Wrapper for UpSetR::upset() with improved default aesthetics.

upset(..., line.size = 1L, main.bar.color = "black",
  matrix.color = "black", matrix.dot.alpha = 1L, mb.ratio = c(0.6,
  0.4), point.size = 3L, sets.bar.color = "black", shade.alpha = 1L,
  shade.color = NA, text.scale = 1.5, decreasing = c(TRUE, FALSE),
  keep.order = FALSE)

Arguments

...

Additional arguments.

line.size

Width of lines in matrix plot

main.bar.color

Color of the main bar plot

matrix.color

Color of the intersection points

matrix.dot.alpha

Transparency of the empty intersections points in the matrix

mb.ratio

Ratio between matrix plot and main bar plot (Keep in terms of hundredths)

point.size

Size of points in matrix plot

sets.bar.color

Color of set size bar plot

shade.alpha

Transparency of shading in matrix

shade.color

Color of row shading in matrix

text.scale

Numeric, value to scale the text sizes, applies to all axis labels, tick labels, and numbers above bar plot. Can be a universal scale, or a vector containing individual scales in the following format: c(intersection size title, intersection size tick labels, set size title, set size tick labels, set names, numbers above bars)

decreasing

How the variables in order.by should be ordered. "freq" is decreasing (greatest to least) and "degree" is increasing (least to greatest)

keep.order

Keep sets in the order entered using the sets parameter. The default is FALSE, which orders the sets by their sizes.

Value

Graphical output, no return.

Details

Visualization of set data in the layout described by Lex and Gehlenborg in http://www.nature.com/nmeth/journal/v11/n8/abs/nmeth.3033.html. UpSet also allows for visualization of queries on intersections and elements, along with custom queries queries implemented using Hadley Wickham's apply function. To further analyze the data contained in the intersections, the user may select additional attribute plots to be displayed alongside the UpSet plot. The user also has the the ability to pass their own plots into the function to further analyze data belonging to queries of interest. Most aspects of the UpSet plot are customizable, allowing the user to select the plot that best suits their style. Depending on how the features are selected, UpSet can display between 25-65 sets and between 40-100 intersections.

References

Lex et al. (2014). UpSet: Visualization of Intersecting Sets IEEE Transactions on Visualization and Computer Graphics (Proceedings of InfoVis 2014), vol 20, pp. 1983-1992, (2014). http://people.seas.harvard.edu/~alex/papers/2014_infovis_upset.pdf

Lex and Gehlenborg (2014). Points of view: Sets and intersections. Nature Methods 11, 779 (2014). http://www.nature.com/nmeth/journal/v11/n8/abs/nmeth.3033.html

Examples

## Refer to UpSetR::upset() documentation for more examples. movies <- read.csv( system.file("extdata", "movies.csv", package = "UpSetR"), header = TRUE, sep = ";" ) upset(movies)