Plot Moran/Geary Monte Carlo results

Plot the simulations as a density plot or histogram compared to the observed Moran's I or Geary's C, with ggplot2 so it looks nicer. Unlike the plotting function in spdep, this function can also plot the same feature in different samples as facets or plot different features or samples together for comparison.

Usage

plotMoranMC(
  sfe,
  features,
  sample_id = "all",
  facet_by = c("sample_id", "features"),
  ncol = NULL,
  colGeometryName = NULL,
  annotGeometryName = NULL,
  reducedDimName = NULL,
  ptype = c("density", "histogram", "freqpoly"),
  swap_rownames = NULL,
  name = "moran.mc",
  ...
)

Arguments

sfe

A SpatialFeatureExperiment object.

features

Features to plot, must be in rownames of the gene count matrix, colnames of colData or a colGeometry, colnames of cell embeddings in reducedDim, or numeric indices of dimension reduction components.

sample_id

Sample(s) in the SFE object whose cells/spots to use. Can be "all" to compute metric for all samples; the metric is computed separately for each sample.

facet_by

Whether to facet by sample_id (default) or features. If facetting by sample_id, then different features will be plotted in the same facet for comparison. If facetting by features, then different samples will be compared for each feature. Ignored if only one sample is specified.

ncol

Number of columns if facetting.

colGeometryName

Name of a colGeometry sf data frame whose numeric columns of interest are to be used to compute the metric. Use colGeometryNames to look up names of the sf data frames associated with cells/spots.

annotGeometryName

Name of a annotGeometry of the SFE object, to annotate the gene expression plot.

reducedDimName

Name of a dimension reduction, can be seen in reducedDimNames. colGeometryName and annotGeometryName have precedence over reducedDimName.

ptype

Plot type, one of "density", "histogram", or "freqpoly".

swap_rownames

Column name of rowData(object) to be used to identify features instead of rownames(object) when labeling plot elements. If not found in rowData, then rownames of the gene count matrix will be used.

name

Name under which the Monte Carlo results are stored, which defaults to "moran.mc". For Geary's C Monte Carlo, the default is "geary.mc".

...

Other arguments passed to geom_density, geom_histogram, or geom_freqpoly, depending on ptype.

Value

A ggplot2 object.

Examples

library(SpatialFeatureExperiment)
library(SFEData)
sfe <- McKellarMuscleData("small")
#> see ?SFEData and browseVignettes('SFEData') for documentation
#> loading from cache
colGraph(sfe, "visium") <- findVisiumGraph(sfe)
sfe <- colDataUnivariate(sfe, type = "moran.mc", "nCounts", nsim = 100)
plotMoranMC(sfe, "nCounts")