GeneTrendHeatmap.Slingshot

[naqvih6]

Hi,

Thanks for the great tool! I have been using the Slingshot functions from your tool, and it was all running smoothly until I got to GeneTrendHeatmap.Slingshot.
When I ran the function following the instructions from the vignette, I got this error:

#Visualizing Gene Trends with Heatmaps
GeneTrendHeatmap.Slingshot(

• so,
• features = c("MKI67", VariableFeatures(so)[1:20]),
• lineage = "slingPseudotime_2"
• )
  Error in dcast(predictions, Gene ~ Pseudotime, value.var = "Predicted") :
  The dcast generic in data.table has been passed a data.frame, but data.table::dcast currently only has a method for data.tables. Please confirm your input is a data.table, with setDT(predictions) or as.data.table(predictions). If you intend to use a method from reshape2, try installing that package first, but do note that reshape2 is superseded and is no longer actively developed.

To try countering this I ran:
so@meta.data[,colnames(sling)] <- as.data.table(sling)
But I still ran into the same issue. I also ran the following functions, but ran into errors:

predictions <- setDT(predictions)
Error in home(x, parent.env(env)) : Cannot find symbol predictions
predictions <- as.data.table(predictions)
Error: object 'predictions' not found

I would appreciate any guidance you can provide on this matter.

Also, is there a way to add curves or branch points with labels on the Slingshot DimPlot to allow for easier readability and visualization of the Pseudotime Trajectories? Please let me know whenever you can!