plotNhoodExpressionDA {miloR} | 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)

### Value

a `ggplot` object

a `ggplot` object

### Author(s)

Emma Dann

Emma Dann

### Examples

    NULL

    NULL

[Package miloR version 1.2.0 Index]