Network Visualization in Cytoscape?Cytoscape 的網(wǎng)絡(luò)可視化?

While we do provide in-browser visualization for networks, these are limited to a single component at a time. Using Cytoscape, we can start visualizing the entire molecular network at once.

雖然我們確實(shí)為網(wǎng)絡(luò)提供了瀏覽器內(nèi)可視化，但是每次只能使用一個(gè)組件。使用細(xì)胞景觀，我們可以立即開始可視化整個(gè)分子網(wǎng)絡(luò)。

Cytoscape is an open source software platform for visualization and annotation of networks. Cytoscape is available for download from?here. The instructions below assume that you have installed Cytoscape 3.6.X.

Cytoscape 是一個(gè)用于網(wǎng)絡(luò)可視化和注釋的開源軟件平臺(tái)。細(xì)胞景觀可從這里下載。下面的說明假設(shè)您已經(jīng)安裝了 Cytoscape 3.6. x。

Cytoscape 3.6 Analysis (Quick)?

To quickly get started with your molecular network in Cytoscape, we have an easy export module from GNPS that previews the molecular network and provides a pre-formatted Cytoscape file. This feature is very much experimental, but from the status page, click the "Direct Cytoscape Preview/Download"

為了快速開始與您的分子網(wǎng)絡(luò)在 Cytoscape，我們有一個(gè)簡單的導(dǎo)出模塊從 GNPS，預(yù)覽分子網(wǎng)絡(luò)，并提供了一個(gè)預(yù)格式化的細(xì)胞景觀文件。這個(gè)特性是非常實(shí)驗(yàn)性的，但是從狀態(tài)頁面，點(diǎn)擊“直接細(xì)胞景觀預(yù)覽/下載”

This will bring you to a new interface where you will see a preview and a download link.

這將帶您到一個(gè)新的界面，您將看到一個(gè)預(yù)覽和下載鏈接。

To re-style it with our presets, at the bottom we have a few styles already populated.

為了重新樣式與我們的預(yù)設(shè)，在底部，我們有一些樣式已經(jīng)填充。

Contributing Alternative Styles

提供不同的風(fēng)格

If you would like to suggest a new style, please send us a .cys file and the name of the style you have created within the Cytoscape file for us to add.

如果你想推薦一種新款式，請(qǐng)寄給我們一份。Cys 文件和樣式的名稱，您已創(chuàng)建的細(xì)胞景觀文件中為我們添加。

Cytoscape 3.6 Analysis (Recommended)?細(xì)胞景觀3.6分析(推薦)?

Downloading Cytoscape Import Files?下載細(xì)胞景觀導(dǎo)入文件?

The first step is to download the correct input to import into Cytoscape. From the results page of molecular networking, you will need to download the graphML file for Cytoscape.

第一步是下載正確的輸入導(dǎo)入到 Cytoscape 中。從分子網(wǎng)絡(luò)的結(jié)果頁面，您將需要下載針對(duì) Cytoscape 的 graphML 文件。

Unzip the content of the zip file. The content will look like this:

解壓 zip 文件的內(nèi)容，內(nèi)容如下:

Importing Network into Cytoscape?將網(wǎng)絡(luò)導(dǎo)入細(xì)胞景觀?

Now open Cytoscape 3.6.1. From the Toolbar go to File / Import / Network / File (or cmd + L) and then select the .graphml file in the root of the unzipped job folder.

現(xiàn)在打開 Cytoscape 3.6.1。從工具欄轉(zhuǎn)到 File/Import/Network/File (或 cmd + l) ，然后選擇。在解壓縮后的作業(yè)文件夾的根目錄中放置 graphml 文件。

The network has been opened and will look like this.

這個(gè)網(wǎng)絡(luò)已經(jīng)打開了，將會(huì)是這個(gè)樣子。

Creating a Cytoscape Style?創(chuàng)建細(xì)胞景觀風(fēng)格?

In Cytoscape 3.6.1, create a new Cytoscape style. As shown below, click on "Create New Style" and provide a name.

在細(xì)胞景觀3.6.1中，創(chuàng)建一個(gè)新的細(xì)胞景觀樣式。如下所示，單擊“創(chuàng)建新樣式”并提供一個(gè)名稱。

Node Styling?節(jié)點(diǎn)樣式?

Node Label to Spectrum Property?頻譜屬性的節(jié)點(diǎn)標(biāo)記?

Within the Node menu, you will be able to Apply a label to each of your nodes, you may select the Attribute from the drop down menu to use as a label and then select Passthrough MApping as the MApping Type. Typically Parent mass or Precursor mass is selected for node labels of networks generated using GNPS.

在 Node 菜單中，你可以對(duì)每個(gè)節(jié)點(diǎn)應(yīng)用一個(gè)標(biāo)簽，你可以從下拉菜單中選擇 Attribute 作為標(biāo)簽，然后選擇 Passthrough MApping 作為映射類型。通常，為使用 GNPS 生成的網(wǎng)絡(luò)的節(jié)點(diǎn)標(biāo)簽選擇父質(zhì)量或前驅(qū)質(zhì)量。

Visualizing Group Abundances as Pie Charts?可視化群組豐度為餅圖?

If you organized your data into cohorts of samples, we can visualize the relative abundance (as measured by spectral counts which is psuedo-quantitative) with pie charts across these groups.

如果你把你的數(shù)據(jù)組織成樣本的隊(duì)列，我們可以用餅圖來顯示這些組中的相對(duì)豐度(通過光譜計(jì)數(shù)量度量)。

Visualizing Structures?可視化結(jié)構(gòu)?

The Cytoscape plugin ChemViz2 can visualize the chemical structure of GNPS spectral library annotation in the nodes. The ChemViz2 plugin can be be installed in the toolbar Apps /Apps manager / and type "ChemViz2" to find and install it.

Cytoscape 插件 chemviz2可以將 GNPS 光譜庫注釋的化學(xué)結(jié)構(gòu)可視化到節(jié)點(diǎn)中?？梢栽诠ぞ邫?Apps/Apps manager/中安裝 chemviz2插件，并鍵入“ ChemViz2”來查找和安裝它。

To visualize chemical structures, select the nodes of interest and do right-click, Apps / Cheminformatics tools / Paint structure on selected nodes.

為了可視化化學(xué)結(jié)構(gòu)，選擇感興趣的節(jié)點(diǎn)，然后右鍵單擊 Apps/Cheminformatics tools/Paint structure on selected nodes。

Also check out their?website.

還可以看看他們的網(wǎng)站。

Edge Styling?邊緣造型?

Edge Thickness based on Spectral Similarity?基于光譜相似度的邊緣厚度?

To aid in the visualization of individual node relatedness within a cluster, the cosine score is used. This value will determine the thickness of the edge between related nodes. The thicker the edge, the higher the cosine score and therefore the more related the two individual nodes are to each other.

為了幫助可視化集群中各個(gè)節(jié)點(diǎn)的相關(guān)性，使用了余弦得分。此值將確定相關(guān)節(jié)點(diǎn)之間邊緣的厚度。邊緣越厚，余弦得分越高，因此兩個(gè)單獨(dú)的節(jié)點(diǎn)之間的相關(guān)性越強(qiáng)。

Again working within the Style Tab, select the Edge menu. From the Width drop down menu, select Cosine for the Column and Continuous MApping for the MApping Type.

再次在“樣式”選項(xiàng)卡中工作，選擇“邊緣”菜單。在 Width 下拉菜單中，為 Column 選擇 Cosine，為 MApping Type 選擇 Continuous MApping。

Double click on the Continuous MApping area of the menu to adjust the thickness of the edge. Click OK to Apply the setting changes.

雙擊菜單的連續(xù)映射區(qū)域來調(diào)整邊緣的厚度。單擊 OK 應(yīng)用設(shè)置更改。

Below is a zoomed in portion of a network demonstrating the use of Cosine score for edge width determination.

下面是網(wǎng)絡(luò)的縮放部分，演示如何使用余弦得分確定邊緣寬度。