Obtain a summarized trajectory data.frame — getTrajectoryDf • SPATA

Computes the expression trends of all specified variables along the direction of the spatial trajectory.

getTrajectoryDf(
  object,
  trajectory_name,
  of_sample = "",
  variables,
  method_gs = "mean",
  accuracy = 5,
  normalize = TRUE,
  verbose = TRUE
)

Arguments

object	A valid spata-object.
trajectory_name	The trajectory of interest specified as a single character value.
of_sample	The sample(s) of interest specified as a single character value or vector. If set to "" (the default) the first sample is chosen.
variables	Character vector. The variables of interest: Gene sets: Must be in `getGeneSets()` Genes: Must be in `getGenes()` Features: Must be numeric ones of `getFeatureNames()`
method_gs	Character value. The method according to which gene sets will be handled specified as a character of length one. This can be either 'mean' or one of 'gsva', 'ssgsea', 'zscore', or 'plage'. The latter four will be given to `gsva::GSVA()`.
accuracy	Numeric. Given to `accuracy`-argument of `plyr::round_any()`. Determines how many barcode-spots will be summarized as one sub-trajectory-part.
normalize	Logical. If set to TRUE values will be scaled to 0-1. Hint: Variables that are uniformly expressed can not be scaled and are discarded.
verbose	Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.)

Value

A summarized trajectory data.frame.

Details

Initially the compiled trajectory data.frame of the specified trajectory is joined with the respective input of variables via joinWithVariables().

The argument accuracy refers to the amount of which the barcode-spots of the given trajectory will be summarized with regards to the trajectory's direction: The amount of accuracy and the previously specified 'trajectory width' in createTrajectories() determine the length and width of the sub-rectangles in which the rectangle the trajectory embraces are splitted and in which all barcode-spots are binned. Via dplyr::summarize() the variable-means of every sub-rectangle are calculated. These mean-values are then arranged according to the trajectory's direction.

Eventually the data.frame is shifted via tidyr::pivot_longer() to a data.frame in which every observation refers to the mean-value of one of the specified variable-elements (e.g. a specified gene set) of the particular sub-rectangle. The returned data.frame contains the following variables:

trajectory_part: Character. Specifies the trajectory's sub-part of the observation. (Negligible if there is only one trajectory part.)
trajectory_part_order: Numeric. Indicates the order within the trajectory-part. (Negligible if there is only one trajectory part.)
trajectory_order: Numeric. Indicates the order within the whole trajectory.
gene_sets, genes or features: Character. The respective gene sets, gene or feature the value refers to.
values: Numeric. The actual summarized values.