annotSummary: Summarize attributes of an annotGeometry for each cell/spot

In pachterlab/SpatialFeatureExperiment: Integrating SpatialExperiment with Simple Features in sf

Summarize attributes of an annotGeometry for each cell/spot

Description

In SFE objects, the annotation geometries don't have to correspond to the dimensions of the gene count matrix, so there generally is no one to one mapping between annotation geometries and cells/spots. However, it may be interesting to relate attributes of annotation geometries to cell/spots so the attributes can be related to gene expression. This function summarizes attributes of an annotGeometry for each cell/spot by a geometric predicate with a colGeometry.

Usage

annotSummary(
  sfe,
  colGeometryName = 1L,
  annotGeometryName = 1L,
  annotColNames = 1L,
  sample_id = "all",
  pred = st_intersects,
  summary_fun = mean
)

Arguments

sfe	An SFE object.
colGeometryName	Name of column geometry for the predicate.
annotGeometryName	Name of annotation geometry for the predicate.
annotColNames	Character, column names of the annotGeometry of interest, to indicate the columns to summarize. Columns that are absent from the annotGeometry are removed. The column cannot be "geometry" or "barcode".
sample_id	Which sample(s) to operate on. Can be "all" to indicate all samples.
pred	Predicate function to use, defaults to st_intersects.
summary_fun	Function for the summary, defaults to mean.

Value

A data frame whose row names are the relevant column names of sfe, and each column of which is the summary of each column specified in annotColName.

Examples

library(SFEData)
sfe <- McKellarMuscleData("small")
s <- annotSummary(sfe, "spotPoly", "myofiber_simplified",
    annotColNames = c("area", "convexity")
)

pachterlab/SpatialFeatureExperiment documentation built on Dec. 20, 2024, 3:41 a.m.