Generate Upset plot for overlapping peaks

Source: R/overlap_upset_plot.R

This function generates upset plot of overlapping peaks files using the ComplexUpset package.

overlap_upset_plot(peaklist, verbose = TRUE)

Arguments

peaklist

A named list of peak files as GRanges object. Objects must be listed and named using list(). e.g. list("name1"=file1, "name2"=file2). If not named, default file names are assigned.

verbose

Print messages

Value

Upset plot of overlapping peaks.

Examples

### Load Data ###
data("encode_H3K27ac") # load example data
data("CnT_H3K27ac") # load example data 
peaklist <- list("encode"=encode_H3K27ac, "CnT"=CnT_H3K27ac) 
my_plot <- overlap_upset_plot(peaklist = peaklist)
#> --- Running overlap_upset_plot() ---
#> Warning: themes$intersections_matrix is not a valid theme.
#> Please use `theme()` to construct themes.
#> Warning: `legend.margin` must be specified using `margin()`
#> ℹ For the old behavior use `legend.spacing`
#> Warning: themes$intersections_matrix is not a valid theme.
#> Please use `theme()` to construct themes.
#> Warning: selected_theme is not a valid theme.
#> Please use `theme()` to construct themes.
#> Warning: `legend.margin` must be specified using `margin()`
#> ℹ For the old behavior use `legend.spacing`
#> Warning: selected_theme is not a valid theme.
#> Please use `theme()` to construct themes.
#> Warning: selected_theme is not a valid theme.
#> Please use `theme()` to construct themes.
#> Warning: `legend.margin` must be specified using `margin()`
#> ℹ For the old behavior use `legend.spacing`
#> Warning: selected_theme is not a valid theme.
#> Please use `theme()` to construct themes.
#> Warning: themes$overall_sizes is not a valid theme.
#> Please use `theme()` to construct themes.
#> Warning: `legend.margin` must be specified using `margin()`
#> ℹ For the old behavior use `legend.spacing`
#> Warning: themes$overall_sizes is not a valid theme.
#> Please use `theme()` to construct themes.
#> overlap_upset_plot(): Done in 0.4s.