gs_multi_plot: Multi-comparison plot

In NateyJay/genesectR: Genesect analyses in the style of virtualplant.org

Multi-comparison plot

Description

Multi-comparison plot

Usage

gs_multi_plot(
  gs,
  expand,
  value.cex = 0.8,
  label.cex = 0.8,
  zlim = NULL,
  palette = "Purple-Green",
  palette_trim = 0.2
)

Arguments

gs	genesectR object
expand	vector of set names which will be plotted along the top axis, comparing against those which are not listed.
value.cex	scaling for values within boxes
label.cex	scaling for axis labels
zlim	a value used to define the maximum colors plotted. Useful for sharing the same color scale between genesects.
palette	hcl.colors palette (found in hcl.pals()) which will be used in colorizing the genesect.
palette_trim	a percentage of the palette which will be trimmed from the most extreme values. This is useful to remove the most dark colors (default top 0.2) from the palette, which can be difficult to read text on.

Examples

master_set <- str_glue("Gene_{1:1000}")

ls <- list(Set_A= sample(master_set, 300),
           Set_B= sample(master_set[1:100], 27),
           Set_C= sample(master_set, 99),
           Set_V= sample(master_set[1:100], 15),
           Set_W= sample(master_set, 201),
           Set_X= sample(master_set, 500),
           Set_Y= sample(master_set, 44),
           Set_Z= sample(master_set, 766))

gs <- gs_import(ls, master_set)
gs <- gs_compute_matricies(gs, mc=T)
par(mar=c(2,2,10,10))
gs_multi_plot(gs, expand=c("Set_V","Set_W","Set_X","Set_Y","Set_Z"),
              zlim=1)

NateyJay/genesectR documentation built on Aug. 22, 2023, 11 a.m.