Demo: Plot a doublet-score

[Muffin2001]

Plot doublet score

Would be cool to have this included in one of the next updates. Very basic score based on the typical doublet gating. Relies on different FSC peak patterns: spehrical singlets have a proportional peak AUC (FSC-A) to peak height (FSC-H) ratio. Doublets have a larger peak AUC, without the peak being proportionally higher. This formula is basically the diagonal doublet gating turned into a formula.

FSC-A ~ FSC-H (singlets)
d-score = FSC-A / FSC-H (constant for singlets, e.g. 1)
d-score doublets > d-score singlets

condor$expr$orig$`d-score` <- condor$expr$orig$`FSC-A` / condor$expr$orig$`FSC-H`  # adjust colnames if neccessary

plot_dim_red(fcd = condor, expr_slot = "orig",
             reduction_method = "umap", reduction_slot = "15_expr_orig",           # reduction method of choice
             param = "d-score", title = "doublet score UMAP")

plot_marker_violinplot(fcd = condor, marker = "d-score", expr_slot = "orig", 
                       cluster_slot = "...", cluster_var = "...")                  # adjust to clustering of choice

Warning: This d-score, when computed this way, is stored alongside the markers. Makes it easy to plug into cyCONDORs functions, but would be used as a marker for future e.g. clustering/dimred runs, when markers to use/exclude are not specified properly.

[lorenzobonaguro]

Hi @Muffin2001, you can add the parameter to the anno table, this way you do not interfere with the other parameters this would be an exemplary code following your example.

condor$anno$cell_anno$`d-score` <- condor$expr$orig$`FSC-A` / condor$expr$orig$`FSC-H`  # adjust colnames if neccessary

plot_dim_red(fcd = condor, expr_slot = "orig",
                      reduction_method = "umap", 
                      reduction_slot = "15_expr_orig",
                      param = "d-score", 
                      title = "doublet score UMAP")

Nevertheless, it's important to note that this approach will only work well on conventional cytometers. Most new spectral machines do not have an area-scaling feature, which would make assessing the ratio you're calculating quite difficult.