plotIntersect() draws an UpSet plot of the gene lists of sc.filter()
with UpSetR::upset(), which needs the suggested package UpSetR, or
returns its data.
Usage
plotIntersect(
scmpObj,
min_intersection_size = 1,
keep_empty_groups = FALSE,
return = FALSE
)Arguments
- scmpObj
A ScMaSigPro object.
- min_intersection_size
The smallest intersection drawn.
- keep_empty_groups
Whether to draw the empty intersections.
- return
Whether to return the data instead of the plot.
Value
An upset object of UpSetR or, with return = TRUE, a data frame
with one row per gene and a 0/1 column per gene list.
References
Conway JR, Lex A, Gehlenborg N (2017). UpSetR: an R package for the visualization of intersecting sets and their properties. Bioinformatics 33(18), 2938-2940. doi:10.1093/bioinformatics/btx364
See also
Other plots:
plotBinTile(),
plotDiagnostics(),
plotTrend(),
plotTrendCluster()
Author
Priyansh Srivastava spriyansh29@gmail.com
Examples
data("scmp.ob", package = "scMaSigPro")
# The genes of each list as 0/1 columns
head(plotIntersect(scmp.ob, return = TRUE))
#> Path2vsPath1 Path1
#> Gene2 1 0
#> Gene3 1 1
#> Gene4 1 0
#> Gene9 1 1
#> Gene10 1 1
#> Gene15 1 1
if (requireNamespace("UpSetR", quietly = TRUE)) {
plotIntersect(scmp.ob)
}
#> Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
#> ℹ Please use tidy evaluation idioms with `aes()`.
#> ℹ See also `vignette("ggplot2-in-packages")` for more information.
#> ℹ The deprecated feature was likely used in the UpSetR package.
#> Please report the issue at <https://github.com/hms-dbmi/UpSetR/issues>.
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the UpSetR package.
#> Please report the issue at <https://github.com/hms-dbmi/UpSetR/issues>.
#> Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
#> ℹ Please use the `linewidth` argument instead.
#> ℹ The deprecated feature was likely used in the UpSetR package.
#> Please report the issue at <https://github.com/hms-dbmi/UpSetR/issues>.
