visualize_interactions {SingleCellSignalR} | R Documentation

## Visualize interactions

### Description

Creates chord diagrams from the interactions tables.

### Usage

    visualize_interactions(
      signal,
      show.in = NULL,
      write.in = NULL,
      write.out = FALSE,
      method = "default",
      limit = 30
    )

### Arguments

`signal` | a list of data frames result of the **cell_signaling()** function
`show.in` | a vector of which elements of “'signal“' must be shown
`write.in` | a vector of which elements of “'signal“' must be written
`write.out` | a logical
`method` | a string (usually relative to the experiment)
`limit` | a value between 1 and number of interactions

### Details

'show.in' gives the elements of 'signal' to be displayed in the plot window.

'write.in' gives the elements of 'signal' to be written as pdf files in the *images* folder.

If 'write.out' is TRUE, then the function writes a pdf file with a summary of the all the interactions of 'signal' as a chord diagram.

'limit' is the maximum number of interactions displayed on one chord diagram. Raising this limit over 30 may decrease the visibility.

### Value

The function returns images in the plot window of Rstudio and images in the pdf format in the *images* folder.

### Examples

    int.1 <- matrix(c("gene 1","gene 1", "gene 2", "gene 3"),ncol=2)
    colnames(int.1) <- c("cluster 1","cluster 2" )
    int.2 <- matrix(c("gene 1","gene 4","gene 4","gene 2","gene 3","gene 3"),
    ncol=2)
    colnames(int.2) <- c("cluster 1","cluster 3" )
    signal <- list(int.1,int.2)
    names(signal) <- c("1-2","1-3")
    visualize_interactions(signal)

[Package SingleCellSignalR version 1.2.0 Index]