Spatiotemporal metabolic networks in a preclinical model of pancreatic cancer and associated cachexia
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README: OVERVIEW: This repository contains code and interactive plots for "“Spatiotemporal metabolic networks in pancreatic cancer and associated cachexia”. SYSTEM REQUIREMENTS: Hardware: Standard computer with enough RAM. Software: MATLAB version R2020b or later. Note: Our scripts were made on MATLAB for macOS. Some modifications for Windows may need to be made. INSTALLATION GUIDE: MATLAB can be downloaded here: https://www.mathworks.com/help/install/ug/install-products-with-internet-connection.html -Follow standard instructions by MathWorks. Time to install: about 10 minutes INSTRUCTIONS FOR USE: Codes are available for 3D scatterplots, Dandelion Plots, Umbrella Plots, and Prediction Models. Codes in Text files can be downloaded for viewing in Text editor apps, but must be copied into MATLAB in order to run. To run each MATLAB script: Download data files from same folder. Copy directory of the data files to the top of the script as prompted. Run script. Graphs/figures from the manuscript will be generated. Expected Run time: <10 minutes for most scripts, up to an hour for prediction models. Note: models that include multiple iterations/random selection of subsampling will yield slightly different results each time it is run. A representative example was used in the manuscript. "Interactive" Plots are in sub-folders in 3DScatterplots, CorrelationPlots, DandelionPlots, and UmbrellaPlots. All interactive plots have a ".fig" extension which also requires MATLAB to open and interact. 3D scatterplots can be rotated, and data tips show each metabolite name and coordinates. Correlations plots can be zoomed in/out and panned. Additionally, Heatmaps are available as .eps files, and can be downloaded and viewed. Source Files include: -Metabolomics for each method per tissue (not normalized or processed). -Tracing source data -Fold-change and p-values for all volcano plots
自述文件： 概述：本仓库收录了题为《胰腺癌及其伴随恶病质的时空代谢网络》的研究配套代码与交互式可视化图表。 系统需求： 硬件：配置充足内存的标准计算机。 软件：MATLAB R2020b及以上版本。 注：本脚本基于macOS平台的MATLAB编写，若需在Windows系统运行则需进行部分适配修改。 安装指南： 可通过以下链接下载MATLAB：https://www.mathworks.com/help/install/ug/install-products-with-internet-connection.html 请遵循MathWorks官方标准安装流程。安装耗时约10分钟。 使用说明： 本仓库提供可绘制三维散点图、蒲公英图（Dandelion Plots）、伞形图（Umbrella Plots）及预测模型的代码。文本文件格式的代码可通过文本编辑器查看，但需复制至MATLAB环境中方可运行。 运行各MATLAB脚本的步骤如下： 1. 从同一文件夹中下载对应数据文件； 2. 按照脚本提示，将数据文件的目录路径复制至脚本头部； 3. 运行脚本，即可生成论文中的对应图表。 预期运行时长：多数脚本耗时不足10分钟，预测模型类脚本最长可达1小时。 注：包含多次迭代或随机子采样的模型，每次运行结果会存在细微差异，论文中采用了代表性示例结果。 交互式图表存放于3DScatterplots、CorrelationPlots、DandelionPlots及UmbrellaPlots的子文件夹中。所有交互式图表均为.fig格式文件，需使用MATLAB打开并进行交互操作。 三维散点图支持旋转操作，数据提示框可显示各代谢物名称与坐标信息。 相关性图表支持缩放与平移操作。 此外，热图以.eps格式文件提供，可直接下载查看。 源文件文件夹包含： - 各组织样本适配不同分析方法的代谢组学数据（未标准化、未预处理） - 示踪源数据
