Rank and quantile plots are important graph types for single cell RNA-sequencing analyses, which facilitate certain quality control filters.


What are these Plot Types?

A rank plot simply places events in descending order, with regard to values on the currently chosen y-axis. Similarly a quantile plot places events in ascending order, with regard to the y-axis parameter:


These plots are available for an individual gene (in Cell View), population/derived-observation (in Gene View), synthetic parameter, or analytical parameter.


Accessing the Plots

To create a rank or quantile plot for a given parameter set the y-axis to your parameter of interest, and then click the x-axis drop down window where you can select “Rank” or “Quantile”:


Knee Plots

A very popular way of performing QC in single cell RNA-sequencing is by filtering on a knee plot, which is simply a rank of the number of genes expressed per cell versus genes expressed per cell. To create the “genes_expressed_per_cell” parameter click the Quality Control button within the Discover band:


For highest ranked quality support please contact: seqgeq@flowjo.com