About Visualization Tools 
The data analysis and visualization tools permit an analysis of data quality and hypothesis generation with dynamic graphs, which can be automatically generated with easy to use graphical user interfaces.Please see below for brief descriptions of options available at Plantmetaolomics.org, or click title link to navigate to the resource page.
Ratio Plots
Users may compare metabolite levels under different experimental conditions through the generation of dynamic ratio plots of the metabolites. This tool provides the names of all experiments along with access to the metadata of a chosen experiment. Users can expand each experiment and choose any two experimental factors to compare from the two drop down lists. They can also select specific analytical platforms. The resulting ratio plot shows the abundance data where each metabolite is depicted by a clickable mark on the ratio plot The x-axis shows the logarithm (base 2) ratio of the relative abundance of each metabolite between the mutant and wild type samples selected. The metabolites that have a relatively low fold change between the two factors are close to the central vertical y-axis and the metabolites that have a relatively high fold change are distant from the central vertical y-axis. The metabolites with one or more replicates with missing values are shown with different colored marks for quick inspection of data quality. A summary of the metabolite abundance data is generated along with the ratio plot. This summary contains clickable names of the metabolites that are grouped according to the number of missing values (1, 2, 3 or more, or all null values). Users can see detailed information about a metabolite by clicking on its name on the list or by clicking on a mark on the ratio plot. Users can also view an error plot, which shows the change in the metabolite abundance level among the replicates. This helps the users to see if the significant change in the metabolite abundance is similar in replicate samples. The link to the error plot is available near the ratio plot and can be opened in a separate window to compare against the ratio plot.
Bar Charts
The metabolite abundance data can also be visualized in a bar chart where metabolite abundance under different experimental parameters is shown for each replicate. This bar graph can be generated by clicking on a metabolite name from the Browse functional area, by clicking a data point on the ratio plot or by clicking a metabolite name from the data summary list. The metabolite details page also provides links to other databases to provide users with more details about the metabolites. These links include metabolic pathway information from Aracyc, KEGG and MetNetDB and compound information from PubChem. The names of all the pathways that contain a metabolite are shown on the metabolite annotation details page.Pathway names are clickable and show experimental data for all the other metabolites that participate in that pathway in a given experiment