A column, may be named, comparison, can be added to the marker data frame. FindAllMarker output which is in general the marker genes for each cluster or cell type can have value "Cluster Marker" in the comparison column. Additionally, DE analysis results can have "Pheno1_vs_HC", "Pheno2_vs_HC" values. So one single data frame will contain multiple DE analysis results to present in the shiny app. The DT table can have a filter option or drop down selector to select comparison.
A column, may be named, comparison, can be added to the marker data frame. FindAllMarker output which is in general the marker genes for each cluster or cell type can have value "Cluster Marker" in the comparison column. Additionally, DE analysis results can have "Pheno1_vs_HC", "Pheno2_vs_HC" values. So one single data frame will contain multiple DE analysis results to present in the shiny app. The DT table can have a filter option or drop down selector to select comparison.