Type: Package
Title: Create Heatmaps Using Base Graphics
Version: 1.1.0
Date: 2026-03-19
Description: Provides a lightweight framework for creating high quality, complex heatmaps using base graphics. Supports hierarchical clustering with dendrograms, column and row scaling, cluster sub-divisions, customizable cell colours, shapes and sizes, legends, and flexible layouts for arranging multiple heatmaps. Designed to return plot objects that can be easily arranged with other plots without sacrificing resolution. Methods for hierarchical clustering and distance computations are described in Murtagh and Contreras (2012) <doi:10.1002/wics.53>. Dendrogram visualisation methods are based on the 'ggdendro' package by de Vries and Ripley (2020) https://CRAN.R-project.org/package=ggdendro.
URL: https://dillonhammill.github.io/HeatmapR/
BugReports: https://github.com/DillonHammill/HeatmapR/issues
Depends: R (≥ 3.5)
Imports: methods, stats, graphics, grDevices, tools
License: GPL-2
Encoding: UTF-8
RoxygenNote: 7.3.3
Language: en-GB
Suggests: covr, testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2026-03-20 02:37:25 UTC; dillon
Author: Dillon Hammill ORCID iD [aut, cre]
Maintainer: Dillon Hammill <dillon.hammill21@gmail.com>
Repository: CRAN
Date/Publication: 2026-03-24 09:20:13 UTC

Create a complex heatmap using base graphics

Description

Create a complex heatmap using base graphics

Usage

heat_map(
  x,
  scale = FALSE,
  scale_method = "range",
  dist_method = "euclidean",
  clust_method = "complete",
  round = 2,
  tree = FALSE,
  tree_x = NULL,
  tree_size_x = 1,
  tree_scale_x = FALSE,
  tree_cut_x = NULL,
  tree_split_x = 1,
  tree_label_x = FALSE,
  tree_label_size_x = 0.1,
  tree_label_col_x = "grey40",
  tree_label_col_alpha_x = 1,
  tree_label_text_x = NA,
  tree_label_text_font_x = 1,
  tree_label_text_size_x = 1,
  tree_label_text_col_x = "black",
  tree_label_text_col_alpha_x = 1,
  tree_y = NULL,
  tree_size_y = 1,
  tree_scale_y = FALSE,
  tree_cut_y = NULL,
  tree_split_y = 1,
  tree_label_y = FALSE,
  tree_label_size_y = 0.1,
  tree_label_col_y = "grey40",
  tree_label_col_alpha_y = 1,
  tree_label_text_y = NA,
  tree_label_text_font_y = 1,
  tree_label_text_size_y = 1,
  tree_label_text_col_y = "black",
  tree_label_text_col_alpha_y = 1,
  cell_shape = "rect",
  cell_size = FALSE,
  cell_col_palette = c("red", "blue", "green", "orange", "magenta", "purple"),
  cell_col_scale,
  cell_col_scale_limits = NULL,
  cell_size_scale_limits = NULL,
  cell_col_alpha = 1,
  cell_col_empty = "white",
  cell_border_line_type = 1,
  cell_border_line_width = 1,
  cell_border_line_col = "black",
  cell_border_line_col_alpha = 1,
  cell_border_mask = NULL,
  cell_text = FALSE,
  cell_text_font = 1,
  cell_text_size = 1,
  cell_text_col = "white",
  cell_text_col_alpha = 1,
  bar_size_x = 1,
  bar_values_x = NULL,
  bar_axis_label_x = NULL,
  bar_axis_label_adj_x = 0,
  bar_axis_label_font_x = 1,
  bar_axis_label_size_x = 1,
  bar_axis_label_col_x = "black",
  bar_axis_label_col_alpha_x = 1,
  bar_fill_x = "grey40",
  bar_fill_alpha_x = 1,
  bar_line_type_x = 1,
  bar_line_width_x = 1,
  bar_line_col_x = "black",
  bar_line_col_alpha_x = 1,
  bar_size_y = 1,
  bar_values_y = NULL,
  bar_axis_label_y = NULL,
  bar_axis_label_adj_y = 0,
  bar_axis_label_font_y = 1,
  bar_axis_label_size_y = 1,
  bar_axis_label_col_y = "black",
  bar_axis_label_col_alpha_y = 1,
  bar_fill_y = "grey40",
  bar_fill_alpha_y = 1,
  bar_line_type_y = 1,
  bar_line_width_y = 1,
  bar_line_col_y = "black",
  bar_line_col_alpha_y = 1,
  axis_text_x = NULL,
  axis_text_side_x = "bottom",
  axis_text_font_x = 1,
  axis_text_size_x = 1,
  axis_text_col_x = "black",
  axis_text_col_alpha_x = 1,
  axis_text_angle_x = 3,
  axis_text_adjust_x = 0.45,
  axis_label_x = NULL,
  axis_label_font_x = 2,
  axis_label_size_x = 1.2,
  axis_label_col_x = "black",
  axis_label_col_alpha_x = 1,
  axis_ticks_length_x = 1,
  axis_text_y = NULL,
  axis_text_side_y = "left",
  axis_text_font_y = 1,
  axis_text_size_y = 1,
  axis_text_col_y = "black",
  axis_text_col_alpha_y = 1,
  axis_text_angle_y = 1,
  axis_text_adjust_y = 0.45,
  axis_label_y = NULL,
  axis_label_font_y = 2,
  axis_label_size_y = 1.2,
  axis_label_col_y = "black",
  axis_label_col_alpha_y = 1,
  axis_ticks_length_y = 1,
  margins = c(NA, NA, NA, NA),
  title = NULL,
  title_text_font = 2,
  title_text_size = 1.5,
  title_text_col = "black",
  title_text_col_alpha = 1,
  legend = TRUE,
  legend_size = 1,
  legend_col_scale_size = 1,
  legend_title = NULL,
  legend_title_text_font = 2,
  legend_title_text_size = 1,
  legend_title_text_col = "black",
  legend_title_text_col_alpha = 1,
  legend_text_font = 1,
  legend_text_size = 1,
  legend_text_col = "black",
  legend_text_col_alpha = 1,
  popup = TRUE,
  popup_size = c(7, 7),
  ...
)

Arguments

x

matrix or data.frame containing the data to display in the heatmap.

scale

logical indicating whether the data should be scaled prior to constructing the heatmap. Addition options include "column" or "row" to indicate whether scaling should be performed across rows or columns.

scale_method

indicates the type of scaling to perform on rows or columns as indicated by scale, options include "range", "mean" or "zscore". Set to "range" by default.

dist_method

indicates the type of distance metric to use when constructing dendrograms, set to "euclidean" distance by default. See ?dist for alternatives. Also supports "cosine" for cosine distance (1 - cosine similarity).

clust_method

indicates the type of agglomeration method to use when constructing performing hierarchical clustering, set to "complete" by default. See ?hclust for alternatives.

round

indicates the number of decimal places to round values when cell_text = TRUE and values are displayed in the heatmap, set to 2 decimal places by default

tree

options include "row", "y", "column", "x" or "both" to indicate the axes for which dendrograms should be constructed, set to FALSE by default. This argument overrides the tree_x and tree_y arguments.

tree_x

logical indicating whether dendrograms should be constructed for the x axis (columns), set to NULL by default.

tree_size_x

numeric to control the height of the dendrogram for the x axis, set to 1 by default.

tree_scale_x

logical indicating whether the branch heights of the x axis dendrogram should be scaled for better visualisation, set to FALSE by default.

tree_cut_x

either a numeric ranging from 0 to 1 indicating the branch cut height for x axis dendrogram (proportional for non-cosine distances, or absolute cosine distance threshold when dist_method = "cosine") or an integer indicating the desired number of clusters to obtain by cutting the x axis dendrogram. Alternatively, clusters can be manually defined by specifying the number of columns to include in each cluster (e.g., c(3,4,5)), or a vector of cluster indices can be supplied to assign each column to a specific cluster (e.g., c(1,1,1,2,2,2,2,3,3,3) for 10 columns in 3 clusters). When a vector of indices is supplied, its length must equal the number of columns in x.

tree_split_x

a numeric to control the spacing between x axis tree splits, set to 1 by default. Setting the argument to 0 will remove axis tree splits.

tree_label_x

logical indicating whether a label should be added for each cluster within the x axis tree when tree_cut_x is specified, set to FALSE by default.

tree_label_size_x

numeric to control the height of the tree cluster labels for the x axis tree, set to 0.1 by default.

tree_label_col_x

vector of colours to use for x axis tree cluster labels, set to "grey40" by default.

tree_label_col_alpha_x

numeric to control the transparency of the x axis tree cluster labels, set to 1 by default to use solid colours.

tree_label_text_x

a vector of text to include in the x axis tree cluster labels, set to NA by default.

tree_label_text_font_x

a vector of font types to use for text in x axis cluster labels, set to 1 by default for plain text. See font in ?par for alternatives.

tree_label_text_size_x

a vector of numerics to control the size of the text in the x axis cluster labels, set to 1 by default.

tree_label_text_col_x

a vector of colours to control the colour of text in x axis cluster labels, set to "black" by default.

tree_label_text_col_alpha_x

a vector of numerics to control the transparency of text in x axis cluster labels, set to 1 by default to use solid colours.

tree_y

logical indicating whether dendrograms should be constructed for the y axis (rows), set to NULL by default.

tree_size_y

numeric to control the width of the dendrogram for the y axis, set to 1 by default.

tree_scale_y

logical indicating whether the branch heights of the y axis dendrogram should be scaled for better visualisation, set to FALSE by default.

tree_cut_y

either a numeric ranging from 0 to 1 indicating the branch cut height for y axis dendrogram (proportional for non-cosine distances, or absolute cosine distance threshold when dist_method = "cosine") or an integer indicating the desired number of clusters to obtain by cutting the y axis dendrogram. Alternatively, clusters can be manually defined by specifying the number of rows to include in each cluster (e.g., c(3,4,5)), or a vector of cluster indices can be supplied to assign each row to a specific cluster (e.g., c(1,1,1,2,2,2) for 6 rows in 2 clusters). When a vector of indices is supplied, its length must equal the number of rows in x.

tree_split_y

a numeric to control the spacing between y axis tree splits, set to 1 by default. Setting the argument to 0 will remove axis tree splits.

tree_label_y

logical indicating whether a label should be added for each cluster within the y axis tree when tree_cut_y is specified, set to FALSE by default.

tree_label_size_y

numeric to control the width of the tree cluster labels for the y axis tree, set to 0.1 by default.

tree_label_col_y

vector of colours to use for y axis tree cluster labels, set to "grey40" by default.

tree_label_col_alpha_y

numeric to control the transparency of the y axis tree cluster labels, set to 1 by default to use solid colours.

tree_label_text_y

a vector of text to include in the y axis tree cluster labels, set to NA by default.

tree_label_text_font_y

a vector of font types to use for text in y axis cluster labels, set to 1 by default for plain text. See font in ?par for alternatives.

tree_label_text_size_y

a vector of numerics to control the size of the text in the y axis cluster labels, set to 1 by default.

tree_label_text_col_y

a vector of colours to control the colour of text in y axis cluster labels, set to "black" by default.

tree_label_text_col_alpha_y

a vector of numerics to control the transparency of text in y axis cluster labels, set to 1 by default to use solid colours.

cell_shape

indicates the shape to use for the cells in the heatmap, options include "rect", "circle" or "diamond".

cell_size

logical indicating whether each cell in the heatmap should be scaled by the value in x, set to FALSE by default. Alternatively, a matrix of the same dimensions as x containing the values by which the size of each cell should be scaled.

cell_col_palette

a vector of colours from which colours are selected for columns containing non-numeric data.

cell_col_scale

a vector of colours to use for the colour scale of numeric values, set to a hybrid colour-blind friendly viridis colour palette by default.

cell_col_scale_limits

a numeric vector of length 2 specifying custom limits for the colour scale as c(min, max). If NULL (default), limits are computed from the data before rounding. Custom limits allow you to set consistent colour scales across multiple heatmaps or override automatic scaling.

cell_size_scale_limits

a numeric vector of length 2 specifying custom limits for the size scale as c(min, max). If NULL (default), limits are computed from the data before rounding. Only used when cell_size is not FALSE. Custom limits allow consistent size scales across multiple heatmaps.

cell_col_alpha

a numeric to control the fill transparency of cells within the heatmap, set to 1 by default to use solid colours.

cell_col_empty

a colour to use for missing values in x, set to "white" by default.

cell_border_line_type

a integer to indicate the type of line to use for cell borders, set to 1 by default for solid lines. See lty in ?par for alternatives.

cell_border_line_width

a numeric to control the with of cell borders, set to 1 by default.

cell_border_line_col

indicates the colour to use for cell borders, set to "black" by default.

cell_border_line_col_alpha

numeric to control the transparency of cell borders, set to 1 by default to use solid colours.

cell_border_mask

a matrix of the same dimensions as x containing TRUE/FALSE values indicating whether each cell should have a colored border (TRUE) or a transparent border (FALSE), set to NULL by default to apply border color to all cells.

cell_text

logical indicating whether the values in x should be displayed in each cell of the heatmap, set to FALSE by default.

cell_text_font

an integer to control the font face of cell text, set to 1 by default. See font in ?par for alternatives.

cell_text_size

numeric to control the size of cell text, set to 1 by default.

cell_text_col

colour to use for cell text, set to "white" by default,

cell_text_col_alpha

numeric ranging from 0 to 1 to control the transparency of cell text, set to 1 by default to use solid colours for cell text.

bar_size_x

numeric to control the height of x axis bar plot, set to 1 by default.

bar_values_x

a vector of values to display in x axis bar plot, supplied in the order matching the original columns of x or named with the column names of x. The values supplied to bar_values_x will be internally reordered to match the order of columns as determined by hierarchical clustering.

bar_axis_label_x

axis label to use for the x axis bar plot.

bar_axis_label_adj_x

scalar [-1, 1] to adjust the position of the x axis bar graph label relative to the x axis, set to 0 by default.

bar_axis_label_font_x

font to use for the axis label of the x axis bar plot, set to 2 by default. See font in ?par for alternatives.

bar_axis_label_size_x

numeric to control the size of the axis text in x axis bar plots, set to 1 by default.

bar_axis_label_col_x

colour to use for the axis text in x axis bar plot, set to "black" by default.

bar_axis_label_col_alpha_x

numeric ranging from 0 to 1 to control the transparency of axis text in x axis bar plot, set to 1 by default to use solid colours.

bar_fill_x

a vector of colours to use for the bars in the x axis bar plot, set to "grey40" by default.

bar_fill_alpha_x

a numeric ranging from 0 to 1 to control the fill transparency of bars in x axis bar plot, set to 1 by default to use solid colours.

bar_line_type_x

integer to control the line type of bar borders in the x axis bar plot, set to 1 by default to use solid lines. See lty in ?par for alternatives.

bar_line_width_x

numeric to control the width bar borders in x axis bar plot, set to 1 by default.

bar_line_col_x

colour to use for bar borders in x axis bar plot, set to "black" by default.

bar_line_col_alpha_x

numeric ranging from 0 to 1 to control the transparency of bar borders in x axis bar plot, set to 1 by default.

bar_size_y

numeric to control the width of y axis bar plot, set to 1 by default.

bar_values_y

a vector of values to display in y axis bar plot, supplied in the order matching the original rownames of x or named with the row names of x. The values supplied to bar_values_y will be internally reordered to match the order of rows as determined by hierarchical clustering.

bar_axis_label_y

axis label to use for the y axis bar plot.

bar_axis_label_adj_y

scalar [-1, 1] to adjust the position of the y axis bar graph label relative to the y axis, set to 0 by default.

bar_axis_label_font_y

font to use for the axis label of the y axis bar plot, set to 2 by default. See font in ?par for alternatives.

bar_axis_label_size_y

numeric to control the size of the axis text in y axis bar plots, set to 1 by default.

bar_axis_label_col_y

colour to use for the axis text in y axis bar plot, set to "black" by default.

bar_axis_label_col_alpha_y

numeric ranging from 0 to 1 to control the transparency of axis text in y axis bar plot, set to 1 by default to use solid colours.

bar_fill_y

a vector of colours to use for the bars in the y axis bar plot, set to "grey40" by default.

bar_fill_alpha_y

a numeric ranging from 0 to 1 to control the fill transparency of bars in y axis bar plot, set to 1 by default to use solid colours.

bar_line_type_y

integer to control the line type of bar borders in the y axis bar plot, set to 1 by default to use solid lines. See lty in ?par for alternatives.

bar_line_width_y

numeric to control the width bar borders in y axis bar plot, set to 1 by default.

bar_line_col_y

colour to use for bar borders in y axis bar plot, set to "black" by default.

bar_line_col_alpha_y

numeric ranging from 0 to 1 to control the transparency of bar borders in y axis bar plot, set to 1 by default.

axis_text_x

vector of text to use for x axis labels supplied in the order matching the constructed heatmap, set to NULL by default to use the column names of x.

axis_text_side_x

indicates whether the x axis text should be on the 1 - "bottom" or 3 - "top" of the heatmap, set to "bottom" by default. All other heatmap components, including the tree, tree labels and bar plot will be positioned on the opposite side to the axis text.

axis_text_font_x

integer to control the font face of x axis labels, set to 1 by default. See font in ?par for alternatives.

axis_text_size_x

numeric to control the size of x axis text, set to 1 by default.

axis_text_col_x

colour to use for x axis text labels, set to "black" by default.

axis_text_col_alpha_x

numeric ranging from 0 to 1 to control the transparency of x axis text labels, set to 1 by default to use solid text colours.

axis_text_angle_x

integer to control the angle of x axis text labels relative to the x axis, set to 3 by default. See las in ?par for alternatives.

axis_text_adjust_x

numeric to adjust position x axis text relative to x axis ticks, set to 0.45 by default.

axis_label_x

label to use for the x axis.

axis_label_font_x

integer to control the font face of the x axis label, set to 2 by default.

axis_label_size_x

numeric to control the size of the x axis label, set to 1.2 by default.

axis_label_col_x

colour to use for x axis label text, set to "black" by default.

axis_label_col_alpha_x

numeric ranging from 0 to 1 to control the transparency of the x axis label text, set to 1 by default to use solid colours.

axis_ticks_length_x

numeric to control the length of the x axis ticks, set to 1 by default.

axis_text_y

vector of text to use for y axis labels supplied in the order matching the constructed heatmap, set to NULL by default to use the row names of x.

axis_text_side_y

indicates whether the y axis text should be on the 2 - "left" or 4 - "right" of the heatmap, set to "left" by default. All other heatmap components, including the tree, tree labels and bar plot will be positioned on the opposite side to the axis text.

axis_text_font_y

integer to control the font face of y axis labels, set to 1 by default. See font in ?par for alternatives.

axis_text_size_y

numeric to control the size of y axis text, set to 1 by default.

axis_text_col_y

colour to use for y axis text labels, set to "black" by default.

axis_text_col_alpha_y

numeric ranging from 0 to 1 to control the transparency of y axis text labels, set to 1 by default to use solid text colours.

axis_text_angle_y

integer to control the angle of y axis text labels relative to the y axis, set to 3 by default. See las in ?par for alternatives.

axis_text_adjust_y

numeric to adjust position y axis text relative to y axis ticks, set to 0.45 by default.

axis_label_y

label to use for the y axis.

axis_label_font_y

integer to control the font face of the y axis label, set to 2 by default.

axis_label_size_y

numeric to control the size of the y axis label, set to 1.2 by default.

axis_label_col_y

colour to use for y axis label text, set to "black" by default.

axis_label_col_alpha_y

numeric ranging from 0 to 1 to control the transparency of the y axis label text, set to 1 by default to use solid colours.

axis_ticks_length_y

numeric to control the length of the y axis ticks, set to 1 by default.

margins

vector of numerics to control the size of the margins around the bottom, left, top and right of the heatmap. Setting any of these values to NA will allow for internal computation of optimal heatmap margins.

title

text to include in the title above the heatmap.

title_text_font

integer to control the font face for the heatmap title, set to 2 by default. See font in ?par for alternatives.

title_text_size

numeric to control the size of the text in the heatmap title, set to 1.2 by default.

title_text_col

colour to use for text in heatmap title, set to "black" by default.

title_text_col_alpha

numeric ranging from 0 to 1 to control the transparency of text in heatmap title, set to 1 by default for solid colours.

legend

logical indicating whether to include a legend in the heatmap, set to TRUE by default. Alternatively, "size", "colour" or "both" to indicate the type(s) of legends to include in the heatmap.

legend_size

numeric to control the amount of space allocated to the legend, set to 1 by default.

legend_col_scale_size

numeric to control the width of the legend colour scale relative to the allocated space for the legend, set to 1 by default. legend_title = NULL,

legend_title

a vector of length two containing text to be displayed above the cell colour and size legends respectively.

legend_title_text_font

integer to control the font face for the heatmap legends, set to 2 by default for bold font. See font in ?par for alternatives.

legend_title_text_size

numeric to control the size of the text in the heatmap legend titles, set to 1 by default.

legend_title_text_col

colour to use for text in heatmap legend titles, set to "black" by default.

legend_title_text_col_alpha

numeric ranging from 0 to 1 to control the transparency of text in heatmap legend titles, set to 1 by default for solid colours.

legend_text_font

integer to control the font face for legend text, set to 1 by default. See font in ?par for alternatives.

legend_text_size

numeric to control the size of text in the legend, set to 1 by default.

legend_text_col

colour to use for text in the legend, set to "black".

legend_text_col_alpha

numeric to control the transparency of text in the legend, set to 1 by default to use solid colours.

popup

logical indicating whether the heatmap should be constructed in a popup window, set to TRUE by default.

popup_size

vector to control the height and width of the popup window in inches, set to c(7,7).

...

not in use.

Value

a recorded heatmap.

Author(s)

Dillon Hammill (dillon.hammill21@gmail.com)

Examples

heat_map(
  mtcars,
  scale = "column",
  cell_shape = "circle",
  cell_size = TRUE,
  tree_x = TRUE,
  tree_cut_x = 3,
  tree_y = TRUE,
  tree_cut_y = 3,
  bar_values_x = 1:11,
  bar_fill_x = rainbow(11),
  bar_values_y = 1:32,
  bar_fill_y = rainbow(32)
 )

Perform hierarchical clustering for heatmap

Description

Perform hierarchical clustering for heatmap

Usage

heat_map_clust(
  x,
  tree = "row",
  dist = "euclidean",
  method = "complete",
  scale = FALSE,
  cut = NULL,
  ...
)

Arguments

x

matrix-like object to cluster. The distance matrix will be computed using dist and passed to hclust for hierarchical clustering.

tree

indicates whether hierarchical clustering should be performed by "row" or "column". Optionally a custom object of class "dist" or "hclust" which will be updated with cluster labels as specified by cut.

dist

method passed to dist to compute distance matrix, set to "euclidean" by default. Also supports "cosine" for cosine distance (1 - cosine similarity).

method

agglomeration method passed to hclust to perform hierarchical clustering, set to "complete" by default.

scale

logical indicating whether branch heights should be scaled for better visualisation, set to FALSE by default.

cut

value less than 1 specifying the tree cutpoint as a proportion of the tree height (for non-cosine distances) or as an absolute cosine distance threshold (when dist = "cosine"), or a value greater than or equal to 1 indicating the number of desired clusters.

...

additional arguments passed to dist or hclust.

Value

object of class hclust which describes the tree produced by the clustering process.

Author(s)

Dillon Hammill (dillon.hammill21@gmail.com)

Examples

# Hierarchical clustering
heat_map_hclust <- heat_map_clust(mtcars, cut = 5)

Indicate when a heatmap is complete and ready for saving

Description

Indicate when a heatmap is complete and ready for saving

Usage

heat_map_complete()

Value

No return value, called for side effects.

Author(s)

Dillon Hammill (dillon.hammill21@gmail.com)

Examples


# Save heatmap
heat_map_save(file.path(tempdir(), "Heatmap.png"),
height = 7, 
width = 15)

# Custom layout
heat_map_layout(layout = c(1,2))

# Construct raw heatmap
heat_map(iris[1:10,],
scale = FALSE,
title = "Iris Raw Heatmap",
axis_label_x = "Plant Parameter",
axis_label_y = "Row ID")

# Construct scaled heatmap
heat_map(iris[1:10,],
scale = "range",
title = "Iris Scaled Heatmap",
axis_label_x = "Plant Parameter",
axis_label_y = "Row ID")

# Signal completion
heat_map_complete()

Create a custom heatmap plot layout

Description

heat_map_custom() is similar to cheat_map_save() with the exception that it doesn't write the plot to a file. heat_map_custom() opens a new graphics device and sets the desired layout in preparation for the addition of heatmaps and other plot objects. Once the custom plot is full users MUST run cyto_plot_complete() to close the graphics device and reset any heat_map() related settings (see example).

Usage

heat_map_custom(popup = TRUE, popup_size = c(8, 8), layout = NULL, ...)

Arguments

popup

logical indicating whether a popup graphics device should be opened.

popup_size

indicates the size of the popup graphics device in inches, set to c(8,8) by default.

layout

either a vector of the form c(nrow, ncol) defining the dimensions of the plot or a matrix defining a more sophisticated layout (see layout). Vectors can optionally contain a third element to indicate whether plots should be placed in row (1) or column (2) order, set to row order by default.

...

additional arguments passed to heat_map_new().

Value

No return value, called for side effects.

Author(s)

Dillon Hammill (dillon.hammill21@gmail.com)

See Also

heat_map_save

heat_map_new

heat_map_complete

Examples


heat_map_custom(
  popup = FALSE,
  layout = c(1,2)
)
heat_map(
  mtcars
)
plot(
  mtcars[, 1:2],
  pch = 16
)
heat_map_complete()

Arrange multiple heatmaps

Description

Arrange multiple heatmaps

Usage

heat_map_layout(layout = NULL)

Arguments

layout

either a vector of the form c(nrow, ncol) defining the dimensions of the plot or a matrix defining a more sophisticated layout (see layout). Vectors can optionally contain a third element to indicate whether plots should be placed in row (1) or column (2) order, set to row order by default.

Value

No return value, called for side effects.

Author(s)

Dillon Hammill (dillon.hammill21@gmail.com)

Examples


# Save heatmap
heat_map_save(file.path(tempdir(), "Heatmap.png"),
height = 7, 
width = 15)

# Custom layout
heat_map_layout(layout = c(1,2))

# Construct raw heatmap
heat_map(iris[1:10,],
scale = FALSE,
title = "Iris Raw Heatmap",
axis_label_x = "Plant Parameter",
axis_label_y = "Row ID")

# Construct scaled heatmap
heat_map(iris[1:10,],
scale = "range",
title = "Iris Scaled Heatmap",
axis_label_x = "Plant Parameter",
axis_label_y = "Row ID")

# Signal completion
heat_map_complete()

Open a pop-up graphics device for heatmaps

Description

Open a pop-up graphics device for heatmaps

Usage

heat_map_new(popup = FALSE, popup_size = c(8, 8), ...)

Arguments

popup

logical indicating whether a popup graphics device should be opened.

popup_size

indicates the size of the popup graphics device in inches, set to c(8,8) by default.

...

additional arguments passed to dev.new.

Value

No return value, called for side effects.

Author(s)

Dillon Hammill, dillon.hammill21@gmail.com

Examples


# Open platform-specific graphics device
heat_map_new(popup = TRUE)

Record a custom heatmap

Description

Record custom heatmap layout on current graphics device and save to an R object for future use.

Usage

heat_map_record()

Value

an object of class recordedplot.

Author(s)

Dillon Hammill (dillon.hammill21@gmail.com)

Examples


# Heatmap layout
heat_map_layout(c(1,2))

# Construct raw heatmap
heat_map(iris[1:10,],
scale = FALSE,
title = "Iris Raw Heatmap",
axis_label_x = "Plant Parameter",
axis_label_y = "Row ID")

# Construct scaled heatmap
heat_map(iris[1:10,],
scale = "range",
title = "Iris Scaled Heatmap",
axis_label_x = "Plant Parameter",
axis_label_y = "Row ID")

# Record heatmap layout
heat_map_plot <- heat_map_record()

Reset all heatmap related settings

Description

Reset all heatmap related settings

Usage

heat_map_reset()

Value

No return value, called for side effects.

Author(s)

Dillon Hammill (dillon.hammill21@gmail.com)

Examples


# Reset HeatmapR settings
heat_map_reset()

Save high resolution images

Description

Save high resolution images

Usage

heat_map_save(
  save_as,
  width = 7,
  height = 7,
  units = "in",
  res = 300,
  multiple = FALSE,
  layout = NULL,
  ...
)

Arguments

save_as

name of the file to which the plot should be saved (including the file extension). Supported file formats include png, tiff, jpeg, svg and pdf.

width

numeric indicating the width of exported plot in units, set to 7 by default for image with width of 7 inches.

height

numeric indicating the height of the exported plot in units, set to 7 by default for image with height of 7 inches.

units

units to be used to set plot size, can be either pixels (px), inches (inches), centimetres (cm) or millimetres (mm). Set to "in" by default. Units cannot be altered for svg and pdf graphics devices.

res

resolution in dpi, set to 300 by default.

multiple

logical indicating whether multiple pages should be saved to separate numbered files, set to TRUE by default.

layout

a vector or matrix defining the custom layout of the plot to be created using heat_map_layout, set to NULL by default.

...

additional arguments for the appropriate png(), tiff(), jpeg(), svg() or pdf graphics devices.

Value

No return value, called for side effects.

Author(s)

Dillon Hammill (dillon.hammill21@gmail.com)

Examples


# Save Heatmap
heat_map_save(file.path(tempdir(), "Heatmap.png"),
height = 7, 
width = 5)

# Construct Heatmap
heat_map(iris[1:10,],
scale = "range",
title = "Iris Heatmap",
axis_label_x = "Plant Parameter",
axis_label_y = "Row ID")

Scale numeric data prior to constructing heat_map

Description

Apply column-wise or row-wise scaling to numeric columns in a matrix or data.frame prior to constructing a heat_map.

Usage

heat_map_scale(x, scale = "column", method = "range")

Arguments

x

matrix-like object to be scaled.

scale

indicates whether the data should be scaled by "row" or "column", set to "column" by default.

method

type of scaling to perform, can be either 'range', 'mean' or 'zscore'. Range scaling normalizes the data to have limits between 0 and 1. Mean scaling subtracts the mean (calculated excluding missing values) from each value. Z-score scaling subtracts the mean from each value and then divides the result by the standard deviation.

Value

a matrix or data.frame containing the scaled data.

Author(s)

Dillon Hammill (dillon.hammill21@gmail.com)

Examples

# Range scaling
mtcars_scale_range <- heat_map_scale(mtcars,
method = "range")

# Mean scaling
mtcars_scale_mean <- heat_map_scale(mtcars,
method = "mean")

# Z-score scaling
mtcars_scale_zscore <- heat_map_scale(mtcars,
method = "zscore")