Type: Package
Title: Interactive, Complex Heatmaps
Version: 0.7.1
Description: Make complex, interactive heatmaps. 'iheatmapr' includes a modular system for iteratively building up complex heatmaps, as well as the iheatmap() function for making relatively standard heatmaps.
License: MIT + file LICENSE
Depends: R (≥ 3.5.0)
Imports: methods, utils, magrittr, stats, ggdendro, fastcluster, RColorBrewer, htmlwidgets, jsonlite, scales, knitr, tools
Suggests: htmltools, datasets, shiny, testthat, rmarkdown, reshape2, roxygen2, covr, webshot
RoxygenNote: 7.3.1
VignetteBuilder: knitr
URL: https://docs.ropensci.org/iheatmapr/ (website) https://github.com/ropensci/iheatmapr
BugReports: https://github.com/ropensci/iheatmapr/issues
Encoding: UTF-8
Collate: 'AllClasses.R' 'AllGenerics.R' 'annotations.R' 'axes.R' 'axis_labels.R' 'axis_titles.R' 'barplot.R' 'clustering.R' 'clusters.R' 'colorbars.R' 'colors.R' 'components.R' 'dendogram.R' 'generic_subplots.R' 'groups.R' 'main_heatmap.R' 'iheatmap.R' 'iheatmapr.R' 'layout.R' 'list_utils.R' 'shiny.R' 'shiny_test.R' 'signal.R' 'subplot.R' 'summary.R' 'to_widget.R' 'utils.R'
X-schema.org-applicationCategory: Visualization
X-schema.org-keywords: heatmap, plotly, r, interactive-visualizations, data-visualization, htmlwidgets
X-schema.org-isPartOf: https://ropensci.org
Language: en-US
NeedsCompilation: no
Packaged: 2024-01-25 23:30:33 UTC; alan
Author: Alicia Schep ORCID iD [aut], Sarah Kummerfeld ORCID iD [aut], Genentech [cph], Andee Kaplan [rev] (Reviewer for rOpensci review process https://github.com/ropensci/onboarding/issues/107), Carl Ganz [rev] (Reviewer for rOpensci review process https://github.com/ropensci/onboarding/issues/107), Alex Johnson [ctb] (plotly.js library), Étienne Tétreault-Pinard [ctb] (plotly.js library), Mikola Lysenko [ctb] (plotly.js library), Ricky Reusser [ctb] (plotly.js library), Robert Monfera [ctb] (plotly.js library), Nicolas Riesco [ctb] (plotly.js library), Miklós Tusz [ctb] (plotly.js library), Chelsea Douglas [ctb] (plotly.js library), Ben Postlethwaite [ctb] (plotly.js library), Chris Parmer [ctb] (plotly.js library), Alex Vados [ctb] (plotly.js library), Plotly [cph] (plotly.js library), Frederick Boehm [ctb] (colorbars & main_heatmap), Alan O'Callaghan [cre]
Maintainer: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Repository: CRAN
Date/Publication: 2024-01-25 23:50:02 UTC

iheatmapr

Description

Interactive complex heatmaps in R

Details

iheatmapr is a package for building complex, interactive heatmaps in R that can be explored in interactive R sessions or incorporated into rmarkdown documents, shiny applications, or standalone html files.

The package includes a modular system for building up complex heatmaps, where subplots get iteratively added to the top/left/right/bottom of the main heatmap(s). The iheatmap function provides a wrapper around many of the common modular subcomponents to build fairly standard, moderately complex heatmap.

See the vignette for detailed instructions for how to use the package.

iheatmapr uses the plotly javascript library (https://plotly.com/) for making the interactive figures and htmlwidgets (http://www.htmlwidgets.org/) for rendering them in R.

Author(s)

Alicia Schep

See Also

main_heatmap, iheatmap, Iheatmap-class

ColumnAnnotation

Description

Class for storing row annotation

Slots

xaxis

name of xaxis

yaxis

name of yaxis

data

vector of annotation values

colorbar

name of colorbar

show_colorbar

show the colorbar?

Author(s)

Alicia Schep

See Also

add_col_annotation, add_col_signal, add_col_groups

ColumnLabels

Description

Class for storing column labels

Slots

xaxis

name of xaxis

yaxis

name of yaxis

data

the names of the tick labels

positions

the positions of the tick labels

side

side of plot on which dendrogram is positioned, controls orientation

textangle

angle for text

font

list of font attributes

Author(s)

Alicia Schep

See Also

add_col_labels

ColumnPlot

Description

Class for storing generic column plot

Slots

xaxis

name of xaxis

yaxis

name of yaxis

data

vector of values

name

tracename

type

trace type

showlegend

show the legend?

additional

additional plotly parameters

Author(s)

Alicia Schep

See Also

add_col_plot, add_col_barplot, add_col_summary

ColumnTitle

Description

Class for storing column title

Slots

xaxis

name of xaxis

yaxis

name of yaxis

data

the title (character)

side

side of plot on which dendrogram is positioned, controls orientation

textangle

angle for text

font

list of font attributes

Author(s)

Alicia Schep

See Also

add_col_title

ContinuousColorbar

Description

Class for storing continuous colorbar information

Slots

title

title for colorbar

position

integer indicating relative position of colorbar

colors

name of color palette or vector of colors

zmid

midpoint of colorbar

zmin

min of colorbar

zmax

max of colorbar

Author(s)

Alicia Schep

Dendrogram

Description

Class for storing dendrogram

Slots

xaxis

name of xaxis

yaxis

name of yaxis

data

hclust object

side

side of plot on which dendrogram is positioned, controls orientation

Author(s)

Alicia Schep

See Also

add_row_dendro, add_col_dendro, add_row_clustering, add_col_clustering

DiscreteColorbar

Description

Class for storing discrete colorbar information

Slots

title

title for colorbar

position

integer indicating relative position of colorbar

colors

name of color palette or vector of colors

ticktext

labels for categories

tickvals

integer values for categories

Author(s)

Alicia Schep

GenericPlot

Description

Class for storing an arbitrary subplot

Slots

xaxis

name of xaxis

yaxis

name of yaxis

data

list of plotly parameters

Author(s)

Alicia Schep

See Also

add_subplot

Iheatmap-class

Description

Class to store complex interactive heatmap objects from iheatmapr package

Details

This is a virtual class with two children classes, IheatmapHorizontal and IheatmapVertical. For IheatmapHorizontal additional main heatmaps are added horizontally, and for IheatmapVertical additional main heatmaps are added vertically. For details on accessing certain slots of this class, see access_component documentation.

Slots

plots

list of plot element in IheatmapPlots format

shapes

list of shape element in IheatmapShapes format

annotations

list of annotation elements in IheatmapAnnotations format

xaxes

list of x axes in IheatmapAxes format

yaxes

list of y axes in IheatmapAxes format

colorbars

list of colorbars in IheatmapColorbars format

colorbar_grid

colorbar grid parameters in IheatmapColorbarGrid format

current_xaxis

name of current x axis

current_yaxis

name of current y axis

layout

list of plotly layout parameters

source

source name, for use with shiny

Author(s)

Alicia Schep

See Also

iheatmap, main_heatmap, access_component

IheatmapAnnotation

Description

Virtual class for storing annotation objects

Slots

xaxis

name of xaxis

yaxis

name of yaxis

data

main annotation data

SubClasses

Author(s)

Alicia Schep

IheatmapAnnotations

Description

Class for storing IheatmapAnnotation objects

See Also

IheatmapAnnotation-class, Iheatmap-class

IheatmapAxes

Description

Class for storing IheatmapAxis objects

Slots

axis

x or y?

Author(s)

Alicia Schep

See Also

IheatmapAxis-class, Iheatmap-class

IheatmapAxis

Description

Class for storing axis information

Slots

id

plotly id for axis

domain_start

start of domain (0 to 1)

domain_end

end of domain (0 to 1)

anchor

anchor for axis

layout

plotly layout parameters

SubClasses

Author(s)

Alicia Schep

See Also

Iheatmap-class

IheatmapColorbar

Description

Virtual class for storing colorbar objects

Slots

title

title for colorbar

position

integer indicating relative position of colorbar

colors

name of color palette or vector of colors

SubClasses

Author(s)

Alicia Schep

IheatmapColorbarGrid

Description

Parameters for setting up colorbars

Slots

nrows

number of rows

x_spacing

spacing between colorbars horizontally

y_spacing

spacing between colorbars vertically

y_length

length of colorbars vertically

x_start

start position horizontally

y_start

start position vertically

Author(s)

Alicia Schep

See Also

setup_colorbar_grid, Iheatmap-class

IheatmapColorbars

Description

Class for storing IheatmapColorbar objects

Author(s)

Alicia Schep

See Also

IheatmapColorbar-class, Iheatmap-class

IheatmapMainX

Description

Class for storing X axis information for "main" x axis– x axis for MainHeatmap-class

Slots

id

plotly id for axis

domain_start

start of domain (0 to 1)

domain_end

end of domain (0 to 1)

anchor

anchor for axis

layout

plotly layout parameters

categorical

is axis categorical?

order

ordering of columns

text

text labels for columns

Author(s)

Alicia Schep

See Also

Iheatmap-class, IheatmapAxis

IheatmapMainY

Description

Class for storing Y axis information for "main" y axis– y axis for MainHeatmap-class

Slots

id

plotly id for axis

domain_start

start of domain (0 to 1)

domain_end

end of domain (0 to 1)

anchor

anchor for axis

layout

plotly layout parameters

categorical

is axis categorical?

order

ordering of rows

text

text labels for rows

Author(s)

Alicia Schep

See Also

Iheatmap-class, IheatmapAxis

IheatmapPlot

Description

Virtual class for storing plot objects

Slots

xaxis

name of xaxis

yaxis

name of yaxis

data

main plot data

SubClasses

Author(s)

Alicia Schep

IheatmapPlots

Description

Class for storing IheatmapPlot objects

Author(s)

Alicia Schep

See Also

IheatmapPlot-class, Iheatmap-class

IheatmapShape

Description

Virtual class for storing shape objects

Slots

xaxis

name of xaxis

yaxis

name of yaxis

data

main shape data

SubClasses

Author(s)

Alicia Schep

IheatmapShapes

Description

Class for storing IheatmapShapes objects

Author(s)

Alicia Schep

See Also

IheatmapShape-class, Iheatmap-class

IheatmapX

Description

Class for storing X axis information

Slots

id

plotly id for axis

domain_start

start of domain (0 to 1)

domain_end

end of domain (0 to 1)

anchor

anchor for axis

layout

plotly layout parameters

Author(s)

Alicia Schep

See Also

Iheatmap-class, IheatmapAxis

IheatmapY

Description

Class for storing Y axis information

Slots

id

plotly id for axis

domain_start

start of domain (0 to 1)

domain_end

end of domain (0 to 1)

anchor

anchor for axis

layout

plotly layout parameters

Author(s)

Alicia Schep

See Also

Iheatmap-class, IheatmapAxis

MainHeatmap

Description

Class for storing main heatmap

Slots

xaxis

name of xaxis

yaxis

name of yaxis

data

matrix of heatmap values

colorbar

name of colorbar

show_colorbar

show the colorbar?

Author(s)

Alicia Schep

See Also

main_heatmap

RowAnnotation

Description

Class for storing row annotation

Slots

xaxis

name of xaxis

yaxis

name of yaxis

data

vector of annotation values

colorbar

name of colorbar

show_colorbar

show the colorbar?

Author(s)

Alicia Schep

See Also

add_row_annotation, add_row_signal, add_row_groups

RowLabels

Description

Class for storing row labels

Slots

xaxis

name of xaxis

yaxis

name of yaxis

data

the names of the tick labels

positions

the positions of the tick labels

side

side of plot on which dendrogram is positioned, controls orientation

textangle

angle for text

font

list of font attributes

Author(s)

Alicia Schep

See Also

add_row_labels

RowPlot

Description

Class for storing generic row plot

Slots

xaxis

name of xaxis

yaxis

name of yaxis

data

vector of values

name

tracename

type

trace type

showlegend

show the legend?

additional

additional plotly parameters

Author(s)

Alicia Schep

See Also

add_row_plot, add_row_barplot, add_row_summary

RowTitle

Description

Class for storing row title

Slots

xaxis

name of xaxis

yaxis

name of yaxis

data

the title (character)

side

side of plot on which dendrogram is positioned, controls orientation

textangle

angle for text

font

list of font attributes

Author(s)

Alicia Schep

See Also

add_row_title

add_col_annotation

Description

Adds annotation heatmaps for one or more qualitative or quantitative annotations for each column of a main heatmap.

Usage

## S4 method for signature 'Iheatmap'
add_col_annotation(
  p,
  annotation,
  colors = NULL,
  side = c("top", "bottom"),
  size = 0.05,
  buffer = 0.015,
  inner_buffer = buffer/2,
  layout = list(),
  show_colorbar = TRUE
)

Arguments

p

link{Iheatmap-class} object

annotation

data.frame or object that can be converted to data frame

colors

list of color palettes, with one color per annotation column name

side

side of plot on which to add column annotation

size

relative size of each row annotation

buffer

relative size of buffer between previous subplot and column annotation

inner_buffer

relative size of buffer between each annotation

layout

layout properties for new y axis

show_colorbar

logical indicator to show or hide colorbar

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

iheatmap, add_row_annotation, add_col_signal, add_col_groups

Examples


mat <- matrix(rnorm(24), ncol = 6)
annotation <- data.frame(gender = c(rep("M", 3),rep("F",3)),
                        age = c(20,34,27,19,23,30))
hm <- iheatmap(mat) %>% add_col_annotation(annotation)

# Print heatmap if interactive session 
if (interactive()) hm

add_col_barplot

Description

Add bar plot with one bar per column above or below a main heatmap

Usage

## S4 method for signature 'Iheatmap'
add_col_barplot(
  p,
  y,
  ...,
  color = NULL,
  tracename = NA_character_,
  showlegend = !is.na(tracename),
  side = c("top", "bottom"),
  layout = list(),
  size = 0.2,
  buffer = 0.02,
  xname = current_xaxis(p),
  yname = NULL,
  pname = if (!is.na(tracename)) tracename else "col_barplot"
)

Arguments

p

iheatmap object

y

y axis values

...

additional arguments to add to plotly scatter trace, see https://plotly.com/javascript/reference/#scatter

color

color of bars

tracename

name of trace (for legend and hover)

showlegend

show in legend?

side

side of plot on which to add subplot

layout

yaxis layout list

size

relative size of subplot relative to main heatmap

buffer

amount of space to leave empty before this plot, relative to size of first heatmap

xname

internal name of xaxis

yname

internal name of yaxis

pname

internal name of plot

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

add_col_signal, iheatmap, add_col_plot

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)  
hm <- iheatmap(mat) %>% add_col_barplot(y = 1:5, tracename = "Strength")

# Print heatmap if interactive session 
if (interactive()) hm

add_col_clustering

Description

add_col_clustering

Usage

## S4 method for signature 'Iheatmap'
add_col_clustering(
  p,
  method = c("hclust", "kmeans", "groups"),
  name = "Col<br>Clusters",
  k = NULL,
  groups = NULL,
  clust_dist = stats::dist,
  colors = NULL,
  show_colorbar = TRUE,
  side = c("top", "bottom"),
  yname = NULL,
  xname = current_xaxis(p)
)

Arguments

p

iheatmap object

method

"hclust" or "kmeans" for hierarchical or k-means clustering, respectively

name

name of colorbar indicating cluster membership

k

number of clusters for rows, needed if order is kmeans or optional if hclust

groups

vector of group assignments

clust_dist

distance function to use for clustering if hierarchical clustering

colors

colors to use for annotation of grouping, can be RColorBrewer palette name or vector of colors

show_colorbar

show the colorbar for the heatmap indicating cluster membership

side

side of plot on which to add subplot

yname

name of yaxis

xname

name of xaxis

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

add_row_clustering, iheatmap

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)
hm <- iheatmap(mat) %>% add_col_clustering(method = "hclust", k = 2)

# Print heatmap if interactive session 
if (interactive()) hm

add_col_clusters

Description

Add column groups and order columns based on groups

Usage

## S4 method for signature 'Iheatmap'
add_col_clusters(
  p,
  clusters,
  name = "Col<br>Clusters",
  reorder = TRUE,
  side = c("top", "bottom"),
  xname = current_xaxis(p),
  ...
)

Arguments

p

iheatmap object

clusters

cluster assignments, should be vector of integers, characters, or factors

name

name of colorbar indicating cluster membership

reorder

reorder rows based on clusters? default is TRUE

side

side of plot on which to add subplot

xname

name of xaxis

...

additional arguments to pass to add_col_groups for creation of annotation heatmap indicating cluster membership

Details

This function is very similar to add_col_groups; the main difference is that with this function column will get reordered based on the groups.

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

add_row_clusters, add_col_clustering, iheatmap

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)
clusters <- c("A","B","A","B","A")

hm <- iheatmap(mat) %>% add_col_clusters(clusters)

# Print heatmap if interactive session 
if (interactive()) hm

add_col_dendro

Description

Adds column dendrogram to iheatmap object

Usage

## S4 method for signature 'Iheatmap,hclust'
add_col_dendro(
  p,
  dendro,
  reorder = TRUE,
  side = c("top", "bottom"),
  size = 0.15,
  buffer = 0.005,
  xname = current_xaxis(p),
  yname = NULL,
  sname = "col_dendro"
)

Arguments

p

iheatmap object

dendro

hclust object

reorder

reorder rows based on dendrogram order?

side

side of plot on which to add dendro

size

relative size of dendrogram (relative to the main heatmap)

buffer

amount of space to leave empty before this plot, relative to size of first heatmap

xname

internal name of xaxis

yname

internal name of yaxis

sname

internal name of shape

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

add_col_clustering, iheatmap, add_row_dendro

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)  
dend <- hclust(dist(t(mat)))
hm <- iheatmap(mat) %>% add_col_dendro(dend)

# Print heatmap if interactive session 
if (interactive()) hm

add_col_groups

Description

Adds annotation to heatmap indicating what group every column of main heatmap belongs to

Usage

## S4 method for signature 'Iheatmap'
add_col_groups(
  p,
  groups,
  name = "Column<br>Groups",
  title = "Groups",
  colors = pick_discrete_colors(groups, p),
  colorbar_position = get_colorbar_position(p),
  show_colorbar = TRUE,
  show_title = TRUE,
  side = c("top", "bottom"),
  layout = list(),
  size = 0.05,
  buffer = 0.015,
  tooltip = setup_tooltip_options(),
  xname = current_xaxis(p),
  yname = NULL,
  pname = name
)

Arguments

p

Iheatmap-class object

groups

vector of group names

name

name of colorbar

title

name of x axis label

colors

palette name or vector of colors

colorbar_position

colorbar placement

show_colorbar

show the colorbar?

show_title

show title as axis label

side

side of plot on which to groups annotation

layout

list of layout parameters for x axis

size

relative size of dendrogram (relative to the main heatmap)

buffer

amount of space to leave empty before this plot, relative to size of first heatmap

tooltip

tooltip options, see setup_tooltip_options

xname

internal name of xaxis

yname

internal name of yaxis

pname

internal name of plot

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

iheatmap, add_row_groups

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)
col_groups <- c("A","A","B","D","B")
hm <- iheatmap(mat) %>% add_col_groups(col_groups, name = "My Groups")

# Print heatmap if interactive session 
if (interactive()) hm

add_col_labels

Description

Add x axis labels to plot

Usage

## S4 method for signature 'Iheatmap'
add_col_labels(
  p,
  tickvals = NULL,
  ticktext = NULL,
  textangle = -90,
  font = get_layout(p)$font,
  side = c("bottom", "top"),
  size = 0.1,
  buffer = 0.005,
  xname = current_xaxis(p),
  yname = NULL
)

Arguments

p

link{Iheatmap-class} object

tickvals

column indices at which to place axis tick labels

ticktext

text for axis tick labels

textangle

angle for ticktext

font

list of plotly font attributes, see https://plotly.com/javascript/reference/#layout-font

side

side of plot on which to add subplot

size

relative size of subplot relative to main heatmap

buffer

amount of space to leave empty before this plot, relative to size of first heatmap

xname

name for xaxis

yname

name for yaxis

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

add_row_title, iheatmap, add_col_labels

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)  
hm1 <- iheatmap(mat) %>% add_col_labels()
hm2 <- iheatmap(mat) %>% add_col_labels(ticktext = letters[22:26])

# Print heatmap if interactive session 
if (interactive()) hm1
if (interactive()) hm2

add_col_plot

Description

Add a scatter or line plot with one point per column of the main heatmap

Usage

## S4 method for signature 'Iheatmap'
add_col_plot(
  p,
  y,
  ...,
  mode = c("lines+markers", "lines", "markers"),
  color = NULL,
  tracename = NA_character_,
  showlegend = !is.na(tracename),
  side = c("top", "bottom"),
  layout = list(),
  size = 0.2,
  buffer = 0.02,
  xname = current_xaxis(p),
  yname = NULL,
  pname = if (!is.na(tracename)) tracename else "col_plot"
)

Arguments

p

iheatmap object

y

y axis values

...

additional arguments to add to plotly scatter trace, see https://plotly.com/javascript/reference/#scatter

mode

mode of plot – one of "lines+markers","lines", or "markers"

color

color of bars

tracename

name of trace (for legend and hover)

showlegend

show in legend?

side

side of plot on which to add subplot

layout

yaxis layout list

size

relative size of subplot relative to main heatmap

buffer

amount of space to leave empty before this plot, relative to size of first heatmap

xname

internal name of xaxis

yname

internal name of yaxis

pname

internal name of plot

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

add_col_signal, iheatmap, add_col_barplot

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)  
hm <- iheatmap(mat) %>% add_col_plot(y = 1:5, tracename = "Strength")

# Print heatmap if interactive session 
if (interactive()) hm

add_col_signal

Description

Adds column signal to iheatmap object

Usage

## S4 method for signature 'Iheatmap'
add_col_signal(
  p,
  signal,
  name,
  title = name,
  yname = NULL,
  xname = current_xaxis(p),
  pname = name,
  colorbar_position = get_colorbar_position(p),
  colors = pick_continuous_colors(zmid, zmin, zmax, p = p),
  zmin = min(signal, na.rm = TRUE),
  zmax = max(signal, na.rm = TRUE),
  zmid = 0,
  side = c("top", "bottom"),
  size = 0.05,
  buffer = 0.015,
  text = signif(signal, digits = 3),
  tooltip = setup_tooltip_options(),
  show_colorbar = TRUE,
  show_title = TRUE,
  layout = list()
)

Arguments

p

iheatmap object

signal

vector of signal

name

name of colorbar

title

label for y axis

yname

internal name of yaxis

xname

internal name of xaxis

pname

internal name of plot

colorbar_position

colorbar placement

colors

palette or vector of colors to use

zmin

minimum for colorscale

zmax

maximum for colorscale

zmid

midpoint for colorscale

side

side of plot on which to add groups

size

relative size of dendrogram (relative to the main heatmap)

buffer

amount of space to leave empty before this plot, relative to size of first heatmap

text

text of value to display for data

tooltip

tooltip options, see setup_tooltip_options

show_colorbar

show the colorbar?

show_title

show title as axis label

layout

y axis layout parameters to use

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

iheatmap, add_row_groups

add_row_signal, iheatmap, add_col_annotation

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)  
hm <- iheatmap(mat) %>% add_col_signal(signal = 1:5, name = "Strength")

# Print heatmap if interactive session 
if (interactive()) hm

add_col_summary

Description

Adds a line plot summarizing the values across columns

Usage

## S4 method for signature 'Iheatmap'
add_col_summary(
  p,
  groups = NULL,
  heatmap_name = NULL,
  colors = NULL,
  tracename = "Col Summary",
  showlegend = FALSE,
  side = c("top", "bottom"),
  layout = list(),
  size = 0.3,
  buffer = 0.02,
  xname = current_xaxis(p),
  yname = NULL,
  type = c("scatter", "bar"),
  summary_function = c("mean", "median", "sd", "var", "mad", "max", "min", "sum"),
  ...
)

Arguments

p

Iheatmap-class object

groups

vector of group labels, name of groups colorbar, or TRUE – see Details

heatmap_name

name of a heatmap within the plot

colors

vector of colors or RColorBrewer palette name

tracename

name of trace

showlegend

show legend?

side

side of plot on which to add subplot

layout

xaxis layout list

size

relative size of subplot relative to main heatmap

buffer

amount of space to leave empty before this plot, relative to size of first heatmap

xname

internal name of xaxis

yname

internal name of yaxis

type

scatter or bar?

summary_function

summary function to use, default is mean, options are mean, median, sd, var, mad, max, min, and sum

...

additional arguments to add_col_plot or add_col_barplot

Details

If adding the column summary to a vertically oriented heatmap, the summary will be based on the topmost heatmap if side is "top" and based on the bottom heatmap if side is "bottom" unless a "heatmap_name" is specified. The heatmap_name should match the "pname" argument given to a previously added heatmap.

The column summary is based on specific rows if a "groups" argument is given. The groups argument can either be a vector of group assignments for each row, the "pname" for an existing set of groups incorporated into the plot using add_row_groups, add_row_annotation, add_row_clusters, or add_row_clustering. If groups is set to TRUE, then the function will use an existing set of row groups added to the plot.

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

add_row_summary, iheatmap, add_col_plot

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)  
hm1 <- iheatmap(mat) %>% add_col_summary()
hm2 <- iheatmap(mat) %>% add_col_summary(groups = c("A","A","B","B"))

# Print heatmap if interactive session 
if (interactive()) hm1
if (interactive()) hm2

add_col_title

Description

Add x axis title to plot

Usage

## S4 method for signature 'Iheatmap'
add_col_title(
  p,
  title,
  textangle = 0,
  font = get_layout(p)$font,
  side = c("bottom", "top"),
  size = 0.1,
  buffer = 0.01,
  xname = current_xaxis(p),
  yname = NULL
)

Arguments

p

iheatmap object

title

title of axis

textangle

angle of text

font

list of plotly font attributes, see https://plotly.com/javascript/reference/#layout-font

side

side of plot on which to add subplot

size

relative size of subplot relative to main heatmap

buffer

amount of space to leave empty before this plot, relative to size of first heatmap

xname

name for xaxis

yname

name for yaxis

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

add_col_labels, iheatmap, add_row_title

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)  
hm <- iheatmap(mat) %>% add_col_title("My x-axis")

# Print heatmap if interactive session 
if (interactive()) hm

Adding plot components to iheatmapr

Description

These are generic methods for adding new plot components to an link{Iheatmap-class} object. Not intended for end users; exported for developers seeking to create new Iheatmap subplots.

Usage

add_axis(p, new_axis, ...)

add_colorbar(p, new_colorbar, ...)

add_plot(p, new_plot, ...)

add_shape(p, new_shape, ...)

add_annotation(p, new_anno, ...)

Arguments

p

Iheatmap-class object

new_axis

new IheatmapAxis-class object

new_colorbar

new IheatmapColorbar-class object

new_plot

new IheatmapPlot-class object

new_shape

new IheatmapShape-class object

new_anno

new IheatmapAnnotation-class object

add_iheatmap

Description

add_iheatmap

Usage

## S4 method for signature 'IheatmapHorizontal,matrix'
add_iheatmap(
  p,
  data,
  x = default_x(data),
  cluster_cols = c("none", "hclust", "kmeans", "groups"),
  col_clusters = NULL,
  col_k = NULL,
  col_clust_dist = stats::dist,
  name = "Signal",
  scale = c("none", "rows", "cols"),
  scale_method = c("standardize", "center", "normalize"),
  colors = NULL,
  col_clusters_colors = NULL,
  col_clusters_name = "Col<br>Clusters",
  show_col_clusters_colorbar = TRUE,
  row_annotation = NULL,
  col_annotation = NULL,
  row_annotation_colors = NULL,
  col_annotation_colors = NULL,
  row_labels = NULL,
  col_labels = NULL,
  row_title = NULL,
  col_title = NULL,
  buffer = 0.2,
  ...
)

## S4 method for signature 'IheatmapVertical,matrix'
add_iheatmap(
  p,
  data,
  y = default_y(data),
  cluster_rows = c("none", "hclust", "kmeans", "groups"),
  row_clusters = NULL,
  row_k = NULL,
  row_clust_dist = stats::dist,
  name = "Signal",
  scale = c("none", "rows", "cols"),
  scale_method = c("standardize", "center", "normalize"),
  colors = NULL,
  row_clusters_colors = NULL,
  row_clusters_name = "Col<br>Clusters",
  show_row_clusters_colorbar = TRUE,
  row_annotation = NULL,
  col_annotation = NULL,
  row_annotation_colors = NULL,
  col_annotation_colors = NULL,
  row_labels = NULL,
  col_labels = NULL,
  row_title = NULL,
  col_title = NULL,
  buffer = 0.2,
  ...
)

Arguments

p

iheatmap object

data

matrix of values to be plotted as heatmap

x

x xaxis labels, by default colnames of data

cluster_cols

"none","hclust", or "k-means" for no clustering, hierarchical clustering, and k-means clustering of columnsrespectively

col_clusters

vector of pre-determined column cluster assignment

col_k

number of clusters for columns, needed if cluster_rows is kmeans or optional if hclust

col_clust_dist

distance function to use for column clustering if hierarchical clustering

name

Name for colorbar

scale

scale matrix by rows, cols or none

scale_method

what method to use for scaling, either standardize, center, normalize

colors

name of RColorBrewer palette or vector of colors for main heatmap

col_clusters_colors

colors for col clusters annotation heatmap

col_clusters_name

name for col clusters colorbar

show_col_clusters_colorbar

show the colorbar for column clusters?

row_annotation

row annotation data.frame

col_annotation

column annotation data.frame

row_annotation_colors

list of colors for row annotations heatmap

col_annotation_colors

list of colors for col annotations heatmap

row_labels

axis labels for y axis

col_labels

axis labels for x axis

row_title

x axis title

col_title

y axis title

buffer

amount of space to leave empty before this plot, relative to size of first heatmap

...

additional argument to add_iheatmap

y

y axis labels, by default rownames of data

cluster_rows

"none","hclust", or "k-means" for no clustering, hierarchical clustering, and k-means clustering of rows respectively

row_clusters

vector of pre-determined row cluster assignment

row_k

number of clusters for rows, needed if cluster_rows is kmeans or optional if hclust

row_clust_dist

distance function to use for row clustering if hierarchical clustering

row_clusters_colors

colors for row clusters annotation heatmap

row_clusters_name

name for row clusters colorbar

show_row_clusters_colorbar

show the colorbar for row clusters?

Details

By default, no scaling is done of rows or columns. This can be changed by specifying the 'scale' argument. There are three options for scaling methods. "standardize" subtracts the mean and divides by standard deviation, "center" just subtracts the mean, and "normalize" divides by the sum of the values. "normalize" should only be used for data that is all positive! If alternative scaling is desired, the scaling should be done prior to calling the iheatmap function.

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

iheatmap, main_heatmap

Examples


mat <- matrix(rnorm(24), nrow = 6)
mat2 <- matrix(rnorm(24), nrow = 6)
annotation = data.frame(gender = c(rep("M", 3),rep("F",3)),
                        age = c(20,34,27,19,23,30))
hm <- iheatmap(mat, 
 cluster_rows = "hclust", 
 cluster_cols = "hclust", 
 col_k = 3) %>%
add_iheatmap(mat2, 
 cluster_cols = "hclust", 
 col_k = 3, 
 row_annotation = annotation)

# Print heatmap if interactive session 
if (interactive()) hm

add_main_heatmap

Description

Adds an additional main heatmap to an iheatmap object

Usage

## S4 method for signature 'IheatmapHorizontal,matrix'
add_main_heatmap(
  p,
  data,
  name = "Signal",
  x = default_x(data),
  colors = pick_continuous_colors(zmid, zmin, zmax, p),
  colorbar_position = get_colorbar_position(p),
  show_colorbar = TRUE,
  zmin = min(data, na.rm = TRUE),
  zmax = max(data, na.rm = TRUE),
  zmid = 0,
  col_order = NULL,
  x_categorical = NULL,
  side = c("right", "left"),
  size = 1,
  buffer = 0.04,
  text = signif(data, digits = 3),
  tooltip = setup_tooltip_options(),
  xname = NULL,
  pname = name,
  ...
)

## S4 method for signature 'IheatmapVertical,matrix'
add_main_heatmap(
  p,
  data,
  name = "Signal",
  y = default_y(data),
  colors = pick_continuous_colors(zmid, zmin, zmax, p),
  colorbar_position = get_colorbar_position(p),
  show_colorbar = TRUE,
  zmin = min(data, na.rm = TRUE),
  zmax = max(data, na.rm = TRUE),
  zmid = 0,
  row_order = NULL,
  y_categorical = NULL,
  side = c("bottom", "top"),
  size = 1,
  buffer = 0.04,
  text = signif(data, digits = 3),
  tooltip = setup_tooltip_options(),
  yname = NULL,
  pname = name,
  ...
)

Arguments

p

Iheatmap-class object

data

matrix

name

name of colorbar, will determine if colorbar is shared with existing plot

x

x axis labels (by default rownames of data); only used if orientation is horizontal

colors

color palette name or vector of colors

colorbar_position

colorbar placement

show_colorbar

display the colorbar?

zmin

minimum for colorscale

zmax

maximum for colorscale

zmid

midpoint for scale

col_order

column ordering for this heatmap; only used if orientation is horizontal

x_categorical

is x categorical? will guess if not provided

side

which side of the current plot to add this heatmap?

size

relative size of plot. size relative to first heatmap

buffer

amount of space to leave empty before this plot, relative to size of first heatmap

text

text of value to display for data

tooltip

tooltip options, see setup_tooltip_options

xname

internal name for x axis

pname

internal name for plot

...

additional arguments (ignored)

y

y axis labels (by default colnames of data); only used if orientation is vertical

row_order

row ordering for this heatmap; only used if orientation is vertical

y_categorical

is y categorical? will guess if not provided

yname

internal name for y axis

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

iheatmap, main_heatmap

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4) 
mat2 <-  matrix(rnorm(24), ncol = 6, nrow = 4) 
hm <- iheatmap(mat) %>% add_main_heatmap(mat2)

# Print heatmap if interactive session 
if (interactive()) hm

add_row_annotation

Description

Adds annotation heatmaps for one or more qualitative or quantitative annotations for each row of a main heatmap.

Usage

## S4 method for signature 'Iheatmap'
add_row_annotation(
  p,
  annotation,
  colors = NULL,
  side = c("right", "left"),
  size = 0.05,
  buffer = 0.015,
  inner_buffer = buffer/2,
  layout = list(),
  show_colorbar = TRUE
)

Arguments

p

link{Iheatmap-class} object

annotation

data.frame or object that can be converted to data frame

colors

list of color palettes, with one color per annotation column name

side

side of plot on which to add row annotation

size

relative size of each row annotation

buffer

relative size of buffer between previous subplot and row annotation

inner_buffer

relative size of buffer between each annotation

layout

layout properties for new x axis

show_colorbar

logical indicator to show or hide colorbar

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

iheatmap, add_row_annotation, add_col_signal, add_col_groups

Examples


mat <- matrix(rnorm(24), nrow = 6)
annotation <- data.frame(gender = c(rep("M", 3),rep("F",3)),
                        age = c(20,34,27,19,23,30))
hm <- iheatmap(mat) %>% add_row_annotation(annotation)

# Print heatmap if interactive session 
if (interactive()) hm

add_row_barplot

Description

add_row_barplot

Usage

## S4 method for signature 'Iheatmap'
add_row_barplot(
  p,
  x,
  ...,
  color = NULL,
  tracename = NA_character_,
  showlegend = !is.na(tracename),
  side = c("right", "left"),
  layout = list(),
  size = 0.2,
  buffer = 0.02,
  xname = NULL,
  yname = current_yaxis(p),
  pname = if (!is.na(tracename)) tracename else "row_barplot"
)

Arguments

p

iheatmap object

x

x axis values

...

additional arguments to add to plotly scatter trace, see https://plotly.com/javascript/reference/#scatter

color

color of bars

tracename

name of trace (for legend and hover)

showlegend

show in legend?

side

side of plot on which to add subplot

layout

yaxis layout list

size

relative size of subplot relative to main heatmap

buffer

amount of space to leave empty before this plot, relative to size of first heatmap

xname

internal name of xaxis

yname

internal name of yaxis

pname

internal name of plot

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

add_row_signal, iheatmap, add_row_plot

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)  
hm <- iheatmap(mat) %>% add_row_barplot(x = 1:4, tracename = "Strength")

# Print heatmap if interactive session 
if (interactive()) hm

add_row_clustering

Description

add_row_clustering

Usage

## S4 method for signature 'Iheatmap'
add_row_clustering(
  p,
  method = c("hclust", "kmeans", "groups"),
  name = "Row<br>Clusters",
  k = NULL,
  groups = NULL,
  clust_dist = stats::dist,
  colors = NULL,
  show_colorbar = TRUE,
  side = c("left", "right"),
  xname = NULL,
  yname = current_yaxis(p)
)

Arguments

p

iheatmap object

method

"hclust" or "kmeans" for hierarchical or k-means clustering, respectively

name

name of colorbar indicating cluster membership

k

number of clusters for rows, needed if order is kmeans or optional if hclust

groups

vector of group assignments

clust_dist

distance function to use for clustering if hierarchical clustering

colors

colors to use for annotation of grouping, can be RColorBrewer palette name or vector of colors

show_colorbar

show the colorbar for the heatmap indicating cluster membership

side

side of plot on which to add subplot

xname

name of xaxis

yname

name of yaxis

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

add_col_clustering, iheatmap

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)
hm <- iheatmap(mat) %>% add_row_clustering(method = "hclust", k = 2)

# Print heatmap if interactive session 
if (interactive()) hm

add_row_clusters

Description

Add row groups and order rows based on groups

Usage

## S4 method for signature 'Iheatmap'
add_row_clusters(
  p,
  clusters,
  name = "Row<br>Clusters",
  reorder = TRUE,
  side = c("left", "right"),
  yname = current_yaxis(p),
  ...
)

Arguments

p

iheatmap object

clusters

cluster assignments, should be vector of integers, characters, or factors

name

name of colorbar indicating cluster membership

reorder

reorder rows based on clusters? default is TRUE

side

side of plot on which to add subplot

yname

name of yaxis

...

additional arguments to pass to add_row_groups for creation of annotation heatmap indicating cluster membership

Details

This function is very similar to add_row_groups; the main difference is that with this function rows will get reordered based on the groups.

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

add_row_clustering, add_col_clusters, iheatmap

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)
clusters <- c("A","B","A","B")

hm <- iheatmap(mat) %>% add_row_clusters(clusters)

# Print heatmap if interactive session 
if (interactive()) hm

add_row_dendro

Description

Adds row dendrogram to iheatmap object

Usage

## S4 method for signature 'Iheatmap,hclust'
add_row_dendro(
  p,
  dendro,
  reorder = TRUE,
  side = c("left", "right"),
  size = 0.15,
  buffer = 0.005,
  xname = NULL,
  yname = current_yaxis(p),
  sname = "row_dendro"
)

Arguments

p

iheatmap object

dendro

hclust object

reorder

reorder rows based on dendrogram order?

side

side of plot on which to add dendrogram

size

relative size of dendrogram (relative to the main heatmap)

buffer

amount of space to leave empty before this plot, relative to size of first heatmap

xname

internal name of xaxis

yname

internal name of yaxis

sname

internal name of shapes

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

add_row_clustering, iheatmap, add_col_dendro

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)  
dend <- hclust(dist(mat))
hm <- iheatmap(mat) %>% add_row_dendro(dend)

# Print heatmap if interactive session 
if (interactive()) hm

add_row_groups

Description

Adds annotation to heatmap indicating what group every row of main heatmap belongs to

Usage

## S4 method for signature 'Iheatmap'
add_row_groups(
  p,
  groups,
  name = "Row<br>Groups",
  title = "Groups",
  colors = pick_discrete_colors(groups, p),
  colorbar_position = get_colorbar_position(p),
  show_colorbar = TRUE,
  show_title = TRUE,
  side = c("right", "left"),
  layout = list(),
  size = 0.05,
  buffer = 0.005,
  tooltip = setup_tooltip_options(),
  xname = NULL,
  yname = current_yaxis(p),
  pname = name
)

Arguments

p

Iheatmap-class object

groups

vector of group names

name

name of colorbar

title

name of x axis label

colors

palette name or vector of colors

colorbar_position

colorbar placement

show_colorbar

show the colorbar?

show_title

show title as axis label

side

side of plot on which to groups annotation

layout

list of layout parameters for x axis

size

relative size of dendrogram (relative to the main heatmap)

buffer

amount of space to leave empty before this plot, relative to size of first heatmap

tooltip

tooltip options, see setup_tooltip_options

xname

internal name of xaxis

yname

internal name of yaxis

pname

internal name of plot

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

iheatmap, add_col_groups

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)
row_groups <- c("A","A","B","D")
hm <- iheatmap(mat) %>% add_row_groups(row_groups, name = "My Groups")

# Print heatmap if interactive session 
if (interactive()) hm

add_row_labels

Description

Add y axis labels to plot

Usage

## S4 method for signature 'Iheatmap'
add_row_labels(
  p,
  tickvals = NULL,
  ticktext = NULL,
  textangle = 0,
  font = get_layout(p)$font,
  side = c("left", "right"),
  size = 0.1,
  buffer = 0.005,
  xname = NULL,
  yname = current_yaxis(p)
)

Arguments

p

Iheatmap-class object

tickvals

row indices at which to place axis tick labels

ticktext

text for axis tick labels

textangle

angle for ticktext

font

list of plotly font attributes, see https://plotly.com/javascript/reference/#layout-font

side

side of plot on which to add subplot

size

relative size of subplot relative to main heatmap

buffer

amount of space to leave empty before this plot, relative to size of first heatmap

xname

internal name for xaxis

yname

internal name for yaxis

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

add_row_title, iheatmap, add_col_labels

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)  
hm1 <- iheatmap(mat) %>% add_row_labels()
hm2 <- iheatmap(mat) %>% add_row_labels(ticktext = letters[23:26])


# Print heatmaps if interactive session 
if (interactive()) hm1
if (interactive()) hm2

add_row_plot

Description

Add a scatter or line plot with one point per row of the main heatmap

Usage

## S4 method for signature 'Iheatmap'
add_row_plot(
  p,
  x,
  ...,
  mode = c("lines+markers", "lines", "markers"),
  color = NULL,
  tracename = NA_character_,
  showlegend = !is.na(tracename),
  side = c("right", "left"),
  layout = list(),
  size = 0.2,
  buffer = 0.02,
  xname = NULL,
  yname = current_yaxis(p),
  pname = if (!is.na(tracename)) tracename else "row_plot"
)

Arguments

p

iheatmap object

x

x axis values

...

additional arguments to add to plotly scatter trace, see https://plotly.com/javascript/reference/#scatter

mode

mode of plot – one of "lines+markers","lines", or "markers"

color

color of bars

tracename

name of trace (for legend and hover)

showlegend

show in legend?

side

side of plot on which to add subplot

layout

yaxis layout list

size

relative size of subplot relative to main heatmap

buffer

amount of space to leave empty before this plot, relative to size of first heatmap

xname

internal name of xaxis

yname

internal name of yaxis

pname

internal name of plot

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

add_row_signal, iheatmap, add_row_barplot

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)  
hm <- iheatmap(mat) %>% add_row_plot(x = 1:4, tracename = "Strength")

# Print heatmap if interactive session 
if (interactive()) hm

add_row_signal

Description

Adds single column heatmap to iheatmap object

Usage

## S4 method for signature 'Iheatmap'
add_row_signal(
  p,
  signal,
  name,
  title = name,
  xname = NULL,
  yname = current_yaxis(p),
  pname = name,
  colorbar_position = get_colorbar_position(p),
  colors = pick_continuous_colors(zmid, zmin, zmax, p = p),
  zmin = min(signal, na.rm = TRUE),
  zmax = max(signal, na.rm = TRUE),
  zmid = 0,
  side = c("right", "left"),
  size = 0.05,
  buffer = 0.015,
  text = signif(signal, digits = 3),
  tooltip = setup_tooltip_options(),
  show_colorbar = TRUE,
  show_title = TRUE,
  layout = list()
)

Arguments

p

iheatmap object

signal

vector of signal

name

name of colorbar

title

label for x axis

xname

internal name of xaxis

yname

internal name of yaxis

pname

internal name of plot

colorbar_position

colorbar placement

colors

color palette or vector of colors

zmin

minimum for colorscale

zmax

maximum for colorscale

zmid

midpoint for colorscale

side

side of plot on which to add dendro

size

relative size of dendrogram (relative to the main heatmap)

buffer

amount of space to leave empty before this plot, relative to size of first heatmap

text

text of value to display for data

tooltip

tooltip options, see setup_tooltip_options

show_colorbar

show the colorbar?

show_title

show title as axis label

layout

list of x axis layout parameters

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

iheatmap, add_col_groups

add_col_signal, iheatmap, add_row_annotation

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)  
hm <- iheatmap(mat) %>% add_row_signal(signal = 1:4, name = "Strength")

# Print heatmap if interactive session 
if (interactive()) hm

add_row_summary

Description

Adds a line plot summarizing the values across rows

Usage

## S4 method for signature 'Iheatmap'
add_row_summary(
  p,
  groups = NULL,
  heatmap_name = NULL,
  colors = NULL,
  tracename = "Row Summary",
  showlegend = FALSE,
  side = c("right", "left"),
  layout = list(),
  size = 0.3,
  buffer = 0.02,
  xname = NULL,
  yname = current_yaxis(p),
  type = c("scatter", "bar"),
  summary_function = c("mean", "median", "sd", "var", "mad", "max", "min", "sum"),
  ...
)

Arguments

p

Iheatmap-class object

groups

vector of group labels, name of groups colorbar, or TRUE – see Details

heatmap_name

name of a heatmap within the Iheatmap-class object

colors

vector of colors or RColorBrewer palette name

tracename

name of trace

showlegend

show legend?

side

side of plot on which to add subplot

layout

xaxis layout list

size

relative size of subplot relative to main heatmap

buffer

amount of space to leave empty before this plot, relative to size of first heatmap

xname

internal name of xaxis

yname

internal name of yaxis

type

scatter or bar?

summary_function

summary function to use, default is mean, options are mean, median, sd, var, mad, max, min, and sum

...

additional arguments to add_row_plot or add_row_barplot

Details

If adding the row summary to a horizontally oriented heatmap, the summary will be based on the right-most heatmap if side is "right" and based on the left heatmap if side is "left" unless a "heatmap_name" is specified. The heatmap_name should match the "pname" argument given to a previously added heatmap.

The row summary is based on specific columns if a "groups" argument is given. The groups argument can either be a vector of group assignments for each row, the "pname" for an existing set of groups incorporated into the plot using add_col_groups, add_col_annotation, add_col_clusters, or add_col_clustering. If groups is set to TRUE, then the function will use an existing set of column groups added to the plot.

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

add_col_summary, iheatmap, add_row_plot

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)  
hm1 <- iheatmap(mat) %>% add_row_summary()
hm2 <- iheatmap(mat) %>% add_row_summary(groups = c("A","A","B","B","B"))

# Print heatmap if interactive session 
if (interactive()) hm1
if (interactive()) hm2

add_row_title

Description

Add y axis title to plot

Usage

## S4 method for signature 'Iheatmap'
add_row_title(
  p,
  title,
  textangle = ifelse(side == "left", -90, 90),
  font = get_layout(p)$font,
  side = c("left", "right"),
  size = 0.1,
  buffer = 0.01,
  xname = NULL,
  yname = current_yaxis(p)
)

Arguments

p

iheatmap object

title

title of axis

textangle

angle of text

font

list of plotly font attributes, see https://plotly.com/javascript/reference/#layout-font

side

side of plot on which to add subplot

size

relative size of subplot relative to main heatmap

buffer

amount of space to leave empty before this plot, relative to size of first heatmap

xname

internal name for xaxis

yname

internal name for yaxis

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

add_col_title, iheatmap, add_row_labels

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)  
hm <- iheatmap(mat) %>% add_row_title("Samples")

# Print heatmap if interactive session 
if (interactive()) hm

add_subplot

Description

Adds an arbitrary subplot to iheatmap

Usage

## S4 method for signature 'Iheatmap'
add_subplot(
  p,
  ...,
  side = c("top", "bottom", "right", "left"),
  layout = list(),
  size = 1,
  buffer = 0.1,
  xname = if (side %in% c("top", "bottom")) current_xaxis(p) else NULL,
  yname = if (side %in% c("left", "right")) current_yaxis(p) else NULL,
  pname = "subplot"
)

Arguments

p

iheatmap object

...

arguments to pass to plotly trace, see plotly.js documentation at https://plotly.com/javascript/reference/

side

which side of the current plot to add this heatmap? "right", "left","top", or "bottom"

layout

axis layout parameters (list)

size

relative size of plot. size relative to first heatmap

buffer

amount of space to leave empty before this plot, relative to size of first heatmap

xname

internal name of xaxis

yname

internal name of yaxis

pname

internal name of plot

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

iheatmap

Examples

mat <- matrix(rnorm(24), ncol = 6)
hm <- iheatmap(mat) %>% add_subplot(x = 1:5, y=1:5, side = "top")

# Print heatmap if interactive session 
if (interactive()) hm

Access subcomponents of Iheatmap object

Description

These are methods for accessing subcomponents of the Iheatmap object

Usage

## S4 method for signature 'Iheatmap'
colorbars(x, what = c("all", "continuous", "discrete"))

## S4 method for signature 'Iheatmap'
yaxes(p, xaxis = NULL)

## S4 method for signature 'Iheatmap'
xaxes(p, yaxis = NULL)

## S4 method for signature 'Iheatmap'
plots(x)

## S4 method for signature 'Iheatmap'
shapes(x)

## S4 method for signature 'Iheatmap'
annotations(x)

Arguments

x

Iheatmap-class object

xaxis

name of xaxis

yaxis

name of yaxis

iheatmap

Description

Make a farily standard interactive heatmap with optional clustering and row and column annotations. For more flexibility and options, see the main_heatmap function and other modular functions as described in vignette.

Usage

## S4 method for signature 'matrix'
iheatmap(
  data,
  x = default_x(data),
  y = default_y(data),
  cluster_rows = c("none", "hclust", "kmeans"),
  cluster_cols = c("none", "hclust", "kmeans"),
  row_clusters = NULL,
  col_clusters = NULL,
  row_k = NULL,
  col_k = NULL,
  row_clust_dist = stats::dist,
  col_clust_dist = stats::dist,
  name = "Signal",
  scale = c("none", "rows", "cols"),
  scale_method = c("standardize", "center", "normalize"),
  colors = NULL,
  col_clusters_colors = NULL,
  col_clusters_name = "Col<br>Clusters",
  row_clusters_colors = NULL,
  row_clusters_name = "Row<br>Clusters",
  show_row_clusters_colorbar = TRUE,
  show_col_clusters_colorbar = TRUE,
  row_annotation = NULL,
  col_annotation = NULL,
  row_annotation_colors = NULL,
  col_annotation_colors = NULL,
  row_labels = NULL,
  col_labels = NULL,
  row_title = NULL,
  col_title = NULL,
  colorbar_grid = setup_colorbar_grid(),
  layout = list(),
  source = "iheatmapr",
  ...
)

Arguments

data

matrix of values to be plotted as heatmap

x

x xaxis labels, by default colnames of data

y

y axis labels, by default rownames of data

cluster_rows

"none","hclust", or "k-means" for no clustering, hierarchical clustering, and k-means clustering of rows respectively

cluster_cols

"none","hclust", or "k-means" for no clustering, hierarchical clustering, and k-means clustering of columnsrespectively

row_clusters

vector of pre-determined row cluster assignment

col_clusters

vector of pre-determined column cluster assignment

row_k

number of clusters for rows, needed if cluster_rows is kmeans or optional if hclust

col_k

number of clusters for columns, needed if cluster_rows is kmeans or optional if hclust

row_clust_dist

distance function to use for row clustering if hierarchical clustering

col_clust_dist

distance function to use for column clustering if hierarchical clustering

name

Name for colorbar

scale

scale matrix by rows, cols or none

scale_method

what method to use for scaling, either none, standardize, center, normalize

colors

name of RColorBrewer palette or vector of colors for main heatmap

col_clusters_colors

colors for col clusters annotation heatmap

col_clusters_name

name for col clusters colorbar

row_clusters_colors

colors for row clusters annotation heatmap

row_clusters_name

name for row clusters colorbar

show_row_clusters_colorbar

show the colorbar for row clusters?

show_col_clusters_colorbar

show the colorbar for column clusters?

row_annotation

row annotation data.frame

col_annotation

column annotation data.frame

row_annotation_colors

list of colors for row annotations heatmap

col_annotation_colors

list of colors for col annotations heatmap

row_labels

axis labels for y axis

col_labels

axis labels for x axis

row_title

x axis title

col_title

y axis title

colorbar_grid

colorbar grid parameters, should be result from setup_colorbar_grid

layout

list of layout attributes to pass to plotly, eg. list(font = list(size = 15))

source

source name for use with shiny

...

additional argument to iheatmap

Details

By default, no scaling is done of rows or columns. This can be changed by specifying the 'scale' argument. There are three options for scaling methods. "standardize" subtracts the mean and divides by standard deviation, "center" just subtracts the mean, and "normalize" divides by the sum of the values. "normalize" should only be used for data that is all positive! If alternative scaling is desired, the scaling should be done prior to calling the iheatmap function.

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

iheatmap, add_iheatmap, to_widget

Examples

mat <- matrix(rnorm(24), nrow = 6)
annotation = data.frame(gender = c(rep("M", 3),rep("F",3)),
 age = c(20,34,27,19,23,30))
hm <- iheatmap(mat, 
 cluster_rows = "hclust",
 cluster_cols = "kmeans", 
 col_k = 3, 
 row_annotation = annotation)

# Print heatmap if interactive session 
if (interactive()) hm

S4 List Utils for Iheatmap classes

Description

These are utility methods for list-like classes in the package.

Usage

## S4 method for signature 'IheatmapList'
length(x)

## S4 method for signature 'IheatmapList'
as.list(x)

## S4 method for signature 'IheatmapList'
x[i]

## S4 replacement method for signature 'IheatmapList'
x[i] <- value

## S4 method for signature 'IheatmapList'
x[[i]]

## S4 replacement method for signature 'IheatmapList'
x[[i]] <- value

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

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

## S4 method for signature 'IheatmapList'
names(x)

## S4 replacement method for signature 'IheatmapList'
names(x) <- value

## S4 method for signature 'IheatmapList'
lapply(X, FUN, ...)

## S4 method for signature 'IheatmapList'
vapply(X, FUN, FUN.VALUE, ..., USE.NAMES = TRUE)

Arguments

x

input

FUN

function to apply to each element of x

...

additional arguments

FUN.VALUE

template for return value from FUN

USE.NAMES

logical, use names?

Shiny bindings for iheatmapr

Description

Output and render functions for using iheatmapr within Shiny

Usage

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

renderIheatmap(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 an Iheatmap object

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.

Access iheatmapr user input event data in shiny

Description

This function must be called within a reactive shiny context.

Usage

iheatmapr_event(
  object,
  event = c("hover", "click", "relayout"),
  session = shiny::getDefaultReactiveDomain()
)

Arguments

object

Iheatmap-class object

event

The type of plotly event. Currently 'plotly_hover', 'plotly_click', 'plotly_selected', and 'plotly_relayout' are supported.

session

a shiny session object (the default should almost always be used).

Examples

## Not run: 
shiny::runApp(system.file("examples", "shiny_example", package = "iheatmapr"))

## End(Not run)

knit_print.Iheatmap

Description

knit_print.Iheatmap

Usage

## S3 method for class 'Iheatmap'
knit_print(x, ...)

Arguments

x

Iheatmap object

...

Passed to knit_print.

main_heatmap

Description

Plots initial heatmap, creates Iheatmap object

Usage

## S4 method for signature 'matrix'
main_heatmap(
  data,
  name = "Signal",
  x = default_x(data),
  y = default_y(data),
  colors = pick_continuous_colors(zmid, zmin, zmax),
  colorbar_grid = setup_colorbar_grid(),
  colorbar_position = 1,
  zmid = 0,
  zmin = min(data, na.rm = TRUE),
  zmax = max(data, na.rm = TRUE),
  orientation = c("horizontal", "vertical"),
  x_categorical = NULL,
  y_categorical = NULL,
  row_order = seq_len(nrow(data)),
  col_order = seq_len(ncol(data)),
  text = signif(data, digits = 3),
  tooltip = setup_tooltip_options(),
  xname = "x",
  yname = "y",
  pname = name,
  source = "iheatmapr",
  show_colorbar = TRUE,
  layout = list()
)

Arguments

data

matrix

name

name of colorbar

x

x axis labels (by default rownames of data)

y

y axis labels (by default colnames of data)

colors

color palette or vector of colors

colorbar_grid

colorbar grid parameters, should be result from setup_colorbar_grid

colorbar_position

colorbar placement, should be positive integer

zmid

midpoint for colorscale

zmin

minimum for colorscale

zmax

maximum for colorscale

orientation

should new main plots be added horizontally or vertically?

x_categorical

is x categorical? will guess if not provided

y_categorical

is y categorical? will guess if not provided

row_order

row ordering for this heatmap– will be used for all subsequent elements sharing y axis

col_order

column ordering for this heatmap– will be used for all subsequent elements sharing x axis

text

text of value to display for data

tooltip

tooltip options, see setup_tooltip_options

xname

internal name for xaxis

yname

internal name for yaxis

pname

internal plot name

source

source name for use with shiny

show_colorbar

logical to indicate whether to show colorbar

layout

list of layout attributes to pass to plotly, eg. list(font = list(size = 15))

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

add_iheatmap, to_widget, iheatmap, Iheatmap-class

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)  
hm <- main_heatmap(mat) 

# Print heatmap if interactive session 
if (interactive()) hm

Convert iheatmapr subcomponents to plotly format

Description

These are generic methods for converting link{Iheatmap-class} plot components to plotly lists. Not intended for end users; exported for developers seeking to create new Iheatmap subplots. Any new link{IheatmapPlot}, link{IheatmapShape}, link{IheatmapAnnotation}, or link{IheatmapColorbar} child class should have one of these methods.

Usage

make_trace(x, ...)

make_shapes(x, ...)

make_annotations(x, ...)

make_colorbar(cb, grid)

Arguments

x

IheatmapPlot-class, IheatmapShape-class, or IheatmapAnnotation-class object

...

additional arguments specific to component

measles

Description

Data on measles cases for different states from 1930 to 2001

Examples

data(measles)

modify_layout

Description

modify_layout

Usage

## S4 method for signature 'Iheatmap'
modify_layout(x, new_layout)

Arguments

x

Iheatmap

new_layout

list of new layout parameter

Value

modified Iheatmap object

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)  
hm <- main_heatmap(mat) %>% modify_layout(list(margin = list(b = 120))) 

# Print heatmap if interactive session 
if (interactive()) hm

Objects exported from other packages

Description

These objects are imported from other packages. Follow the links below to see their documentation.

magrittr

%>%

reorder_cols

Description

Reorder the columns of an Iheatmap-class object

Usage

## S4 method for signature 'IheatmapHorizontal,integer'
reorder_cols(p, col_order, xname = current_xaxis(p))

## S4 method for signature 'IheatmapVertical,integer'
reorder_cols(p, col_order)

Arguments

p

Iheatmap-class object

col_order

integer vector

xname

name of xaxis to reorder, only applicable if object is oriented horizontally

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

add_row_clustering, reorder_cols

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)  
dend <- hclust(dist(t(mat)))
hm <- iheatmap(mat) %>% reorder_cols(dend$order)

# Print heatmap if interactive session 
if (interactive()) hm

reorder_rows

Description

Reorder the rows of an Iheatmap-class object

Usage

## S4 method for signature 'IheatmapHorizontal,integer'
reorder_rows(p, row_order)

## S4 method for signature 'IheatmapVertical,integer'
reorder_rows(p, row_order, yname = current_yaxis(p))

Arguments

p

Iheatmap-class object

row_order

integer vector

yname

name of yaxis to reorder, only applicable if object is oriented vertically

Value

Iheatmap-class object, which can be printed to generate an interactive graphic

Author(s)

Alicia Schep

See Also

add_row_clustering, reorder_cols

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)  
dend <- hclust(dist(mat))
hm <- iheatmap(mat) %>% reorder_rows(dend$order)

# Print heatmap if interactive session 
if (interactive()) hm

save_iheatmap

Description

save an link{Iheatmap-class} object, either as standalone HTML or as static pdf/png/jpeg

Usage

## S4 method for signature 'Iheatmap,character'
save_iheatmap(p, filename, ...)

Arguments

p

link{Iheatmap-class} object

filename

name of file

...

additional arguments to saveWidget for saving as html or webshot for saving as pdf/png/jpeg

Details

Note that this function requires the webshot package. If deploying a shiny app that calls this function in shinyapps.io, loading the webshot library and calling webshot::install_phantomjs() is needed for the the save functionality to work.

Author(s)

Alicia Schep

Examples

mat <- matrix(rnorm(24), nrow = 6)
hm <- iheatmap(mat)
## Not run: 
save_iheatmap(hm, "example_iheatmap.png")

## End(Not run)

setup_colorbar_grid

Description

function to set parameters controlling colorbar placement in Iheatmap object

Usage

setup_colorbar_grid(
  nrows = 3,
  y_length = y_spacing * 0.9,
  x_spacing = 0.16,
  y_spacing = y_start/nrows,
  x_start = 1.05,
  y_start = 0.9
)

Arguments

nrows

number of rows in colorbar grid

y_length

length of colorbar

x_spacing

spacing along horizontal axis between colorbars

y_spacing

spacing along vertical axis between colorbars

x_start

left most position of colorbar grid

y_start

top most position of colorbar grid

Value

IheatmapColorbarGrid-class object

Examples


cb_grid <- setup_colorbar_grid(nrows = 2, x_spacing = 0.2)
mat <- matrix(rnorm(24), nrow = 6)
hm <- iheatmap(mat, colorbar_grid = cb_grid, cluster_rows = "kmeans",
         cluster_cols = "kmeans", row_k = 3, col_k = 2)

# Print heatmap if interactive session 
if (interactive()) hm

Tooltip Options

Description

This function setups tooltip options for heatmap components of iheatmapr complex heatmaps.

Usage

setup_tooltip_options(
  row = TRUE,
  col = TRUE,
  value = TRUE,
  prepend_row = "Row: ",
  prepend_col = "Col: ",
  prepend_value = "Value: "
)

Arguments

row

logical, include row name in tooltip?

col

logical, include column name in tooltip?

value

logical, include value in tooltip?

prepend_row

text to prepend to row name

prepend_col

text to prepend to column name

prepend_value

text to prepend to value

Value

a HeatmapTooltipOptions object which stores these options and can be passed to 'tooltip' argument to main_heatmap and other functions.

Examples


mat <- matrix(rnorm(20), ncol = 5, nrow = 4)  
hm1 <- main_heatmap(mat, 
   tooltip = setup_tooltip_options(row = FALSE, col = FALSE,
                                   prepend_value = "Value is ")) 

# Print heatmap if interactive session 
if (interactive()) hm1

test_iheatmapr_event

Description

test_iheatmapr_event

Usage

test_iheatmapr_event(ihm, event = c("click", "hover", "relayout"))

Arguments

ihm

Iheatmap object

event

name of event, either "click","hover", or "relayout"

Value

shiny app

Examples


## Not run: 
  mat <- matrix(rnorm(20), ncol = 5, nrow = 4)  
  hm <- main_heatmap(mat) 
  test_iheatmapr_event(hm, "click")

## End(Not run)

Convert Iheatmap to plotly spec

Description

Function to convert link{Iheatmap-class} object to a plotly spec either as a list or json

Usage

to_plotly_list(p)

to_plotly_json(p)

Arguments

p

Iheatmap-class object to convert

Value

Returns a JSON for a plotly spec for to_plotly_spec and as a list of same plotly object for to_plotly_list.

Examples


mat <- matrix(rnorm(24), nrow = 6)
hm_json <- iheatmap(mat) %>% to_plotly_json()
hm_list <- iheatmap(mat) %>% to_plotly_list()

to_widget

Description

Function to convert link{Iheatmap-class} object to widget object

Usage

## S4 method for signature 'Iheatmap'
to_widget(p)

Arguments

p

Iheatmap-class object to convert

Value

htmlwidgets object

Author(s)

Alicia Schep

See Also

iheatmap, main_heatmap

Examples


mat <- matrix(rnorm(24), nrow = 6)
hm <- iheatmap(mat) %>% to_widget()
class(hm)

# Print heatmap if interactive session 
if (interactive()) hm