Description Usage Arguments Details Value Author(s) See Also Examples

Summarize the velocity vectors into a grid, usually for easy plotting.

1 2 3 4 5 6 7 | ```
gridVectors(x, embedded, ...)
## S4 method for signature 'ANY'
gridVectors(x, embedded, resolution = 40, scale = TRUE, as.data.frame = TRUE)
## S4 method for signature 'SingleCellExperiment'
gridVectors(x, embedded, ..., use.dimred = 1)
``` |

`x` |
A numeric matrix of low-dimensional coordinates, e.g., after t-SNE.
Alternatively, a SingleCellExperiment containing such coordinates in its |

`embedded` |
A low-dimensional projection of the velocity vectors into the embedding of |

`...` |
For the generic, further arguments to pass to specific methods. For the SingleCellExperiment method, further arguments to pass to the ANY method. |

`resolution` |
Integer scalar specifying the resolution of the grid, in terms of the number of grid intervals along each axis. |

`scale` |
Logical scalar indicating whether the averaged vectors should be scaled by the grid resolution. |

`as.data.frame` |
Logical scalar indicating whether the output should be a data.frame.
If |

`use.dimred` |
String or integer scalar specifying the reduced dimensions to retrieve from |

This partitions the bounding box of `x`

into a grid with `resolution`

units in each dimension.
The locations and vectors of all cells in each block are averaged to obtain a representative of that block.
This is most obviously useful for visualization to avoid overplotting of velocity vectors.

If `scale=TRUE`

, per-block vectors are scaled so that the median vector length is comparable to the spacing between blocks.
This improves visualization when the scales of `x`

and `embedded`

are not immediately comparable.

If `as.data.frame=FALSE`

, a list is returned containing `start`

and `end`

,
two numeric matrices with one row per non-empty block in the grid and one column per column in `x`

.
`start`

contains the mean location of all cells inside that block,
and `end`

contains the endpoint after adding the (scaled) average of the block's cell's velocity vectors.

If `as.data.frame=TRUE`

, a data.frame is returned with numeric columns of the same contents as the list above.
Column names are prefixed by `start.*`

and `end.*`

.

Aaron Lun

`embedVelocity`

, to generate `embedded`

.

1 2 3 4 5 6 7 8 |

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