plotNhoodExpressionDA: Visualize gene expression in neighbourhoods
In MarioniLab/miloR: Differential neighbourhood abundance testing on a graph

plotNhoodExpressionDA

R Documentation

Visualize gene expression in neighbourhoods

Description

Plots the average gene expression in neighbourhoods, sorted by DA fold-change

Plots the average gene expression in neighbourhood groups

Usage

plotNhoodExpressionDA(
  x,
  da.res,
  features,
  alpha = 0.1,
  subset.nhoods = NULL,
  cluster_features = FALSE,
  assay = "logcounts",
  scale_to_1 = FALSE,
  show_rownames = TRUE,
  highlight_features = NULL
)

plotNhoodExpressionGroups(
  x,
  da.res,
  features,
  alpha = 0.1,
  subset.nhoods = NULL,
  cluster_features = FALSE,
  assay = "logcounts",
  scale_to_1 = FALSE,
  show_rownames = TRUE,
  highlight_features = NULL,
  grid.space = "free"
)

Arguments

`x`	A `Milo` object
`da.res`	a data.frame of DA testing results
`features`	a character vector of features to plot (they must be in rownames(x))
`alpha`	significance level for Spatial FDR (default: 0.1)
`subset.nhoods`	A logical, integer or character vector indicating a subset of nhoods to show in plot (default: NULL, no subsetting)
`cluster_features`	logical indicating whether features should be clustered with hierarchical clustering. If FALSE then the order in `features` is maintained (default: FALSE)
`assay`	A character scalar that describes the assay slot to use for calculating neighbourhood expression. (default: logcounts) Of note: neighbourhood expression will be computed only if the requested features are not in the `nhoodExpression` slot of the milo object. If you wish to plot average neighbourhood expression from a different assay, you should run `calcNhoodExpression(x)` with the desired assay.
`scale_to_1`	A logical scalar to re-scale gene expression values between 0 and 1 for visualisation.
`show_rownames`	A logical scalar whether to plot rownames or not. Generally useful to set this to `show_rownames=FALSE` when plotting many genes.
`highlight_features`	A character vector of feature names that should be highlighted on the right side of the heatmap. Generally useful in conjunction to `show_rownames=FALSE`, if you are interested in only a few features
`grid.space`	a character setting the `space` parameter for `facet.grid` (`'fixed'` for equally sized facets, `'free'` to adapt the size of facent to number of neighbourhoods in group)