getVelocityGridAlongThirdDimensions: Calculate the velocity grid along a third dimension.
In danielschw188/Revelio:

Description Usage Arguments Details Value

'getVelocityGridAlongThirdDimensions' places a regular grid on the two-dimensional plot consisting of cell cycle pseudotime and a higher order DC and calculates the average velocity for each grid point as described in La Manno et al. 2018 ('RNA velocity of single cells').

getVelocityGridAlongThirdDimensions(
  dataList,
  whichThirdDimension = 3,
  sigma = 1,
  numberOfGridPointsOneSide = 20,
  boolPlotResults = FALSE
)

`dataList`	A Revelio object that contains information about the extrapolated state of cells.
`whichThirdDimension`	The number of the dimension to be investigated. Needs to be an integer.
`sigma`	The smoothing parameter for the Gaussian kernel.
`numberOfGridPointsOneSide`	The number of grid points along one side. The total grid will be a numberOfGridPointsOneSide-by-numberOfGridPointsOneSide grid.
`boolPlotResults`	TRUE/FALSE if the velocity grid plot should be shown.

A grid is generated overlaying the two-dimensional plot of cell cycle pseudotime and a higher order DC. For each grid point, the RNA velocity is calculated by using a Gaussian kernel as explained in La Manno et al. 2018 ('RNA velocity of single cells').

Returns the same Revelio object given as input with the additional information about the RNA velocity at grid points.

danielschw188/Revelio documentation built on April 30, 2021, 1:02 p.m.