This tool gives you plots showing user defined markers/genes across the conditions. This tool can be used for two sample combined Seurat objects.
As inputs, give a combined Seurat object.
Select the markers you want to inspect by listing them in the parameter row. Separate the names with space and comma. As an example, the parameter is set to markers "CD3D, CREM, HSPH1, SELL, GIMAP5".
The "SplitDotPlotGG" can be useful for viewing conserved cell type markers across conditions, showing both the expression level and the percentage of cells in a cluster expressing any given gene. The size of the dot encodes the percentage of cells within a class (=cluster), while the color encodes the AverageExpression level of 'expressing' cells (stronger color, more experssion).
Another useful way to visualize the changes in gene expression is with the FeatureHeatmap function. This will display FeaturePlots of the list of given genes, split by the condition.
For more details, please check the Seurat tutorials for multiple sample analysis.