Package 'hicVennDiagram'

Browse the venn plot

Description

Brow the venn plot in a web browser to adjust the plot and export the result.

Usage

browseVenn(plot, width = NULL, height = NULL)

Arguments

plot	plots of vennPlot or upsetPlot
width	width of the figure
height	height of the figure

Value

An object of class htmlwidget that will intelligently print itself into HTML in a variety of contexts including the R console, within R Markdown documents, and within Shiny output bindings.

Examples

pd <- system.file("extdata", package = "hicVennDiagram", mustWork = TRUE)
fs <- dir(pd, pattern = ".bedpe", full.names = TRUE)
vc <- vennCount(fs)
p <- vennPlot(vc)
browseVenn(p)

---

Shiny bindings for browseVenn

Description

Output and render functions for using browseVenn within Shiny applications and interactive Rmd documents.

Usage

browseVennOutput(outputId, width = "100%", height = "400px")

renderbrowseVenn(expr, env = parent.frame(), quoted = FALSE)

Arguments

outputId	output variable to read from
width, height	Must be a valid CSS unit (like '100%', '400px', 'auto') or a number, which will be coerced to a string and have 'px' appended.
expr	An expression that generates a browseVenn
env	The environment in which to evaluate expr.
quoted	Is expr a quoted expression (with quote())? This is useful if you want to save an expression in a variable.

---

Create background by input GInteractions

Description

Create background based on the distance distribution of input GInteractions.

Usage

createGIbackground(gi, size = 2 * lengths(gi))

Arguments

gi	A vector of bedpe files or a list of genomic interaction data (Pairs or GInteractions).
size	The maximal size of the background

Examples

pd <- system.file("extdata", package = "hicVennDiagram", mustWork = TRUE)
fs <- dir(pd, pattern = ".bedpe", full.names = TRUE)[1]
set.seed(123)
# createGIbackground(fs)

---

Perform GLEAM test

Description

Run Genomic Loops Enrichment Analysis Method test

Usage

gleamTest(query, subject, background, method = c("binom", "hyper"), ...)

Arguments

query, subject	A vector of bedpe files or a list of genomic interaction data (Pairs or GInteractions) or a list of GRanges object. 'subject' is optional if length of query > 1.
background	The test will restricted within the region. The background is the background of subject if subject is available. Otherwise, the background is the the background of second element of comparison group.
method	Distribution type for p-value.
...	parameters used by findOverlaps.

Examples

# example code
pd <- system.file("extdata", package = "hicVennDiagram", mustWork = TRUE)
fs <- dir(pd, pattern = ".bedpe", full.names = TRUE)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
## set.seed(123)
## background <- createGIbackground(fs)
## gleamTest(fs, background = background)
## gleamTest(fs, background = background, method = 'hyper')
grl <- GRangesList(exons=reduce(exons(TxDb.Hsapiens.UCSC.hg38.knownGene)),
 genes=reduce(genes(TxDb.Hsapiens.UCSC.hg38.knownGene)))
gleamTest(fs[seq_along(grl)], grl, background = grl[['exons']])
gleamTest(grl[c(2, 1)], grl, background = grl[['exons']])
gleamTest(grl, background = grl[['genes']])

---

UpSet plot for the Venn count table

Description

Plot the overlaps counts by ComplexUpset.

Usage

upsetPlot(
  vennTable,
  label_all = list(na.rm = TRUE, color = "gray30", alpha = 0.7, label.padding = unit(0.1,
    "lines")),
  coln_prefix = NULL,
  ...
)

Arguments

vennTable	An vennTable object, the first element in the output of vennCount.
label_all	A list of parameters used by geom_label for text labels of counts for each group. If it set to FALSE or length of the list is zero, the labels will be ignored.
coln_prefix	The prefix to be removed for colnumn names of vennTable.
...	Parameters could be passed to upset except data and intersect.

Value

A ggplot object.

Examples

pd <- system.file("extdata", package = "hicVennDiagram", mustWork = TRUE)
fs <- dir(pd, pattern = ".bedpe", full.names = TRUE)
vc <- vennCount(fs)
upset_themes_fix <- lapply(ComplexUpset::upset_themes, function(.ele){
.ele[names(.ele) %in% names(formals(ggplot2::theme))]
})
upsetPlot(vc, theme = upset_themes_fix)
## change the font size of lables and numbers
themes <- ComplexUpset::upset_modify_themes(
 ## get help by vignette('Examples_R', package = 'ComplexUpset')
        list('intersections_matrix'=
            ggplot2::theme(axis.text.y=ggplot2::element_text(size=24)))
)
themes <- lapply(themes, function(.ele){
.ele[names(.ele) %in% names(formals(ggplot2::theme))]
})
upsetPlot(vc, label_all=list(
                        na.rm = TRUE,
                        color = 'gray30',
                        alpha = .7,
                        label.padding = grid::unit(0.1, "lines"),
                        size = 5
), themes = themes)

---

Construct intersections of sets

Description

Given a collection of bedpe files or a list of genomic interaction data, vennCount will compute all possible combinations of interactions and return an object of class vennTable, storing the combinations as well as the number of elements in each intersection.

Usage

vennCount(gi, FUN = min, ...)

Arguments

gi	A vector of bedpe files or a list of genomic interaction data (Pairs or GInteractions)
FUN	Function to summarize the overlapping number.
...	parameters used by findOverlaps

Value

An object of vennTable

Examples

pd <- system.file("extdata", package = "hicVennDiagram", mustWork = TRUE)
fs <- dir(pd, pattern = ".bedpe", full.names = TRUE)
vc <- vennCount(fs)

---

Venn diagram for the Venn count table

Description

Plot the overlaps counts by eulerr.

Usage

vennPlot(vennTable, shape = "circle", ...)

Arguments

vennTable	An vennTable object, the first element in the output of vennCount.
shape	Geometric shape used in the diagram used by euler.
...	parameters to update fills and edges with and thereby a shortcut to set these parameters plot.euler.

Value

A grid object.

Examples

pd <- system.file("extdata", package = "hicVennDiagram", mustWork = TRUE)
fs <- dir(pd, pattern = ".bedpe", full.names = TRUE)
vc <- vennCount(fs)
vennPlot(vc)
## change the font size of venn plot lables and numbers,
## both cex or fontsize should work
vennPlot(vc, quantities=list(fontsize=24), labels=list(cex=1.5))

---

Class "vennTable"

Description

An object of class "vennTable" represents Venn counts.

Usage

vennTable(...)

## S4 method for signature 'vennTable'
x$name

## S4 replacement method for signature 'vennTable'
x$name <- value

## S4 method for signature 'vennTable,ANY,ANY'
x[[i]]

## S4 replacement method for signature 'vennTable,ANY,ANY'
x[[i]] <- value

## S4 method for signature 'vennTable'
show(object)

Arguments

...	Each argument in ... becomes an slot in the new vennTable.
x	an object of vennTable
name	slot name of vennTable
value	values to assign
i	slot name of vennTable
object	an object of vennTable.

Value

An object of vennTable.

Slots

combinations

A logical "matrix", specify the combinations.

counts

A "numeric" vector, the overall counts number for each combination.

vennCounts

A "matrix" object, specify the counts number for each sample in the combination.

overlapList

"list", overlapping list of the genomic interactions.

Examples

vt <- vennTable()

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