S4 wrapper for
UpSetR::upset() with improved default aesthetics.
plotUpset(object, ...) # S4 method for data.frame plotUpset( object, 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, ... ) # S4 method for DataFrame plotUpset( object, 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, ... )
Width of lines in matrix plot
Color of the main bar plot
Color of the intersection points
Transparency of the empty intersections points in the matrix
Ratio between matrix plot and main bar plot (Keep in terms of hundredths)
Size of points in matrix plot
Color of set size bar plot
Transparency of shading in matrix
Color of row shading in matrix
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)
How the variables in order.by should be ordered. "freq" is decreasing (greatest to least) and "degree" is increasing (least to greatest)
Keep sets in the order entered using the sets parameter. The default is FALSE, which orders the sets by their sizes.
Graphical output, no return.
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.
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
## Refer to 'UpSetR::upset()' documentation for more examples. movies <- import(system.file("extdata", "movies.csv", package = "UpSetR"))#>plotUpset(movies)