velocyto.R spliced/unspliced figures for cluster specific genes with low expression

[RodrigoGM]

Hi !
I'm a little stuck figuring out how to plot the spliced and unspliced data for six genes of interest. The main issue is they are not present in the Seurat emat or nmat created by RunVelocity.

Is there a way to perform this analysis with genes not currently present by default in the filtered expression matrices ? i.e. can I force the set of six genes of interest to become part of the emat and nmat? These genes are expressed in about 10% of the total cell population but are cluster specific (95% are solely on 2 clusters), albeit have low transcript abundance.

Any help and/or suggestions would be much appreciated. Thank you in advance,

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I'm implementing this example code from the the velocyto.R vignette to plot a few of my genes of interest (my code below).

gene <- "Nfib"
gene.relative.velocity.estimates(emat, nmat, deltaT = 1, kCells = 20 , kGenes = 1, 
   fit.quantile = fit.quantile, cell.emb = emb, cell.colors = cell.colors, cell.dist = cell.dist, 
   show.gene = gene, old.fit = rvel.cd, do.par = TRUE)

With my data I'm running this code, which works for genes present in the emat and nmat, but fails with my genes of interest.

276 gene.relative.velocity.estimates(
277     emat = seu@tools$RunVelocity$conv.emat.norm,
278     nmat = seu@tools$RunVelocity$conv.nmat.norm,
279     cellKNN = seu@tools$RunVelocity$cellKNN,
280     fit.quantile = 0.2,
281     cell.emb = Embeddings(object = seu, reduction = "umap"),
282     show.gene = "CDK4", do.par = TRUE)
283 * Error in gene.relative.velocity.estimates(emat = seu@tools$RunVelocity$conv.emat.norm,  :
284   gene CDK4 is not present in the filtered expression matrices