base_FastUpset: Give a fast way to draw an Upset plot base on upsetR

In shijianasdf/BasicBioinformaticsAnalysisFromZhongShan: Launch Usual Clinical tool for Kind Yield

Description

FastUpset is based on upsetR and give a fast way to draw an Upset plot

Usage

FastUpset(data,
          nsets = NULL,nintersects =NA,
          matrix.color = NULL,
          main.bar.color = NULL,
          mainbar.y.label = "Intersection Size",
          sets.bar.color = NULL,
          sets.x.label = "Set Size",
          order.by = c("freq","degree")[1],
          point.size = 3,line.size =1,
          decreasing = c(T,F),
          shade.color = mycolor[30], shade.alpha = 0.25,
          text.scale = 2)

Arguments

data	a list of character vector like markers or genes.The names of list was recommanded to be set
nsets	If NULL,all combs was printed
nintersects	Number of intersections to plot. If set to NA, all intersections will be plotted
matrix.color	Color of the intersection points
main.bar.color	Color of the main bar plot
mainbar.y.label	The y-axis label of the intersection size bar plot
sets.bar.color	Color of set size bar plot
sets.x.label	The x-axis label of the set size bar plot
order.by	How the intersections in the matrix should be ordered by. Options include frequency (entered as "freq"), degree, or both in any order
point.size	Size of points in matrix plot
line.size	Width of lines in matrix plot
decreasing	How the variables in order.by should be ordered. "freq" is decreasing (greatest to least) and "degree" is increasing (least to greatest)
shade.color	Color of row shading in matrix
shade.alpha	Transparency of 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)

"

Value

an Upset Plot

Author(s)

Weibin Huang<[e-mail]>

See Also

upsetR::upset()

Examples

## make a data list
data <- list(
  Cohort1 = sample(1:100,50),
  Cohort2 = sample(1:120,60),
  Cohort3 = sample(1:150,75)
  )

## A simple setting
win.graph(width = 12,height = 8);
FastUpset(data,
          mainbar.y.label = "Intersection Size",
          sets.x.label = "Set Size",
          order.by = c("freq","degree")[1])

## More complex setting
FastUpset(data,
          nsets = NULL,nintersects =NA,
          matrix.color = NULL,
          main.bar.color = NULL,
          mainbar.y.label = "Intersection Size",
          sets.bar.color = NULL,
          sets.x.label = "Set Size",
          order.by = c("freq","degree")[1],
          point.size = 3,line.size =1,
          decreasing = c(T,F),
          shade.color = mycolor[30], shade.alpha = 0.25,
          text.scale = 2)

shijianasdf/BasicBioinformaticsAnalysisFromZhongShan documentation built on Jan. 3, 2020, 10:08 p.m.