visualize_interactions: Visualize interactions

In SingleCellSignalR: Cell Signalling Using Single Cell RNAseq Data Analysis

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)

Example output

`major.tick.percentage` is not used any more, please directly use argument `major.tick.length`.
`major.tick.percentage` is not used any more, please directly use argument `major.tick.length`.
`major.tick.percentage` is not used any more, please directly use argument `major.tick.length`.
insufficient memory

SingleCellSignalR documentation built on Nov. 8, 2020, 5:17 p.m.