aggregateNeighbors {imcRtools} | R Documentation |
Function to summarize categorical or expression values of all neighbors of each cell.
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 )
object |
a |
colPairName |
single character indicating the |
aggregate_by |
character specifying whether the neighborhood should be
summarized by cellular features stored in |
count_by |
for |
proportions |
single logical indicating whether aggregated metadata should be returned in form of proportions instead of absolute counts. |
assay_type |
for |
subset_row |
for |
statistic |
for |
name |
single character specifying the name of the data frame to be
saved in the |
returns an object of class(object)
containing the aggregated
values in form of a DataFrame
object in
colData(object)[[name]]
.
Daniel Schulz (daniel.schulz@uzh.ch)
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