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1. Launching NetCrafter
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1.1 Installating NetCrafter on Windows
- To launch NetCrafter:
- 1) Go to the the main NetCrafter page.
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2) Click the button to download the NetCrafter Desktop Application.
- 3) Open ‘NetCrafter.zip’ file and uncompress the file.
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4) Click the right button on the mouse to install
NetCrafter1.21.exe and select Run as administrator.
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Guide to all process for installation are started from the following
window.
- *다운로드 사진 필요
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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.
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2.1 Running NetCrafter
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When NetCrafter starts, the main windows will appear that looks like this (captured on
Window):
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2.2 Loading Data
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To obtain the sample loading data, you can download the file from the main page of
NetCrafter.
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1) Select the data type; Gene or GOBP or HPO.
- 2) Click the [Import data] button.
- 3) Select your input file as csv format.
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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
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You can deselect genes or functions that you don't want to display in the network. Here’s
how:
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1) You can sort the data by clicking on the column names,
[Gene symbol] and [# Total functions].
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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.
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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.
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Click the [Selected] button to confirm your choices.
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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 ]
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2) Criterion for node size : [ ontology count / your custom basis ]
• Customization : Node size can be adjusted
based on input file data.
- 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.
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1) By clicking the [Network] button, a new window will pop
up, displaying the network.
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2) You can view names of each node by hovering your mouse over it.
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3) The number of nodes displayed in the network is shown in the
upper right corner.
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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.
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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
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1) Click the [Save Plot] button at the bottom of the control
panel on the right.
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You can save your data file as PDF, JPG, and
PNG format.
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Format |
Description |
PDF |
Portable Document Format, ideal for sharing and printing
|
JPG |
Image file of high-quality resolution |
PNG |
Image file with lossless compression |
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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.
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3.1 Control Panel
- 1) Network connection threshold
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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:
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• 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.
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Once you’ve adjusted the settings, click the [UPDATE] button to apply your changes.
- 3) Two options for edge
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• Edge thickness - Adjust the scale to make edges thicker or thinner.
• Edge length - Increase the scale to spread clusters further
apart in the network.
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After adjusting the settings, click the [UPDATE] button to confirm your changes.
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3.2 Cluster Selection
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The NetCrafter software automatically calculates similarity using Tanimoto coefficients to
form clusters.
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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.
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1) Deselect the clusters which you don't want to display on the
network.
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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
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4.1 Detailed Cluster List
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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 Reclustering Network (Gene Network)
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After drawing a gene network, you can redraw an ontology network included in the cluster.
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1) Select the cluster you want to explore further, then open its
ontology list window as described in Section 4.1.
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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.
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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.
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If you want to include data for node size, you must also provide the node shape index.
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Last update: August. 23, 2024