cluster.
• Click the blue words in the cluster section to see detailed cluster information.
• The image below presents an example ontology list:
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4.2 Visualize Ontology-Associated Genes (Gene Network)

• After drawing a gene network, you can visualize the genes on the network that are associated with an ontology to see where they are positioned in the network.
•    1)  Select the cluster you want to explore further, then open its ontology list window as described in Section 4.1.
•    2)  Click the ontology row to see where its genes are loacted in the network.
•    2)  Click the [Highlight genes] button to generate an image.
• A new window will appear, as shown below :
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4.3 Network Reclustering (Gene Network)

• After drawing a gene network, you can redraw an ontology network included in the cluster.
•    1)  Select the cluster you want to explore further, then open its ontology list window as described in Section 4.1.
•    2)  Click the [Clustering ontology terms] button to generate an ontology network.
• A new window will appear, as shown below :
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5. Notice for using NetCrafter

There are several notice points to use the NetCrafter.

5.1 Input File Format

• NetCrafter only recognize the input file with extension type of 'csv'.
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• For GO or HPO input data, the input file should include only the first column.
• For gene input data, the first column must include the gene symbol.
• If you want to include data for node size, you must also provide the node shape index.

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Last update: 2025-04-08