heatmaps: Flexible Heatmaps for Functional Genomics and Sequence Features

Package ‘heatmaps’

September 30, 2024

Title Flexible Heatmaps for Functional Genomics and Sequence Features

Version 1.29.0

Date 2021-11-21

Author Malcolm Perry <[email protected]>

Maintainer Malcolm Perry <[email protected]>

Depends R (>= 3.4)

Imports methods, grDevices, graphics, stats, Biostrings,

GenomicRanges, IRanges, KernSmooth, plotrix, Matrix, EBImage,

RColorBrewer, BiocGenerics, GenomeInfoDb

Suggests BSgenome.Drerio.UCSC.danRer7, knitr, rmarkdown, testthat

biocViews Visualization, SequenceMatching, FunctionalGenomics

License Artistic-2.0

Description This package provides functions for plotting heatmaps of genome-wide

data across genomic intervals, such as ChIP-seq signals at peaks or across promoters.

Many functions are also provided for investigating sequence features.

VignetteBuilder knitr

Collate Heatmap-class.R PlotHeatmap.R PlotHeatmapList.R

PlotPatternDensityMap.R PWMScanHeatmap.R PatternHeatmap.R

CoverageHeatmap.R SmoothHeatmap.R PlotHeatmapMeta.R Data.R

NeedsCompilation no

RoxygenNote 6.0.1

git_url https://git.bioconductor.org/packages/heatmaps

git_branch devel

git_last_commit 6974f83

git_last_commit_date 2024-04-30

Repository Bioconductor 3.20

Date/Publication 2024-09-29

Contents

coords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

CoverageHeatmap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

default_color . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

2 coords

getScale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Heatmap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Heatmap-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

HeatmapExamples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

heatmapOptions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

label . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

length,Heatmap-method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

nseq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

PatternHeatmap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

plotHeatmap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

plotHeatmapList . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

plotHeatmapMeta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

plotPatternDensityMap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

plot_clusters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

plot_legend . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

PWMScanHeatmap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

rev,Heatmap-method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

scale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

smoothHeatmap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

width,Heatmap-method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

xm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

ym . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Index 24

coords Return or set the coords in a Heatmap

Description

Return or set the coords in a Heatmap

Usage

coords(x)

## S4 method for signature 'Heatmap'

coords(x)

coords(x) <- value

## S4 replacement method for signature 'Heatmap'

coords(x) <- value

Arguments

x A heatmap

value Replacement value

CoverageHeatmap 3

Value

integer, length 2, value of x@coords

Examples

data(HeatmapExamples)

coords(hm) = c(-100, 100)

CoverageHeatmap Generate a Heatmap of coverage

Description

Generate a Heatmap of coverage

Usage

CoverageHeatmap(windows, track, ...)

## S4 method for signature 'GenomicRanges,GenomicRanges'

CoverageHeatmap(windows, track,

coords = NULL, weight = 1, label = NULL, nbin = 0)

## S4 method for signature 'GenomicRanges,RleList'

CoverageHeatmap(windows, track,

coords = NULL, label = NULL, nbin = 0)

Arguments

windows A set of GRanges of equal length

track A GRanges or RleList object specifying coverage

... additional arguments used by methods

This function generates a Heatmap object from a set of windows and an object

containing genome-wide information about coverage. Either a GRanges or an

RleList can be used. In the former case, the "weight" paramter is passed directly

to the ‘coverage‘ function. If nbin is set, binned coverage is calculated which

will save memory and time when plotting and average out varible data.

If the coverage track contains negative values, then the scale will be centered

on zero, ie. c(-max(abs(image(hm))), max(abs(image(hm)))). This makes more

sense for most color schemes which are centered on zero, and avoids mislead-

ing plots where either positive or negative values are over-emphasised. See

?getScale for details. The scale can be manually reset if desired using the "scale"

method.

coords Co-ordinates for the heatmap, defaults to c(0, width(windows))

weight Passed to coverage(track) constructor if class(track) == "GRanges"

label Label for the heatmap

nbin If set, number of bins to use across each window

4 default_color

Value

A Heatmap object

Methods (by class)

• windows = GenomicRanges,track = GenomicRanges: Heatmap of Coverage from 2 GRanges

• windows = GenomicRanges,track = RleList: Heatmap of Coverage from GRanges + RleList

Examples

data(HeatmapExamples)

CoverageHeatmap(windows, rle_list, coords=c(-100, 100), label="Example")

default_color Prediﬁned color palettes from RColorBrewer + Rainbow

Description

Prediﬁned color palettes from RColorBrewer + Rainbow

Usage

default_color(col)

Arguments

col Character, RColorBrewer colorscheme or "Rainbow"

This function provides a convenient function to all color palettes from RColor-

Brewer, and a better version of R’s rainbow function (speciﬁcally rev(rainbow(9,

start=0, end=4/6)), so it starts blue and ends with red).

Value

character, a length-9 color palette

Examples

default_color("Blues")

default_color("Rainbow")

getScale 5

getScale Make an appropriate scale for a heatmap

Description

Make an appropriate scale for a heatmap

Usage

getScale(x, y)

Arguments

x Min/max values for the heatmap

y Min/max values for the heatmap

This function takes min/max values for a heatmap and generates a scale either

starting, ending or centered on zero.

Value

numeric, length 2, a new scale

Examples

getScale(0.5, 5) # c(0, 5)

getScale(-6, -2) # c(-6, 6)

getScale(-6, 2) # c(-6, 6)

Heatmap Function to create a heatmap object

Description

Function to create a heatmap object

Usage

Heatmap(image, coords = NULL, label = "", nseq = NULL, scale = NULL,

metadata = list())

Arguments

image A numeric Matrix

coords A length-2 integer vector

label A character vector

nseq An integer

scale A length-2 vector

metadata A list containing arbitrary metadata

Using this function avoids calling ’new’ directly or manually setting coords and

nseq to integers. Other constructors exist for creating heatmaps from data, rather

than a raw matrix.

6 Heatmap-class

Value

A Heatmap object

See Also

PatternHeatmap CoverageHeatmap PWMScanHeatmap

Examples

data(HeatmapExamples)

hm = Heatmap(mat, coords=c(-100, 100), label="Test")

Heatmap-class An S4 class to represent a heatmap

Description

An S4 class to represent a heatmap

Slots

image A numeric Matrix

scale A length-2 vector

coords A length-2 integer vector

nseq An integer

label A character vector

metadata A list containing arbitrary metadata

A class used to represent a heatmap in a simple, self-contained way

Slots can be accessed and set using getters and setters with the same name.

See Also

CoverageHeatmap PatternHeatmap plotHeatmap plotHeatmapMeta

Examples

data(HeatmapExamples)

hm = new("Heatmap",

image=mat,

scale=c(0,max(mat)),

coords=c(-100L, 100L),

nseq=1000L,

label="Test",

metadata=list())

# or use the constructor:

hm = Heatmap(mat, coords=c(-100, 100), label="Test")

HeatmapExamples 7

HeatmapExamples Data for man page examples

Description

Generated Data for examples

An example heatmap

A second example heatmap

An example matrix

An example RleList

An example DNAStringSet

An example PWM

An example GRanges

Usage

hm2

mat

rle_list

string_set

tata_pwm

windows

Format

An object of class Heatmap of length 500.

Value

invisible("HeatmapExamples")

heatmapOptions Generate default options for a Heatmap

Description

Generate default options for a Heatmap

Usage

heatmapOptions(...)

8 heatmapOptions

Arguments

... options to set manually

Guide to Heatmap options

This is an reference to all the possible options for plotting heatmaps. Some op-

tions are handled by heatmaps functions (either plotHeatmap or plotHeatmapList),

others are passed directly to plotting functions. Further explanation is available

in the vignette. Arguments are numeric if not otherwise stated.

color: A vector of colors or a default color, see ?default_color. plotHeatmap will

interpolate between these colors to form a scale.

box.width: width of box around the heatmap, passed to box()

x.ticks: Logical, plot x axis ticks

x.tick.labels: Character, labels to use for x ticks, (default blank)

tcl: Length of x axis ticks

padj: Vertical adjustment of x axis labels

cex.axis: cex for axis labels

scale: Logical, Plot scale or not

scale.label: Character, label for scale

scale.lwd: Width for line around scale

cex.scale: Cex for Scale

label: Logical, plot label or not

label.xpos: x position for label, from left

label.ypos: y position for label, from top

cex.label: cex for axis labels

label.col: Color for label, white is often useful for dark plots

legend: Logical, plot legend (scale indicating values for colors)

legend: Color for label, white is often useful for dark plots

legend.pos: Character, position of legend relative to heatmap: ’l’ for left, ’r’ for

right

legend.ticks: Number of ticks to use on legend.

cex.legend: cex to use for legend marks

reﬂine: Logical, Draw dashed line at coords = 0 label: Logical, plot label or not

label.xpos: x position for label, from left

label.ypos: y position for label, from top

cex.label: cex for axis labels

label.col: Color for label, white is often useful for dark plots

legend: Logical, plot legend (scale indicating values for colors)

legend: Color for label, white is often useful for dark plots

legend.pos: Character, position of legend relative to heatmap: ’l’ for left, ’r’ for

right

legend.ticks: Number of ticks to use on legend.

cex.legend: cex to use for legend marks

reﬂine: Logical, Draw dashed line at coords = 0

reﬂine.width: Width of reference line

transform: Function to transform values before plotting

plot.mai: Length-4 numeric, margins around plot

legend.mai: Length-4 numeric, margins around legend

image 9

partition: Numeric, relative sizes of clusters

partition.lines: Logical, plot lines delineating clusters

partition.legend: Logical, plot cluster legend in HeatmapList

partition.col: Character, colours to use for plotting clusters. Defaults to RColor-

Brewer’s Set1

hook: Function called after plotting is complete.

Value

a list containing the speciﬁed options

See Also

plotHeatmap plotHeatmapList

Examples

myOptions = heatmapOptions()

myOptions$color = "Reds"

# plotHeatmap(hm, options=myOptions)

image Return or set the image in a Heatmap

Description

Return or set the image in a Heatmap

Usage

## S4 method for signature 'Heatmap'

image(x)

image(x) <- value

## S4 replacement method for signature 'Heatmap'

image(x) <- value

Arguments

x A heatmap

value Replacement value

Value

matrix, from hm@image

Examples

data(HeatmapExamples)

image(hm) = log(image(hm))

scale(hm) = c(0, max(image(hm)))

10 length,Heatmap-method

label Return or set the label in a Heatmap

Description

Return or set the label in a Heatmap

Usage

label(x)

## S4 method for signature 'Heatmap'

label(x)

label(x) <- value

## S4 replacement method for signature 'Heatmap'

label(x) <- value

Arguments

x A heatmap

value Replacement value

Value

character, value of hm@label

Examples

data(HeatmapExamples)

label(hm) = "NewLabel"

label(hm) # "NewLabel"

length,Heatmap-method Return the number of sequences in a heatmap

Description

Return the number of sequences in a heatmap

Usage

## S4 method for signature 'Heatmap'

length(x)

Arguments

x A heatmap

metadata 11

Value

integer, value of x@nseq

metadata Return or set the metadata in a Heatmap

Description

Store arbitrary metadata in a list, if desired.

Usage

metadata(x)

## S4 method for signature 'Heatmap'

metadata(x)

metadata(x) <- value

## S4 replacement method for signature 'Heatmap'

metadata(x) <- value

Arguments

x A heatmap

value Replacement value

Value

list, value of hm@metadata

Examples

data(HeatmapExamples)

metadata(hm) = list(replicate=1, cell_line="ESC")

metadata(hm)$replicate == 1

nseq Return or set nseq in a Heatmap

Description

Return or set nseq in a Heatmap

12 PatternHeatmap

Usage

nseq(x)

## S4 method for signature 'Heatmap'

nseq(x)

nseq(x) <- value

## S4 replacement method for signature 'Heatmap'

nseq(x) <- value

Arguments

x A heatmap

value Replacement value

Value

integer, value of hm@nseq

Examples

data(HeatmapExamples)

nseq(hm) = 1000

PatternHeatmap Generate a Heatmap of patterns in DNA sequence

Description

Generate a Heatmap of patterns in DNA sequence

Usage

PatternHeatmap(seq, pattern, ...)

## S4 method for signature 'DNAStringSet,character'

PatternHeatmap(seq, pattern, coords = NULL,

min.score = NULL, label = NULL)

## S4 method for signature 'DNAStringSet,matrix'

PatternHeatmap(seq, pattern, coords = NULL,

min.score = "80%", label = NULL)

Arguments

seq A DNAString of equal length

pattern A nucleotide pattern or PWM

plotHeatmap 13

... additional arguments used by methods

This function creates a Heatmap from a set of DNA sequences. The resulting

heatmap will be binary, with 1 representing a match and 0 otherwise. Patterns

can be speciﬁed as a character vectore, eg. "CTCCC", or as a PWM. These ar-

guments are passed to Biostrings functions, ‘vmatchPattern‘ and ‘matchPWM‘.

Character arguments can contain standard ambiguity codes. PWMs must be 4

by n matricies with columns names ACGT. "min.score" is speciﬁed either as an

absolute value, or more commonly as a percentage e.g. "80 for details.

PatternHeatmaps often look much better after smoothing.

coords Co-ordinates for the heatmap, defaults to c(0, width(windows))

min.score Minimum score for PWM match

label Label for the heatmap

Value

A heatmap

Methods (by class)

• seq = DNAStringSet,pattern = character: Heatmap of sequence patterns from sequence

and character

• seq = DNAStringSet,pattern = matrix: Heatmap of sequence patterns from sequence and

matrix

See Also

smoothHeatmap

Examples

data(HeatmapExamples)

PatternHeatmap(string_set, "TA", coords=c(-100, 100), label="TA")

PatternHeatmap(string_set, tata_pwm, coords=c(-100, 100), min.score="80%", label="TATA PWM")

plotHeatmap Plot a Heatmap object to the device

Description

Plot a Heatmap object to the device

Usage

plotHeatmap(heatmap, options = NULL, ...)

## S4 method for signature 'Heatmap'

plotHeatmap(heatmap, options = NULL, ...)

14 plotHeatmapList

Arguments

heatmap A heatmap object

options A list containing plotting options

... Used for passing individual options

This function will take a heatmap and plot it to the device with the speciﬁed

options. Options can be passed together in a list or individually as additional

arguments. If passing options as a list, it’s best to ﬁrst create a list contain-

ing the default settings using heatmapOptions() andmethod then setting options

individually.

plotHeatmap() does not control device settings at all, these can be set using

plotHeatmapList() and the relevant options in heatmapOptions()

See ?heatmapOptions for a full list of options.

Value

invisible(0)

Methods (by class)

• Heatmap: Plot a Heatmap object to the device

See Also

heatmapOptions plotHeatmapList

Examples

data(HeatmapExamples)

plotHeatmap(hm, color="Blues")

plotHeatmapList Plot a list of heatmaps

Description

Plot a list of heatmaps

Usage

plotHeatmapList(heatmap_list, groups = 1:length(heatmap_list),

options = heatmapOptions(), ...)

Arguments

heatmap_list A list of Heatmaps

groups Optionally group heatmaps together

options Heatmap options

plotHeatmapMeta 15

... Additional options

This function takes a list of one or more heatmaps and plots them to a single

image tiled horizontally.

The "groups" argument speciﬁes heatmaps to be grouped together and plotted

using the same display parameters and a uniﬁed scale. plotHeatmapList will try

to guess the best scale, either starting or ﬁnishing at zero, or symetrical aronud

zero - if this is not the desired behaviour, make sure the scales are identical

before the heatmaps are passed to the function.

Options are speciﬁed as for plotHeatmap, but can be speciﬁed per group by

passing a list of options instead of a single vector. Note the difference between a

length-2 character vector, c("Reds", "Blues"), and a list contatining two length-1

character vectors: list("Reds", "Blues").

These are generally large, complex plots, so it can better to plot straight to a

ﬁle. PNG is preferred since pdf ﬁles generated can be if the images are not

downsized. The default settings are designed for plots of about 10cm x 20cm per

heatmap, but all of the relevant settigns can be tweaked using the options. For

display-quality images, it helps to increase the resolution at to at least 150ppi,

double the default of 72ppi on most systems.

Value

invisible(0)

See Also

plotHeatmap heatmapOptions plot_legend

Examples

data(HeatmapExamples)

plotHeatmapList(list(hm, hm2), groups=c(1,2), color=list("Reds", "Blues"))

plotHeatmapMeta Plot a Meta-region plot from heatmaps

Description

Plot a Meta-region plot from heatmaps

Usage

plotHeatmapMeta(hm_list, binsize = 1, colors = gg_col(length(hm_list)),

addReferenceLine = FALSE)

Arguments

hm_list A list of heatmaps

binsize Integer, size of bins to use in plot

colors Color to use for each heatmap

16 plotPatternDensityMap

addReferenceLine

Logical, add reference line at zero or not

This function creates a meta-region plot from 1 or more heatmaps with the same

coordinates. A meta-region plot graphs the sum of the signal at each position

in each heatmap rather than visualising the signal in two dimensions. Often

binning is required to smooth noisy signal.

Value

invisible(0)

Examples

data(HeatmapExamples)

plotHeatmapMeta(hm, color="steelblue")

plotPatternDensityMap Plot heatmaps for several patterns in DNA sequence

Description

Plot heatmaps for several patterns in DNA sequence

Usage

plotPatternDensityMap(seq, patterns, ...)

## S4 method for signature 'DNAStringSet'

plotPatternDensityMap(seq, patterns, coords = NULL,

min.score = "80%", sigma = c(3, 3), output.size = NULL,

options = NULL, ...)

Arguments

seq DNAStringSet of equal width

patterns A vector or list of patterns

... Additional Heatmap plotting options

This function is a convenient wrapper for plotting many different patterns for

the same set of sequences. PatternHeatmap() is applied to the sequence for

each pattern in the list, they are passed to smoothHeatmap() with the supplied

parameters and ﬁnally PlotHeatmapList().

If ﬁne-grained control is desired, or you want to mix other plot types, then more

information is available in the vignette.

coords Heatmap coords

min.score Minimum score for PWM match

sigma Bandwith for smoothing kernel

output.size Output size of ﬁnal image

options Heatmap plotting options

plot_clusters 17

Value

invisible(0)

Methods (by class)

• DNAStringSet: Plot heatmaps for several patterns in DNA sequence

See Also

PatternHeatmap plotHeatmapList smoothHeatmap

Examples

data(HeatmapExamples)

plotPatternDensityMap(string_set, c("AT", "CG"), coords=c(-200, 200))

plot_clusters Plot partition in a separate panel

Description

Plot partition in a separate panel

Usage

plot_clusters(options)

Arguments

options heatmapOptions passed as a list

Two heatmapOptions values are relevant:

* partition Numeric vector containing relative sizes of the clusters * colors Col-

ors to use for clusters, additional colors are discarded

This function plots a vertical color scale (or legend). With the default parame-

ters, it looks good at about 1/5 the width of a heatmap, about 1cm x 10cm. This

function only plots the legend, it does not set margin parameters.

Value

invisible(0)

See Also

plotHeatmapList

Examples

data(HeatmapExamples)

opts = heatmapOptions()

opts$partition = c(1,2,3,4)

par(mai=opts$legend.mai)

plot_clusters(opts)

18 PWMScanHeatmap

plot_legend Plot a color legend for a heatmap

Description

Plot a color legend for a heatmap

Usage

plot_legend(scale, options)

Arguments

scale Numeric vector contain min and max for the scale

options heatmapOptions passed as a list

This function plots a vertical color scale (or legend). With the default parame-

ters, it looks good at about 1/5 the width of a heatmap, about 1cm x 10cm. This

function only plots the legend, it does not set margin parameters.

Value

invisible(0)

See Also

plotHeatmapList

Examples

data(HeatmapExamples)

opts = heatmapOptions()

opts$color = "Rainbow"

par(mai=opts$legend.mai)

plot_legend(c(0,1), opts)

PWMScanHeatmap Generate a Heatmap of PWM Scores in DNA sequnce

Description

Generate a Heatmap of PWM Scores in DNA sequnce

Usage

PWMScanHeatmap(seq, pwm, ...)

## S4 method for signature 'DNAStringSet,matrix'

PWMScanHeatmap(seq, pwm, coords = NULL,

label = "")

rev,Heatmap-method 19

Arguments

seq A DNAString of equal length

pwm A PWM

... additional arguments used by methods

This function creates a heatmap where each point is the score of a PWM match

starting from that position, which can visualise regions of enrichment or exclu-

sion of certain motifs

coords Co-ordinates for the heatmap, defaults to c(0, width(windows))

label Label for the heatmap

Value

A heatmap

Methods (by class)

• seq = DNAStringSet,pwm = matrix: Heatmap of PWM Scores

See Also

PatternHeatmap

Examples

data(HeatmapExamples)

PatternHeatmap(string_set, tata_pwm, coords=c(-100, 100), label="TATA Scan")

rev,Heatmap-method Reﬂect a heatmap in the x axis

Description

Reﬂect a heatmap in the x axis

Usage

## S4 method for signature 'Heatmap'

rev(x)

Arguments

x A heatmap

Value

A heatmap

20 smoothHeatmap

scale Return or set the scale in a Heatmap

Description

Return or set the scale in a Heatmap

Usage

scale(x)

## S4 method for signature 'Heatmap'

scale(x)

scale(x) <- value

## S4 replacement method for signature 'Heatmap'

scale(x) <- value

Arguments

x A heatmap

value Replacement value

Value

numeric, length 2, the value of hm@scale

Examples

data(HeatmapExamples)

scale(hm) = c(-1000, 1000)

smoothHeatmap Smooth a heatmap

Description

Smooth a heatmap

Usage

smoothHeatmap(heatmap, ...)

## S4 method for signature 'Heatmap'

smoothHeatmap(heatmap, sigma = c(3, 3),

output.size = dim(image(heatmap)), algorithm = NULL)

width,Heatmap-method 21

Arguments

heatmap A heatmap object

... additional arguments to S4 methods

This function smooths a heatmap using either binned kernel density (more efﬁ-

cient for binary heatmaps) or gaussian blur.

Sigma controls the SD of the kernel in both cases, deﬁned in terms of pix-

els. This means that if you have very difﬁrent x and y dimensions (eg. a

200bp heatmap around 10000 promoters) you will need to compensate by set-

ting sigma[2] higher to get the same visual effect in both dimensions

"output.size" speciﬁes the dimensions of the output matrix. This can be useful

to reduce plotting time signiﬁcantly.

Smoothing can use either a kernel density estimate or a blurring function. The

methods implemented are KernSmooth:bkde2D and EBImage::ﬁlter2 with a

gaussian ﬁlter. The kernel based method assumes we are smoothing individual

points so the value of these points are ignored. This is most useful for smoothing

PatternHeatmaps where each cell in the matrix is either 1 or 0. For non-binary

heatmaps, blur is most appropriate. Not setting this parameter will choose the

method automatically.

Scaling the output heatmap is handled as in CoverageHeatmap.

sigma Numeric, lengt2, (recycled if length 1)

output.size Numeric, length 2

algorithm "kernel" or "blur"

Value

A heatmap

Methods (by class)

• Heatmap: Smooth a heatmap

Examples

data(HeatmapExamples)

hm_smoothed = smoothHeatmap(hm, sigma=c(5,5), algorithm="blur")

width,Heatmap-method Return the width of sequence represented in a heatmap

Description

Return the width of sequence represented in a heatmap

Usage

## S4 method for signature 'Heatmap'

width(x)

22 xm

Arguments

x A heatmap

Value

integer

xm Generate co-ordinates for each row of the image matrix of a Heatmap

Description

Generate co-ordinates for each row of the image matrix of a Heatmap

Usage

xm(x)

## S4 method for signature 'Heatmap'

xm(x)

Arguments

x A Heatmap

Value

numeric, a list of co-ordinates for plotting values in hm@image

Methods (by class)

• Heatmap: Generate co-ordinates for each frow of the image matrix of a Heatmap

Examples

data(HeatmapExamples)

xm(hm)

ym 23

ym Generate co-ordinates for each column of the image matrix of a

Heatmap

Description

Generate co-ordinates for each column of the image matrix of a Heatmap

Usage

ym(x)

## S4 method for signature 'Heatmap'

ym(x)

Arguments

x A Heatmap

Value

numeric, a list of co-ordinates for plotting values in hm@image

Methods (by class)

• Heatmap: Generate co-ordinates for each column of the matrix

Examples

data(HeatmapExamples)

ym(hm)

Index

∗ datasets

HeatmapExamples, 7

coords, 2

coords,Heatmap-method (coords), 2

coords<- (coords), 2

coords<-,Heatmap-method (coords), 2

CoverageHeatmap, 3

CoverageHeatmap,GenomicRanges,GenomicRanges-method

(CoverageHeatmap), 3

CoverageHeatmap,GenomicRanges,RleList-method

(CoverageHeatmap), 3

default_color, 4

getScale, 5

Heatmap, 5

Heatmap-class, 6

HeatmapExamples, 7

heatmapOptions, 7

hm (HeatmapExamples), 7

hm2 (HeatmapExamples), 7

image, 9

image,Heatmap-method (image), 9

image<- (image), 9

image<-,Heatmap-method (image), 9

label, 10

label,Heatmap-method (label), 10

label<- (label), 10

label<-,Heatmap-method (label), 10

length,Heatmap-method, 10

mat (HeatmapExamples), 7

metadata, 11

metadata,Heatmap-method (metadata), 11

metadata<- (metadata), 11

metadata<-,Heatmap-method (metadata), 11

nseq, 11

nseq,Heatmap-method (nseq), 11

nseq<- (nseq), 11

nseq<-,Heatmap-method (nseq), 11

PatternHeatmap, 12

PatternHeatmap,DNAStringSet,character-method

(PatternHeatmap), 12

PatternHeatmap,DNAStringSet,matrix-method

(PatternHeatmap), 12

plot_clusters, 17

plot_legend, 18

plotHeatmap, 13

plotHeatmap,Heatmap-method

(plotHeatmap), 13

plotHeatmapList, 14

plotHeatmapMeta, 15

plotPatternDensityMap, 16

plotPatternDensityMap,DNAStringSet-method

(plotPatternDensityMap), 16

PWMScanHeatmap, 18

PWMScanHeatmap,DNAStringSet,matrix-method

(PWMScanHeatmap), 18

rev,Heatmap-method, 19

rle_list (HeatmapExamples), 7

scale, 20

scale,Heatmap-method (scale), 20

scale<- (scale), 20

scale<-,Heatmap-method (scale), 20

smoothHeatmap, 20

smoothHeatmap,Heatmap-method

(smoothHeatmap), 20

string_set (HeatmapExamples), 7

tata_pwm (HeatmapExamples), 7

width,Heatmap-method, 21

windows (HeatmapExamples), 7

xm, 22

xm,Heatmap-method (xm), 22

ym, 23

ym,Heatmap-method (ym), 23