Effect plot
Effect plots are useful at showing the size of effect for between group differences. It differs from a Volcano plot, since the effect size is plotted rather than the p-value, giving information about the size of the effect. Gloor et al. 2016 details the differences between effect plots and volcano plots, and what information you can actually obtain from them.
Select conditions
Since ALDEx2 compares the difference between two groups, you need to set up two conditions to be compared. To do this manually, the columns in the data set must be ordered by condition (columns 1-7 are samples under condition 1 and columns 8-14 are samples under condition 2). You can then input how many columns there are for group 1 and group 2 and click Generate effect plot. Below is an example of the two conditions.
Alternatively, you can use your metadata file to select your conditions. Dropdown menus allow you to choose the column and values you wish to compare. Choose your column, and then your two groups from the drop down menus. The data will be filtered based on the sample names, so the samples names in the metadata must be identical to the data.
The default colour scheme for ALDEx2 plots are as follows:
Choose ALDEx2 method
You can change how ALDEx2 calculates the geometric mean. This changes the "denom" input for aldex.clr function. Type ?aldex.clr into your console for more details.
You can hover you mouse over a dot on the effect plot to display the name of the OTU and the effect size between conditions below the plot. This will also show you a stripchart of this OTU, displaying each samples expected CLR values to give an idea of the size of the difference for each sample. This helps interpreting whether there is a true difference in the selected OTU.