- 1. Launching NetCrafter
- 1.1 Install NetCrafter on Windows
- To launch NetCrafter:
- 1) Go to the the main NetCrafter page.
- 2) Click the button to download the NetCrafter Desktop Application.
- 3) Open ‘NetCrafter.zip’ file and uncompress the file.
- 4) Click the right button on the mouse to install NetCrafter1.21.exe and select Run as administrator.
- Guide to all process for installation are started from the following window.
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- *내용 변경 및 다운로드 화면 사진 필요
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- 2. Main Functions of NetCrafter
- This program is mainly draw network automatically based on Tanimoto coefficients using Gene and GO 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 Function.
- 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 Visualization of 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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- 2.5 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.
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- 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.
- 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. Notice for using NetCrafter
- There are several notice points to use the NetCrafter.
- 4.1 Input File
- NetCrafter only recognize the input file with extension type of 'csv'.
- And the input file does not need to include column names in the first row or column.
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- Last update: August. 23, 2024 by
