What is a Cloud Plot?
The cloud plot generated automatically in XCMSplus software is a graphical way to portray which significantly differentiated features are being up-regulated (in green) or down-regulated (in red) across your sample groups. The plot is organized with mass-to-charge ratio (m/z) on the y-axis and by retention time on the x-axis. Each circle on this plot represents a feature (either a metabolite, another compound and/or their adducts). The fold change is represented by the radius of each feature, the larger the circle the larger the mean fold change. The p-value is represented by the depth of color, the darker the color the lower the p-value. The cloud plot is completely interactive and can be filtered by various settings, such as p-value, fold change or mass-to-charge ratio. This allows you to be more stringent regarding what is displayed on the plot, filtering such only the more significant features are displayed.
Thank you for the very simple and comprehensive answer. I know it may seem basic for experienced researchers but for students only starting out, it really helps a lot to understand the output of your data.