aggregateNeighbors {imcRtools} | R Documentation

## Function to aggregate all neighbors of each cell.

### Description

Function to summarize categorical or expression values of all neighbors of each cell.

### Usage

    aggregateNeighbors(
      object,
      colPairName,
      aggregate_by = c("metadata", "expression"),
      count_by = NULL,
      proportions = TRUE,
      assay_type = NULL,
      subset_row = NULL,
      statistic = c("mean", "median", "sd", "var"),
      name = NULL
    )

### Arguments

`object` | a `SingleCellExperiment` or `SpatialExperiment` object
`colPairName` | single character indicating the `colPair(object)` entry containing the neighbor information.
`aggregate_by` | character specifying whether the neighborhood should be summarized by cellular features stored in `colData(object)` (`aggregate_by = "metdata"`) or by marker expression of the neighboring cells (`aggregate_by = "expression"`).
`count_by` | for `summarize_by = "metadata"`, a single character specifying the `colData(object)` entry containing the cellular metadata that should be summarized across each cell's neighborhood.
`proportions` | single logical indicating whether aggregated metadata should be returned in form of proportions instead of absolute counts.
`assay_type` | for `summarize_by = "expression"`, single character indicating the assay slot to use.
`subset_row` | for `summarize_by = "expression"`, an integer, logical or character vector specifying the features to use. If NULL, defaults to all features.
`statistic` | for `summarize_by = "expression"`, a single character specifying the statistic to be used for summarizing the expression values across all neighboring cells. Supported entries are "mean", "median", "sd", "var". Defaults to "mean" if not specified.
`name` | single character specifying the name of the data frame to be saved in the `colData(object)`. Defaults to "aggregatedNeighbors" when `summarize_by = "metadata"` or "statistic_aggregatedExpression" when `summarize_by = "expression"`.

### Value

returns an object of `class(object)` containing the aggregated values in form of a `DataFrame` object in `colData(object)[[name]]`.

### Author(s)

Daniel Schulz (daniel.schulz@uzh.ch)

### Examples

    library(cytomapper)
    data(pancreasSCE)

    sce <- buildSpatialGraph(pancreasSCE, img_id = "ImageNb",
                             type = "knn", k = 3)

    # Aggregating neighboring cell-types
    sce <- aggregateNeighbors(sce, colPairName = "knn_interaction_graph",
                             aggregate_by = "metadata",
                             count_by = "CellType")
    sce$aggregatedNeighbors

    # Aggregating neighboring expression values
    sce <- aggregateNeighbors(sce, colPairName = "knn_interaction_graph",
                             aggregate_by = "expression",
                             assay_type = "exprs",
                             statistic = "mean")
    sce$mean_aggregatedExpression

[Package imcRtools version 1.0.2 Index]