interaction_maps {IrisSpatialFeatures} | R Documentation

## Plot interaction maps for all samples

### Description

Plot interaction maps for all samples

### Usage

    interaction_maps(x, ...)

    ## S4 method for signature 'ImageSet'
    interaction_maps(x, int_markers, int_marker_cols,
      silent_markers = c(), silent_col = c(), outline_transparency = 0.9,
      use_dapi = FALSE, outdir = "interaction_maps", useMask = NULL,
      format = ".png")

### Arguments

`x` | An IrisSpatialFeatures ImageSet object
`...` | Additional arguments.
`int_markers` | Cell-types that should be considered. If two cells from different cell-types interact they are filled in, if a cell is not interacting it is just outlined.
`int_marker_cols` | Colors for the cell-types
`silent_markers` | Cell-types that should only be outlined (Default: c())
`silent_col` | Colors for silent markers (Default: c())
`outline_transparency` | Dimming factor for the outlines cells(Default: 0.9)
`use_dapi` | Use the DAPI channel as a background (Default: FALSE)
`outdir` | Output directory (Default: './interaction_maps')
`useMask` | (Default: NULL)
`format` | Output format of the images. Can be '.png' or '.tiff' (Default: '.png')

### Value

plot of interactions for all samples

### Examples

    #' #loading pre-read dataset
    dataset <- IrisSpatialFeatures_data
    dataset <- extract_interactions(dataset)
    get_interactions(dataset,'CD8+ PD1+')
    int_markers <- c('CD8+ PD1+','SOX10+ PDL1+')
    int_marker_cols <- c('#dd1c77','#99d8c9')
    silent_markers <- c('CD8+ PD1-')
    silent_col=c('yellow')
    p <- interaction_maps(dataset,int_markers,int_marker_cols,silent_markers,
                          silent_col)

[Package IrisSpatialFeatures version 1.3.0 Index]