Access NormCounts data used by plotTrajectory function

[jblich870]

Hi,

I wondered how to access the 'NormCounts' data that is used in the plotTrajectory function?

It does not appear to be identical to the data stored in "GeneExpressionMatrix".

Many thanks,
J

[rcorces]

plotTrajectory() obtains the values from the specified matrix here:

ArchR/R/Trajectory.R

Line 778 in 968e442

plotParams$color <- .getMatrixValues(ArchRProj, name = name, matrixName = colorBy, log2Norm = FALSE)

If you follow what happens to plotParams$color, The additional manipulations after getting these matrix values include:

1. applying imputeWeights which will happen automatically if they are available and you havent set imputeWeights = NULL.

   ArchR/R/Trajectory.R

   Line 824 in 968e442

   plotParams$color <- imputeMatrix(mat = mat, imputeWeights = imputeWeights, logFile = logFile)

2. quantile cut which will happen when plotting things like gene expression.

   ArchR/R/Trajectory.R

   Line 831 in 968e442

   plotParams$color <- .quantileCut(plotParams$color, min(quantCut), max(quantCut))

If you wanted to obtain these values, you should be able to get them from the plot object for the particular gene you are plotting or perform the manipulations yourself after looking at the code links above.

[jblich870]

Brilliant, really helpful - thank you!