![]() ![]() We can plot individual gates: note the scale of the transformed axes. # name Population Parent Count ParentCount We can retrieve the population statistics : getPopStats(gs) # Polygonal gate 'APC' with 14 vertices in dimensions and We only need to know the path to, and filename of the flowJo workspace. We represent flowJo workspaces using flowJoWorkspace objects. The following section walks through opening and importing a flowJo workspace. You will have to save them in XML workspace format. The GatingSet can be built from scratch within R or imported from flowJo XML workspaces (i.e.xml or. By this we mean, accessing the samples, groups, transformations, compensation matrices, gates, and population statistics in the gating tree, which is represented as GatingSet object in R. Just perform compensation on your single stain controls like you normally would and overwrite the acquisition matrix that was applied automatically when you loaded the data.The purpose of this package is to provide the infrastructure to store, represent and exchange the gated flow data. New Files have an acquisition defined matrix, but you want to do compensation in FlowJo This allows you to still use FlowJo for compensation, but it adds one extra step to the template. However, since we loaded the data without compensation, we have to apply a matrix first AND THEN unify the analysis. This would happen automatically if your files had a acquisition defined compensation matrix associated with them because compensated parameters would exist in the files and FlowJo would automatically apply the gates. This command will commit all of those group’s gates to all of the samples in the group. Once you apply a matrix to your samples, you can right click on any group and select “Unify Analysis”. You can compensate in FlowJo either by creating a new matrix from compensation controls run with these new data (recommended) or you can load a matrix exported from a previous experiment. New Files don’t have an acquisition matrix (uncompensated) Therefore, we need to compensate these new data first. However, if you load data into a template that has not yet been compensated, the gates will not automatically apply because the gates in the template were created on compensated parameters and these new data don’t have any compensated parameters yet. When a template is created on compensated parameters, and new data is loaded that was compensated on the machine (includes an acquisition matrix), these data will load right into the template and gates will be applied. Applying new compensation matrices to data loaded into templates can be a bit confusing. ![]()
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