sp_upsetview: Generating upsetView plot

In Tong-Chen/YSX: For Yishengxin Training

Description

Input file is a matrix:

Usage

sp_upsetview(
  data,
  vennFormat = 0,
  pointsize = 8,
  keep_empty = FALSE,
  sets = NULL,
  nintersects = NA,
  order.by = "freq",
  decreasing = TRUE,
  scale.intersections = "identity",
  scale.sets = "identity",
  queries_bar1 = NULL,
  queries_bar2 = NULL,
  queries_bar3 = NULL,
  queries_bar1_color = NULL,
  queries_bar2_color = NULL,
  queries_bar3_color = NULL,
  saveplot = NULL,
  debug = FALSE,
  saveppt = FALSE,
  main_bar_color_vector = "gray23",
  constantColor = T,
  ...
)

Arguments

data	Data file. Receive long and wide table forms.
vennFormat	Venn diagram format without header line. Default 0 represents normal data. Accept 1,2. 0: represents wide data listed above. 1: represents venn diagram format without header line. 2: represents venn diagram format with header line.
pointsize	Point size. Default 8.
keep_empty	Keep empty intersections. Default FALSE. Accept TRUE to remove empty intersections.
sets	Specific sets to look at (Include as combinations. Ex: c('Name1', 'Name2')).
nintersects	Number of intersections to plot. If set to NA, all intersections will be plotted.
order.by	How the intersections in the matrix should be ordered by. Options include frequency (entered as 'freq'), degree.
decreasing	How the variables in order.by should be ordered. 'freq' is decreasing (greatest to least) and 'degree' is increasing (least to greatest).
scale.intersections	The scale to be used for the intersection sizes. Options: 'identity', 'log10', 'log2'.
scale.sets	The scale to be used for the set sizes. Options: 'identity', 'log10', 'log2'.
queries_bar1	Specifies an intersection. Changes the column color.
queries_bar1_color	Input color. Specifies an intersection to use this color.
saveplot	Save plot to given file "a.pdf", "b.png".
...	Other parameters given to base_plot_save

Details

vennFormat 0

(First row would be treated as header line. First column is just a normal column (but needed). 0 represents the sample does not contain the genes in row. 1 represents the containing relationship)

ID Samp1 Samp2 Samp3 Samp4 Samp5

G1 1 0 1 0 1

G2 0 0 1 1 1

G3 1 1 1 0 1

G4 1 1 1 0 0

G5 0 1 0 1 1

G6 1 0 1 0 0

vennFormat 1 or 2

The output contains two barplots, horizontal bar represents the number of genes in each sample, which is the sum of all 1 in sample column. Vertical bar represents the number of sample specific and common genes as indicated by linking vertical lines and points (just as the overlapping regions of venndiagram).

Value

A pdf file.

Examples

upsetview_data <- data.frame(elements=c("1","2","2","2","3"), sets=c("A","A","B","C","C"))
sp_upsetview(data = upsetview_data, vennFormat=2, saveplot = "upsetView_long.pdf")


## Not run:
upsetview_data = "upsetview.data"
sp_upsetview(data = upsetview_data, saveplot = "upsetView_wide.pdf")
## End(Not run)

Tong-Chen/YSX documentation built on Jan. 25, 2021, 2:49 a.m.