Summarize attributes of an annotGeometry for each cell/spot
Source:R/geometry_operation.R
annotSummary.Rd
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 theannotGeometry
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")
#> see ?SFEData and browseVignettes('SFEData') for documentation
#> loading from cache
s <- annotSummary(sfe, "spotPoly", "myofiber_simplified",
annotColNames = c("area", "convexity")
)