Help for package ggcorrheatmap

Title:

Make Flexible 'ggplot2' Correlation Heatmaps

Version:

0.2.0

Description:

Create correlation heatmaps with 'ggplot2' and customise them with flexible annotation and clustering. Symmetric heatmaps can use triangular or mixed layouts, removing redundant information or displaying complementary information in the two halves. There is also support for general heatmaps not displaying correlations.

License:

MIT + file LICENSE

Encoding:

UTF-8

RoxygenNote:

7.3.2

URL:

https://github.com/leod123/ggcorrheatmap, https://leod123.github.io/ggcorrheatmap/

BugReports:

https://github.com/leod123/ggcorrheatmap/issues

Imports:

ggplot2, scales, dplyr, dendextend, ggnewscale, stats, rlang (≥ 1.1.0), cli

Suggests:

testthat (≥ 3.0.0), vdiffr

Config/testthat/edition:

Config/Needs/website:

rmarkdown, patchwork, cowplot, tibble, tidyr

NeedsCompilation:

Packaged:

2025-08-24 17:53:39 UTC; leodahl

Author:

Leo Dahl [aut, cre, cph]

Maintainer:

Leo Dahl <leokosdah@gmail.com>

Repository:

CRAN

Date/Publication:

2025-08-24 18:10:02 UTC

ggcorrheatmap: Make Flexible 'ggplot2' Correlation Heatmaps

Description

Author(s)

Maintainer: Leo Dahl leokosdah@gmail.com [copyright holder]

Add annotations to ggplot heatmap

Description

Add annotations to ggplot heatmap

Usage

add_annotation(
  plt,
  context = c("rows", "cols"),
  annot_df,
  annot_pos,
  annot_size,
  annot_border_lwd = 0.5,
  annot_border_col = "grey",
  annot_border_lty = 1,
  show_annot_names = TRUE,
  na_remove = FALSE,
  col_scale = NULL,
  names_side,
  name_params = NULL,
  names_strategy = "geom"
)

Arguments

plt

ggplot object with geom_tile layer to add annotations to.

context

Dimension to add annotations to, either "rows" or "columns".

annot_df

Data frame containing the annotations. The first column must contain the labels used in the heatmap rows or columns. Each of the other columns should contain corresponding annotations. The column names are used as labels in the legend.

annot_pos

Positions of annotations. x positions if row annotations, y positions if column annotations. Positions are given by the middle coordinate of the annotation cells.

annot_size

Size of annotations, width of row annotations, height if column annotations.

annot_border_lwd

Linewidth of border lines of annotation cells.

annot_border_col

Colour of border lines of annotation cells.

annot_border_lty

Linetype of border lines of annotation cells.

show_annot_names

Logical indicating if the annotation names should be drawn.

na_remove

Logical indicating if NA values should be removed.

col_scale

Named list of fill scales to use, named after the columns in the annotation data frame. Each element should either be a ⁠scale_fill_*⁠ object or a string specifying a brewer palette or viridis option.

names_side

String specifying which side the labels should be drawn on. "top" or "bottom" for row annotation, "left" or "right" for column annotation.

name_params

A named list of parameters to give to ggplot2::geom_text or grid::textGrob to modify annotation label appearance.

names_strategy

String stating which strategy to use for drawing names (geom, grid).

Value

ggplot object with added annotations.

Add dendrogram to ggplot object.

Description

Add dendrogram to ggplot object.

Usage

add_dendrogram(plt, dendro, dend_col = "black", dend_lwd = 0.3, dend_lty = 1)

Arguments

plt

ggplot object to add dendrogram to.

dendro

Dendrogram segment and node data obtained from the prepare_dendrogram function.

dend_col

String specifying colour of dendrogram (used if the colours have not been changed using other options).

dend_lwd

Line width of dendrogram segments (used if not changed using other options).

dend_lty

Line type of dendrogram (used if not changed using other options).

Value

A ggplot object with a dendrogram added.

Add diagonal names to heatmap.

Description

Add diagonal names to heatmap.

Usage

add_diag_names(plt, x_long, names_diag_params = NULL)

Arguments

plt

Plot object to add names to.

x_long

Long format plotting data.

names_diag_params

Parameters for diagonal names.

Value

Plot with labels added.

Add a layout column to long format data for mixed layouts.

Description

Add a layout column to long format data for mixed layouts.

Usage

add_mixed_layout(
  x,
  rows = "row",
  cols = "col",
  values = "value",
  layout,
  name = "layout"
)

Arguments

x

Long format data frame of a symmetric matrix.

rows, cols, values

Columns containing rows, columns, and values.

layout

Character vector of length two with a mixed layout (two opposing triangles).

name

Name of the column that should contain the layouts.

Value

The input data frame with a new column added, showing in which triangle each value would be in a mixed layout.

Examples

# Make long format symmetric data
long_df <- data.frame(rw = rep(letters[1:4], 4),
                      cl = rep(letters[1:4], each = 4),
                      val = 0)

long_df <- add_mixed_layout(long_df, rw, cl, val,
                            layout = c("topleft", "bottomright"))

head(long_df)

Successively apply dendextend functions to a dendrogram.

Description

Successively apply dendextend functions to a dendrogram.

Usage

apply_dendextend(dend_list, dendro)

Arguments

dend_list

List specifying dendextend functions to apply. For usage see the details of gghm.

dendro

Dendrogram object obtained from stats::as.dendrogram.

Value

A dendrogram object modified with dendextend functions.

Check names of annotation

Description

Check names of annotation

Usage

check_annot_df(annot_df, names_in, context)

Arguments

annot_df

Annotation data frame (annot_rows_df, annot_cols_df).

names_in

Names that exist in the data (rownames, colnames).

Value

Annotation data frame (rownames moved to column named '.names' if necessary).

Check annotation name parameters for deprecated usage.

Description

Check annotation name parameters for deprecated usage.

Usage

check_annot_names_deprecated(
  new_params = NULL,
  old_params = NULL,
  context = c("rows", "cols")
)

Arguments

new_params

New argument input.

old_params

Deprecated argument input.

context

Context (rows or cols).

Value

A string stating which strategy to use for drawing names.

Check cell labels if they are ok.

Description

Check cell labels if they are ok.

Usage

check_cell_labels(cell_labels, x_long)

Arguments

cell_labels

The cell_labels input to gghm().

x_long

Long format input data.

Value

Long format data frame containing cell labels.

Check that dendrograms are positioned correctly

Description

Check that dendrograms are positioned correctly

Usage

check_dendrogram_pos(dat, context = c("row", "col"), dendro)

Arguments

dat

Long format data for plotting.

context

Dimension to which the dendrogram is added. These are used to directly get the columns in the long data and thus need to be "row" or "col".

dendro

The dendrogram segments and nodes list.

Value

dendro is returned as is if the positions are correct. Otherwise there is an error.

Check that layout and mode are correct

Description

Check that layout and mode are correct

Usage

check_layout(layout, mode)

Arguments

layout

Plot layout.

mode

Plot mode.

Value

Error if incorrect layout or mode, otherwise nothing.

Check (supposed) logical values.

Description

Check (supposed) logical values.

Usage

check_logical(..., list_allowed = FALSE, call = NULL)

Arguments

...

Should be a single named argument, where the name is the variable name displayed in the error message. The value is the (supposed) logical.

list_allowed

Logical indicating if the argument is allowed to be a list. If TRUE each element will be checked.

call

Call to use for the call in the error message (used in rlang::abort). Default is rlang::caller_env() resulting in the function that called check_logical().

Value

Error if not logical or longer than 1, otherwise nothing.

Check input numeric arguments for class and length.

Description

Check input numeric arguments for class and length.

Usage

check_numeric(
  ...,
  allow_null = FALSE,
  allowed_lengths = 1,
  list_allowed = FALSE,
  call = NULL
)

Arguments

...

Should be a single named argument, where the name is the variable name displayed in the error message. The value is the (supposed) logical.

allow_null

Logical indicating if NULL is allowed as input for the argument.

allowed_lengths

The allowed lengths of the argument.

list_allowed

Logical indicating if the argument is allowed to be a list. If TRUE each element will be checked.

call

Call to use for the call in the error message (used in rlang::abort). Default is rlang::caller_env() resulting in the function that called check_logical().

Value

Error if not numeric, NULL when not allowed, or too long/too short.

Cluster data using hierarchical clustering or use provided clustering.

Description

Cluster data using hierarchical clustering or use provided clustering.

Usage

cluster_data(
  cluster_input,
  mat,
  cluster_distance,
  cluster_method,
  dend_options = NULL
)

Arguments

cluster_input

Either a logical indicating if data should be clustered, or a hclust or dendrogram object.

mat

Matrix to cluster.

cluster_distance

Distance metric for clustering.

cluster_method

Clustering method for hclust.

dend_options

List or functional sequence specifying dendextend functions to use.

Value

List containing the dendrogram and clustering objects.

Make a correlation matrix from long format data.

Description

Make a correlation matrix from long format data.

Usage

cor_long(
  x,
  rows,
  cols,
  values,
  y = NULL,
  rows2 = NULL,
  cols2 = NULL,
  values2 = NULL,
  out_format = c("long", "wide"),
  method = "pearson",
  use = "everything",
  p_values = FALSE,
  p_adjust = "none",
  p_thresholds = c(`***` = 0.001, `**` = 0.01, `*` = 0.05, 1),
  p_sym_add = NULL,
  p_sym_digits = 2
)

Arguments

x

A long format data frame containing the data to correlate.

rows, cols

The columns in x containing the values that should be in the rows and columns of the correlation matrix.

values

Name of the column in x containing the values of the correlation matrix.

y

Optional second data frame for correlating with the data frame from x.

rows2, cols2

Optional names of columns with values for the rows and columns of a second matrix (taken from y).

values2

Optional column for the values of a second matrix.

out_format

Format of output correlation matrix ("long" or "wide").

method

Correlation method given to stats::cor().

use

Missing value strategy of stats::cor().

p_values

Logical indicating if p-values should be calculated.

p_adjust

String specifying the multiple testing adjustment method to use for the p-values (default is "none"). Passed to stats::p.adjust().

p_thresholds

Named numeric vector specifying p-value thresholds (in ascending order) to mark. The last element must be 1 or higher (to set the upper limit). Names must be unique, but one element can be left unnamed (by default 1 is unnamed, meaning values between the threshold closest to 1 and 1 are not marked in the plot). If NULL, no thresholding is done and p-value intervals are not marked with symbols.

p_sym_add

String with the name of the column to add to p-value symbols from p_thresholds (one of 'values', 'p_val', 'p_adj'). NULL (default) results in just the symbols.

p_sym_digits

Number of digits to use for the column in p_sym_add.

Details

If there is only one input data frame (x), a wide matrix is constructed from x and passed to stats::cor(), resulting in a correlation matrix with the column-column correlations.

If y is a data frame and rows2, cols2 and values2 are specified, the wide versions of x and y are correlated (stats::cor(wide_x, wide_y)) resulting in a correlation matrix with the columns of x in the rows and the columns of y in the columns.

Value

A correlation matrix (if wide format) or a long format data frame with the columns 'row', 'col', and 'value' (containing correlations).

Examples

set.seed(123)
cor_in <- data.frame(row = rep(letters[1:10], each = 5),
                     col = rep(LETTERS[1:5], 10),
                     val = rnorm(50))
# Wide format output (default)
corr_wide <- cor_long(cor_in, row, col, val)

# Long format output
corr_long <- cor_long(cor_in, row, col, val,
                      out_format = "long")

# Correlation between two matrices
cor_in2 <- data.frame(rows = rep(letters[1:10], each = 10),
                      cols = rep(letters[1:10], 10),
                      values = rnorm(100))
corr2 <- cor_long(cor_in, row, col, val,
                  cor_in2, rows, cols, values)

Get default colour scale for non-correlation heatmaps.

Description

Get default colour scale for non-correlation heatmaps.

Usage

default_col_scale(
  val_type,
  aes_type,
  leg_order = 1,
  title = ggplot2::waiver(),
  na_col = "grey50",
  bins = NULL,
  limits = NULL
)

Arguments

val_type

Value type ('continuous' or 'discrete').

aes_type

Aesthetic type ('fill', 'col' or 'size).

leg_order

Order of legend.

title

Legend title.

na_col

Colour of NA values.

bins

Number of bins in scale(s).

limits

Limits of scales.

Value

ggplot2 colour scale for non-correlation heatmaps.

Get a default colour scale for correlation heatmaps.

Description

Get a default colour scale for correlation heatmaps.

Usage

default_col_scale_corr(
  aes_type,
  bins = NULL,
  limits = c(-1, 1),
  high = "sienna2",
  mid = "white",
  low = "skyblue2",
  midpoint = 0,
  na_col = "grey50",
  leg_order = 1,
  title = ggplot2::waiver()
)

Arguments

aes_type

Type of aesthetic ('fill', 'col', or 'size').

bins

Number of bins (for fill and colour scales).

limits

Scale limits (fill and colour).

high

Colours at higher end of fill or colour scale.

mid

Colours at middle point of fill or colour scale.

low

Colours at lower end of fill or colour scale.

midpoint

Middle point of colour scale.

na_col

Colour of NAs.

leg_order

Order of legend.

title

Title of legend.

Value

ggplot2 scale for correlation heatmap.

Get default size scale for non-correlation heatmaps.

Description

Get default size scale for non-correlation heatmaps.

Usage

default_size_scale(val_type, leg_order = 1, title = ggplot2::waiver())

Arguments

val_type

Value type ('continuous' or 'discrete').

leg_order

Order of legend.

title

Legend title.

Value

ggplot2 size scale for non-correlation heatmaps.

Get a default size scale for correlation heatmaps.

Description

Get a default size scale for correlation heatmaps.

Usage

default_size_scale_corr(
  size_range = NULL,
  leg_order = 1,
  title = ggplot2::waiver()
)

Arguments

size_range

Numeric vector of length 1 or 2 for size limits.

leg_order

Order of legend.

title

Title of legend.

Value

ggplot2 size scale for correlation heatmap (absolute value transform).

Pick out relevant scales and format for mixed layout.

Description

Pick out relevant scales and format for mixed layout.

Usage

extract_scales(main_scales, scale_order, aes_type, layout)

Arguments

main_scales

Scales for main plot as obtained from prepare_scales.

scale_order

List with order of scales as obtained from make_legend_order.

aes_type

Aesthetic for which to pick out scales.

layout

Layout of heatmap.

Value

List of scales to use.

Calculate positions of annotations for heatmap.

Description

Calculate positions of annotations for heatmap.

Usage

get_annotation_pos(
  annot_side = TRUE,
  annot_names,
  annot_size,
  annot_dist,
  annot_gap,
  data_size
)

Arguments

annot_side

Logical specifying annotation position. TRUE is left of the heatmap if row annotation, bottom of heatmap if column annotation

annot_names

Names of the annotations.

annot_size

Size of annotation cells where 1 is the size of a heatmap cell.

annot_dist

Distance between heatmap and first annotation.

annot_gap

Size of gap between annotations.

data_size

Number of rows or columns in the main heatmap (which is symmetric). Used to get starting position of annotations.

Value

Numeric vector of annotation cell positions

Get a Brewer or Viridis colour scale.

Description

Get a Brewer or Viridis colour scale.

Usage

get_colour_scale(
  name,
  val_type,
  aes_type,
  limits = NULL,
  bins = NULL,
  leg_order = 1,
  title = ggplot2::waiver(),
  na_col = "grey50"
)

Arguments

name

Scale palette/option name.

val_type

Value type ('continuous' or 'discrete').

aes_type

Aesthetic type ('fill' or 'col').

limits

Limits for scale.

bins

Number of bins if binned scale.

leg_order

Order of legend.

title

Legend title.

na_col

Colour of NA cells.

Value

ggplot2 scale using Brewer or Viridis.

Colour scale dispenser.

Description

Colour scale dispenser.

Usage

get_default_annot_scale(num, type)

Arguments

num

Integer between 1 and 8.

type

String specifying data type (discrete or continuous).

Value

Brewer or Viridis ggplot2 scale name.

Make a correlation heatmap with ggplot2.

Description

Make a correlation heatmap from input matrices. Uses a diverging colour scale centered around 0.

Usage

ggcorrhm(
  x,
  y = NULL,
  cor_method = "pearson",
  cor_use = "everything",
  cor_in = FALSE,
  high = "sienna2",
  mid = "white",
  low = "skyblue2",
  midpoint = 0,
  limits = c(-1, 1),
  bins = NULL,
  layout = "full",
  mode = if (length(layout) == 1) "heatmap" else c("heatmap", "text"),
  include_diag = TRUE,
  na_col = "grey50",
  na_remove = FALSE,
  return_data = FALSE,
  col_scale = NULL,
  col_name = NULL,
  size_range = c(4, 10),
  size_scale = NULL,
  size_name = NULL,
  legend_order = NULL,
  p_values = FALSE,
  p_adjust = "none",
  p_thresholds = c(`***` = 0.001, `**` = 0.01, `*` = 0.05, 1),
  cell_labels = FALSE,
  cell_label_p = FALSE,
  cell_label_col = "black",
  cell_label_size = 3,
  cell_label_digits = 2,
  cell_bg_col = "white",
  cell_bg_alpha = 0,
  border_col = "grey",
  border_lwd = 0.1,
  border_lty = 1,
  show_names_diag = TRUE,
  names_diag_params = NULL,
  show_names_x = FALSE,
  names_x_side = "top",
  show_names_y = FALSE,
  names_y_side = "left",
  annot_rows_df = NULL,
  annot_cols_df = NULL,
  annot_rows_col = NULL,
  annot_cols_col = NULL,
  annot_rows_side = "right",
  annot_cols_side = "bottom",
  annot_dist = 0.2,
  annot_gap = 0,
  annot_size = 0.5,
  annot_border_col = if (length(border_col) == 1) border_col else "grey",
  annot_border_lwd = if (length(border_lwd) == 1) border_lwd else 0.5,
  annot_border_lty = if (length(border_lty) == 1) border_lty else 1,
  annot_na_col = na_col,
  annot_na_remove = na_remove,
  annot_rows_params = NULL,
  annot_cols_params = NULL,
  show_annot_names = TRUE,
  annot_names_size = 3,
  annot_rows_names_side = "bottom",
  annot_cols_names_side = "left",
  annot_rows_names_params = NULL,
  annot_cols_names_params = NULL,
  annot_rows_name_params = NULL,
  annot_cols_name_params = NULL,
  cluster_rows = FALSE,
  cluster_cols = FALSE,
  cluster_distance = "euclidean",
  cluster_method = "complete",
  show_dend_rows = TRUE,
  show_dend_cols = TRUE,
  dend_rows_side = "right",
  dend_cols_side = "bottom",
  dend_col = "black",
  dend_dist = 0,
  dend_height = 0.3,
  dend_lwd = 0.3,
  dend_lty = 1,
  dend_rows_params = NULL,
  dend_cols_params = NULL,
  dend_rows_extend = NULL,
  dend_cols_extend = NULL,
  split_rows = NULL,
  split_cols = NULL
)

Arguments

x

Matrix or data frame in wide format containing the columns to correlate against each other or against the columns in y.

y

Optional matrix or data frame in wide format containing columns to correlate with the columns in x.

cor_method

String specifying correlation method to use in the stats::cor() function. Default is 'pearson'.

cor_use

String specifying the use argument of stats::cor(), which defines how to deal with missing values. Default is 'everything'.

cor_in

Logical indicating if the input data contains correlation values and any correlation computations (including p-values) should be skipped. Default is FALSE.

high

Colour to use for the highest value of the colour scale.

mid

Colour to use for 0 in the colour scale.

low

Colour to use for the lowest value of the colour scale.

midpoint

Value for the middle point of the colour scale.

limits

Numeric vector of length two for the limits of the colour scale. NULL uses the default.

bins

Number of bins to divide the scale into (if continuous values). A 'double' class value uses 'nice.breaks' to put the breaks at nice numbers which may not result in the specified number of bins. If an integer the number of bins will be prioritised.

layout

String specifying the layout of the output heatmap. Possible layouts include 'topleft', 'topright', 'bottomleft', 'bottomright', or the 'whole'/'full' heatmap (default and only possible option if the matrix is asymmetric). A combination of the first letters of each word also works (i.e. f, w, tl, tr, bl, br). If layout is of length two with two opposing triangles, a mixed layout will be used. For mixed layouts, mode needs a vector of length two (applied in the same order as layout). See details of gghm() for more information.

mode

A string specifying plotting mode. Possible values are heatmap/hm for a normal heatmap, a number from 1 to 25 to draw the corresponding shape, text to write the cell values instead of filling cells (colour scaling with value), and none for blank cells.

include_diag

Logical indicating if the diagonal cells should be plotted (if the matrix is symmetric).

na_col

Colour to use for cells with NA (both main heatmap and annotation).

na_remove

Logical indicating if NA values in the heatmap should be omitted (meaning no cell border is drawn). This does not affect how NAs are handled in the correlation computations, use the cor_use argument for NA handling in correlation.

return_data

Logical indicating if the data used for plotting (i.e. the correlation values and, if computed, clustering and p-values) should be returned.

col_scale

Scale to use for cell colours. If NULL (default), a divergent scale is constructed from the high, mid, low, midpoint, limits, and bins arguments. These arguments are ignored if a ⁠ggplot2::scale_*⁠ function is provided instead. If a string, the corresponding Brewer or Viridis scale is used. A string with a scale name with "rev_" in the beginning or "_rev" at the end will result in the reversed scale. In mixed layouts, can also be a list of length two containing the two scales to use.

col_name

String to use for the correlation scale. If NULL (default) the text will depend on the correlation method. Can be two values in mixed layouts for dual scales.

size_range

Numeric vector of length 2, specifying lower and upper ranges of shape sizes. Ignored if size_scale is not NULL.

size_scale

⁠ggplot2::scale_size_*⁠ call to use for size scaling if mode is a number from 1 to 25 (R pch). The default behaviour (NULL) is to use a continuous scale with the absolute values of the correlation.

size_name

String to use for the size scale legend title. Can be two values in mixed layouts for dual scales.

legend_order

Integer vector specifying the order of legends (first value is for the first legend, second for the second, etc). The default (NULL) shows all but size legends. NAs hide the corresponding legends, a single NA hides all. Ignored for ggplot2 scale objects in col_scale and size_scale.

p_values

Logical indicating if p-values should be calculated. Use with p_thresholds to mark cells, and/or return_data to get the p-values in the output data.

p_adjust

String specifying the multiple testing adjustment method to use for the p-values (default is "none"). Passed to stats::p.adjust().

p_thresholds

cell_labels

Logical specifying if the cells should be labelled with the correlation values. Alternatively, a matrix or data frame with the same shape and dimnames as x containing values to write in the cells. If mode is text, the cell label colours will scale with the correlation values and cell_label_col is ignored.

cell_label_p

Logical indicating if, when cell_labels is TRUE, p-values should be written instead of correlation values.

cell_label_col

Colour to use for cell labels, passed to ggplot2::geom_text().

cell_label_size

Size of cell labels, used as the size argument in ggplot2::geom_text().

cell_label_digits

Number of digits to display when cells are labelled (if numeric values). Default is 2, passed to base::round(). NULL for no rounding.

cell_bg_col

Colour to use for cell backgrounds in modes 'text' and 'none'.

cell_bg_alpha

Alpha for cell colours in modes 'text' and 'none'.

border_col

Colour of cell borders. If mode is not a number, border_col can be set to NA to remove borders completely.

border_lwd

Size of cell borders. If mode is a number, border_col can be set to 0 to remove borders.

border_lty

Line type of cell borders. Either a number or its corresponding name, or a string of length 2, 4, 6, or 8. See 'lty' of graphics::par() for details. Not supported for numeric mode.

show_names_diag

Logical indicating if names should be written in the diagonal cells (for symmetric input).

names_diag_params

List with named parameters (such as size, angle, etc) passed on to geom_text when writing the column names in the diagonal.

show_names_x, show_names_y

Logical indicating if names should be written on the x and y axes. Labels can be customised using ggplot2::theme() on the output plot.

names_x_side

String specifying position of the x axis names ("top" or "bottom").

names_y_side

String specifying position of the y axis names ("left" or "right").

annot_rows_df, annot_cols_df

Data frame for row and column annotations. The names of the columns in the data must be included, either as row names or in a column named .names. Each other column specifies an annotation where the column name will be used as the annotation name (in the legend and next to the annotation). Numeric columns will use a continuous colour scale while factor or character columns use discrete scales.

annot_rows_col, annot_cols_col

Named list for row and column annotation colour scales. The names should specify which annotation each scale applies to. Elements can be strings or ggplot2 "Scale" class objects. If a string, it is used as the brewer palette or viridis option. If a scale object it is used as is, allowing more flexibility. This may change the order that legends are drawn in, specify order using the guide argument in the ggplot2 scale function.

annot_rows_side

String specifying which side row annotation should be drawn ('left' or 'right', defaults to 'left').

annot_cols_side

String specifying which side column annotation should be drawn ('bottom' or 'top', defaults to 'bottom').

annot_dist

Distance between heatmap and first annotation cell where 1 is the size of one heatmap cell. Used for both row and column annotation.

annot_gap

Distance between each annotation where 1 is the size of one heatmap cell. Used for both row and column annotation.

annot_size

Size (width for row annotation, height for column annotation) of annotation cells compared to a heatmap cell. Used for both row and column annotation.

annot_border_col

Colour of cell borders in annotation. By default it is the same as border_col of the main heatmap if it is of length 1, otherwise uses default (grey).

annot_border_lwd

Line width of cell borders in annotation. By default it is the same as border_lwd of the main heatmap if it is of length 1, otherwise uses default (0.5).

annot_border_lty

Line type of cell borders in annotation. By default it is the same as border_lty of the main heatmap if it is of length 1, otherwise uses default (solid).

annot_na_col

Colour to use for NA values in annotations. Annotation-specific colour can be set in the ggplot2 scales in the ⁠annot_*_fill⁠ arguments.

annot_na_remove

Logical indicating if NAs in the annotations should be removed (producing empty spaces).

annot_rows_params, annot_cols_params

Named list with parameters for row or column annotations to overwrite the defaults set by the ⁠annot_*⁠ arguments, each name corresponding to the * part (see details of gghm() for more information).

show_annot_names

Logical controlling if names of annotations should be shown in the drawing area.

annot_names_size

Size of annotation names.

annot_rows_names_side

String specifying which side the row annotation names should be on. Either "top" or "bottom".

annot_cols_names_side

String specifying which side the column annotation names should be on. Either "left" or "right".

annot_rows_names_params, annot_cols_names_params

Named list of parameters for row and column annotation names. Given to ggplot2::geom_text().

annot_rows_name_params, annot_cols_name_params

Deprecated and kept for backward compatibility. Named list of parameters given to grid::textGrob() for annotation names. Does not work well with heatmap splits.

cluster_rows, cluster_cols

Logical indicating if rows or columns should be clustered. Can also be hclust or dendrogram objects.

cluster_distance

String with the distance metric to use for clustering, given to stats::dist().

cluster_method

String with the clustering method to use, given to stats::hclust().

show_dend_rows, show_dend_cols

Logical indicating if a dendrogram should be drawn for the rows or columns.

dend_rows_side

Which side to draw the row dendrogram on ('left' or 'right', defaults to 'left').

dend_cols_side

Which side to draw the column dendrogram on ('bottom' or 'top', defaults to 'bottom').

dend_col

Colour to use for dendrogram lines, applied to both row and column dendrograms.

dend_dist

Distance from heatmap (or annotation) to leaves of dendrogram, measured in heatmap cells (1 is the size of one cell).

dend_height

Number by which to scale dendrogram height, applied to both row and column dendrograms.

dend_lwd

Linewidth of dendrogram lines, applied to both row and column dendrograms.

dend_lty

Dendrogram line type, applied to both row and column dendrograms.

dend_rows_params, dend_cols_params

Named list for row or column dendrogram parameters. See details of gghm() for more information.

dend_rows_extend, dend_cols_extend

Named list or functional sequence for specifying dendextend functions to apply to the row or column dendrogram. See details of gghm() and ggcorrhm() for usage.

split_rows, split_cols

Vectors for splitting the rows and columns into facets. Can be a numeric vector shorter than the number of rows/columns to split the heatmap after those indices, or a vector of the same length as the number of rows/columns containing the facet memberships. In the latter case names can be used to match with rows/columns. Alternatively, if clustering is applied a single numeric value is accepted for the number of clusters to divide the plot into.

Details

ggcorrhm() makes it convenient to make correlation heatmaps, taking the input matrix or data frame to visualise the correlations between columns with the gghm() function. The input values can either be one matrix or data frame with columns to correlate with each other, or two matrices or data frames with columns to correlate between the matrices. No rownames are needed, but if two matrices are provided they should have the same number of rows and the rows should be ordered in a meaningful way (i.e. same sample/individual/etc in the same row in both).

Row and column names are displayed in the diagonal by default if the correlation matrix is symmetric (only x is provided or x and y are identical).

The colour scale is set to be a diverging gradient around 0, with options to change the low, mid, and high colours, the midpoint, and the limits (using the arguments of the same names). The bins argument converts the scale to a discrete scale divided into bins equally distributed bins (if an integer the breaks may be at strange numbers, if a double the number of bins may be different but the breaks are at nicer numbers). These arguments can be of length two (limits a list of length two) two apply to each triangle in a mixed layout (detailed more in the details section of gghm()). The size_range argument (for size scales) can also be a list of length two like limits.

The size scale, used when a numeric cell shape is specified, is set to vary the shape size between 4 and 10 (can be changed with the size_range argument) and to transform the values to absolute values (so that both positive and negative correlations are treated equally). This behaviour can be overwritten by setting size_scale to another ⁠ggplot2::scale_size_*⁠ function with the desired arguments, or ggplot2::scale_size() for no special behaviour. ggplot2::scale_size_area() also scales with the absolute value, but only the upper size limit can be set. When the absolute value transformation is used the legend for sizes loses its meaning (only displaying positive values) and is therefore set to not be shown if legend_order is NULL.

For symmetric correlation matrices, the dendrogram customisation arguments dend_rows_extend and dend_cols_extend work best with functions that only change the dendrogram cosmetically such as the colours, linetypes or node shapes. While it is possible to reorder (using e.g. 'rotate', 'ladderize') or prune (using e.g. 'prune'), anything that changes the structure of the dendrogram may end up looking strange for symmetric matrices if only applied to one dimension (e.g. the diagonal may not be on the diagonal, triangular or mixed layouts may not work). The same applies if the cluster_rows and cluster_cols arguments are hclust or dendrogram objects.

Value

The correlation heatmap as a ggplot object. If return_data is TRUE the output is a list containing the plot (named 'plot'), the correlations ('plot_data', with factor columns 'row' and 'col' and a column 'value' containing the cell values), and the result of the clustering ('row_clustering' and 'col_clustering', if clustered). If p-values were calculated, two additional columns named 'p_val' and 'p_adj' are included in 'plot_data', containing nominal and adjusted p-values. If the layout is mixed, an extra factor column named 'layout' is included, showing which triangle each cell belongs to.

Examples

# Basic usage
ggcorrhm(mtcars)

# With two matrices
ggcorrhm(iris[1:32, -5], mtcars)

# Different layout
ggcorrhm(mtcars, layout = "br")

# With clustering
ggcorrhm(mtcars, layout = "tl", cluster_rows = TRUE, cluster_cols = TRUE)

# With annotation
set.seed(123)
annot <- data.frame(.names = colnames(mtcars),
                    annot1 = rnorm(ncol(mtcars)),
                    annot2 = sample(letters[1:3], ncol(mtcars), TRUE))
ggcorrhm(mtcars, layout = "tr", annot_cols_df = annot)

# Both
ggcorrhm(mtcars, layout = "full", cluster_rows = TRUE, cluster_cols = TRUE,
         annot_rows_df = annot[, -3], annot_cols_df = annot[, -2])

# Mixed layout
ggcorrhm(mtcars, layout = c("tl", "br"))

`ggcorrhm()` for long format data.

Description

ggcorrhm() for long format data.

Usage

ggcorrhm_tidy(
  x,
  rows,
  cols,
  values,
  annot_rows = NULL,
  annot_cols = NULL,
  labels = NULL,
  facet_rows = NULL,
  facet_cols = NULL,
  cor_in = TRUE,
  ...
)

Arguments

x

Data containing data to plot or to correlate.

rows, cols, values

Columns to use as rows, columns, and values in the plotted matrix (if cor_in is TRUE) or the matrix to compute correlations from (cor_in is FALSE).

annot_rows, annot_cols

Columns containing values for row and column annotations.

labels

Column to use for cell labels, NULL for no labels, or TRUE to use the cell values. If cor_in is FALSE, only NULL, TRUE or FALSE is supported.

facet_rows, facet_cols

Columns to use for row/column facets.

cor_in

Logical indicating if the values are correlation values (TRUE, default) or values to be correlated. See details for more information.

...

Additional arguments for ggcorrhm().

Details

If cor_in is TRUE (the default), ggcorrhm_tidy() behaves similarly to gghm_tidy() but with the colour scales and arguments of ggcorrhm() instead of gghm().

If cor_in FALSE, the data is converted to wide format and the column-column correlations are computed. This means that if asymmetric correlation matrices are to be plotted the correlations have to be computed in advance and plotted with cor_in as TRUE. Additionally, annot_rows and annot_cols will both use the cols column for names, and labels can only take TRUE or FALSE.

On the other hand, if cor_in is TRUE any computation of correlations is skipped, meaning that p-values cannot be computed and would have to be generated in advance and passed as cell labels.

Value

A ggplot2 object with the heatmap. If return_data is TRUE, plotting data is returned as well.

Examples

library(dplyr)
# Basic example with long format correlation data
# Make some correlation data in long format
cor_dat <- cor(mtcars)
hm_in <- data.frame(row = rep(colnames(cor_dat), ncol(cor_dat)),
                    col = rep(colnames(cor_dat), each = ncol(cor_dat)),
                    val = as.vector(cor_dat))

ggcorrhm_tidy(hm_in, row, col, val,
              # Indicate that the data consists of correlation coefficients
              cor_in = TRUE)

# Or let the function compute the correlations
# (this limits some other functionality, see details)
raw_dat <- data.frame(row = rep(rownames(mtcars), ncol(mtcars)),
                      col = rep(colnames(mtcars), each = nrow(mtcars)),
                      val = unlist(mtcars))
ggcorrhm_tidy(raw_dat, row, col, val, cor_in = FALSE)

Make a heatmap with ggplot2.

Description

Make a heatmap with ggplot2.

Usage

gghm(
  x,
  layout = "full",
  mode = if (length(layout) == 1) "heatmap" else c("heatmap", "text"),
  scale_data = NULL,
  col_scale = NULL,
  col_name = "value",
  limits = NULL,
  bins = NULL,
  size_scale = NULL,
  size_name = "value",
  legend_order = NULL,
  include_diag = TRUE,
  show_names_diag = FALSE,
  names_diag_params = NULL,
  show_names_x = TRUE,
  names_x_side = "top",
  show_names_y = TRUE,
  names_y_side = "left",
  na_col = "grey50",
  na_remove = FALSE,
  return_data = FALSE,
  cell_labels = FALSE,
  cell_label_col = "black",
  cell_label_size = 3,
  cell_label_digits = 2,
  border_col = "grey",
  border_lwd = 0.1,
  border_lty = 1,
  cell_bg_col = "white",
  cell_bg_alpha = 0,
  annot_rows_df = NULL,
  annot_cols_df = NULL,
  annot_rows_col = NULL,
  annot_cols_col = NULL,
  annot_rows_side = "right",
  annot_cols_side = "bottom",
  annot_dist = 0.2,
  annot_gap = 0,
  annot_size = 0.5,
  annot_border_col = if (length(border_col) == 1) border_col else "grey",
  annot_border_lwd = if (length(border_lwd) == 1) border_lwd else 0.5,
  annot_border_lty = if (length(border_lty) == 1) border_lty else 1,
  annot_na_col = na_col,
  annot_na_remove = na_remove,
  annot_rows_params = NULL,
  annot_cols_params = NULL,
  show_annot_names = TRUE,
  annot_names_size = 3,
  annot_rows_names_side = "bottom",
  annot_cols_names_side = "left",
  annot_rows_names_params = NULL,
  annot_cols_names_params = NULL,
  annot_rows_name_params = NULL,
  annot_cols_name_params = NULL,
  cluster_rows = FALSE,
  cluster_cols = FALSE,
  cluster_distance = "euclidean",
  cluster_method = "complete",
  show_dend_rows = TRUE,
  show_dend_cols = TRUE,
  dend_rows_side = "right",
  dend_cols_side = "bottom",
  dend_col = "black",
  dend_dist = 0,
  dend_height = 0.3,
  dend_lwd = 0.3,
  dend_lty = 1,
  dend_rows_params = NULL,
  dend_cols_params = NULL,
  dend_rows_extend = NULL,
  dend_cols_extend = NULL,
  split_rows = NULL,
  split_cols = NULL,
  split_rows_side = "right",
  split_cols_side = "bottom"
)

Arguments

x

Matrix or data frame in wide format to make a heatmap of. If rownames are present they are used for the y axis labels, otherwise the row number is used. If a column named .names (containing unique row identifiers) is present it will be used as rownames.

layout

mode

scale_data

Character string specifying scaling of the matrix. NULL or "none" for no scaling, "rows" for rows, and "columns" for columns. Can also be a substring of the beginning of the words.

col_scale

Colour scale to use for cells. If NULL, the default ggplot2 scale is used. If a string, the corresponding Brewer or Viridis scale is used. A string with a scale name with "rev_" in the beginning or "_rev" at the end will result in the reversed scale. Can also be a ggplot2 scale object to overwrite the scale. In mixed layouts, a list of two scales can be provided.

col_name

String to use for the colour scale legend title. Can be two values in mixed layouts for dual scales.

limits

Numeric vector of length two for the limits of the colour scale. NULL uses the default.

bins

size_scale

⁠ggplot2::scale_size_*⁠ call to use for size scaling if mode is a number from 1 to 25 (R pch). In mixed layouts, can also be a list of length two containing the two scales to use.

size_name

String to use for the size scale legend title. Can be two values in mixed layouts for dual scales.

legend_order

Integer vector specifying the order of legends (first value is for the first legend, second for the second, etc). The default (NULL) shows all legends. NAs hide the corresponding legends, a single NA hides all. Ignored for ggplot2 scale objects in col_scale and size_scale.

include_diag

Logical indicating if the diagonal cells (of a symmetric matrix) should be plotted. Mostly only useful for getting a cleaner look with symmetric correlation matrices with triangular layouts, where the diagonal is known to be 1.

show_names_diag

Logical indicating if names should be written in the diagonal cells (for symmetric input).

names_diag_params

List with named parameters (such as size, angle, etc) passed on to geom_text when writing the column names in the diagonal.

show_names_x, show_names_y

Logical indicating if names should be written on the x and y axes. Labels can be customised using ggplot2::theme() on the output plot.

names_x_side

String specifying position of the x axis names ("top" or "bottom").

names_y_side

String specifying position of the y axis names ("left" or "right").

na_col

Colour to use for cells with NA (both main heatmap and annotation).

na_remove

Logical indicating if NA values in the heatmap should be omitted (meaning no cell border is drawn). If NAs are kept, the fill colour can be set in the ggplot2 scale.

return_data

Logical indicating if the data used for plotting and clustering results should be returned.

cell_labels

Logical specifying if the cells should be labelled with the values. Alternatively, a matrix or data frame with the same shape and dimnames as x containing values to write in the cells. If mode is text, the cell label colours will scale with the cell values and cell_label_col is ignored.

cell_label_col

Colour to use for cell labels, passed to ggplot2::geom_text().

cell_label_size

Size of cell labels, used as the size argument in ggplot2::geom_text().

cell_label_digits

Number of digits to display when cells are labelled (if numeric values). Default is 2, passed to base::round(). NULL for no rounding.

border_col

Colour of cell borders. If mode is not a number, border_col can be set to NA to remove borders completely.

border_lwd

Size of cell borders. If mode is a number, border_col can be set to 0 to remove borders.

border_lty

Line type of cell borders. Either a number or its corresponding name, or a string of length 2, 4, 6, or 8. See 'lty' of graphics::par() for details. Not supported for numeric mode.

cell_bg_col

Colour to use for cell backgrounds in modes 'text' and 'none'.

cell_bg_alpha

Alpha for cell colours in modes 'text' and 'none'.

annot_rows_df, annot_cols_df

annot_rows_col, annot_cols_col

annot_rows_side

String specifying which side row annotation should be drawn ('left' or 'right', defaults to 'left').

annot_cols_side

String specifying which side column annotation should be drawn ('bottom' or 'top', defaults to 'bottom').

annot_dist

Distance between heatmap and first annotation cell where 1 is the size of one heatmap cell. Used for both row and column annotation.

annot_gap

Distance between each annotation where 1 is the size of one heatmap cell. Used for both row and column annotation.

annot_size

Size (width for row annotation, height for column annotation) of annotation cells compared to a heatmap cell. Used for both row and column annotation.

annot_border_col

Colour of cell borders in annotation. By default it is the same as border_col of the main heatmap if it is of length 1, otherwise uses default (grey).

annot_border_lwd

Line width of cell borders in annotation. By default it is the same as border_lwd of the main heatmap if it is of length 1, otherwise uses default (0.5).

annot_border_lty

Line type of cell borders in annotation. By default it is the same as border_lty of the main heatmap if it is of length 1, otherwise uses default (solid).

annot_na_col

Colour to use for NA values in annotations. Annotation-specific colour can be set in the ggplot2 scales in the ⁠annot_*_fill⁠ arguments.

annot_na_remove

Logical indicating if NAs in the annotations should be removed (producing empty spaces).

annot_rows_params, annot_cols_params

Named list with parameters for row and column annotations to overwrite the defaults set by the ⁠annot_*⁠ arguments, each name corresponding to the * part (see details for more information).

show_annot_names

Logical controlling if names of annotations should be shown in the drawing area.

annot_names_size

Size of annotation names.

annot_rows_names_side

String specifying which side the row annotation names should be on. Either "top" or "bottom".

annot_cols_names_side

String specifying which side the column annotation names should be on. Either "left" or "right".

annot_rows_names_params, annot_cols_names_params

Named list of parameters for row and column annotation names. Given to ggplot2::geom_text().

annot_rows_name_params, annot_cols_name_params

Deprecated and kept for backward compatibility. Named list of parameters given to grid::textGrob() for annotation names. Does not work well with heatmap splits.

cluster_rows, cluster_cols

Logical indicating if rows or columns should be clustered. Can also be hclust or dendrogram objects.

cluster_distance

String with the distance metric to use for clustering, given to stats::dist().

cluster_method

String with the clustering method to use, given to stats::hclust().

show_dend_rows, show_dend_cols

Logical indicating if a dendrogram should be drawn for the rows or columns.

dend_rows_side

Which side to draw the row dendrogram on ('left' or 'right', defaults to 'left').

dend_cols_side

Which side to draw the column dendrogram on ('bottom' or 'top', defaults to 'bottom').

dend_col

Colour to use for dendrogram lines, applied to both row and column dendrograms.

dend_dist

Distance from heatmap (or annotation) to leaves of dendrogram, measured in heatmap cells (1 is the size of one cell).

dend_height

Number by which to scale dendrogram height, applied to both row and column dendrograms.

dend_lwd

Linewidth of dendrogram lines, applied to both row and column dendrograms.

dend_lty

Dendrogram line type, applied to both row and column dendrograms.

dend_rows_params, dend_cols_params

Named list for row or column dendrogram parameters to overwrite common parameter values. See details for more information.

dend_rows_extend, dend_cols_extend

Named list or functional sequence for specifying dendextend functions to apply to the row or column dendrogram. See details for usage.

split_rows, split_cols

split_rows_side, split_cols_side

Which side the row/column facet strips should be drawn on ('left'/'right', 'top'/'bottom').

Details

When using mixed layouts (layout is length two), mode needs to be length two as well, specifying the mode to use in each triangle. The ⁠cell_label_*⁠ and ⁠border_*⁠ arguments can all be length one to apply to the whole heatmap, length two vectors to apply to each triangle, or lists of length two, each element containing one value (apply to whole triangle) or a value per cell (apply cell-wise in triangle). cell_labels can also be specified per triangle, either as a logical vector of length two, or a list of length two containing a mix of logicals and matrices/data frames.

It is also possible to provide two scales for filling or colouring the triangles differently. In this case the col_scale must be one character value (scale used for both triangles) or NULL or a list of length two containing the scales to use (character or scale object, or NULL for default). size_scale works in the same way (but takes no character values). In addition, the scale-modifying arguments bins, na_col and limits can also be specified per triangle. limits must be a list of length two (or one) where each element is a numeric vector of length two.

The annotation parameter arguments annot_rows_params and annot_cols_params should be named lists, where the possible options correspond to the different ⁠annot_*⁠ arguments. The possible options are "dist" (distance between heatmap and annotation), "gap" (distance between annotations), "size" (cell size), "show_names" (logical, if the annotation names should be displayed), "border_col" (colour of border) and "border_lwd" (border line width). Any unused options will use the defaults set by the ⁠annot_*⁠ arguments.

The dendrogram parameters arguments dend_rows_params and dend_cols_params should be named lists, analogous to the annotation parameter arguments. Possible options are "col" (line colour), "dist" (distance from heatmap to dendrogram), "height" (height scaling), "lwd" (line width), and "lty" (line type).

The dend_rows_extend and dend_cols_extend arguments make it possible to customise the dendrograms using the dendextend package. The argument should be a named list, each element named after the dendextend function to use (consecutive usage of the set function is supported due to duplicate list names being possible). Each element should contain any arguments given to the dendextend function, such as the what argument used in the set function. Alternatively, dendextend functions can be provided in a functional sequence ("fseq" object) by piping together functions using the ⁠%>%⁠ pipe. Functions modifying the labels do not work as the dendrogram labels are not displayed (they are in the axis text). As dendextend::as.ggdend() is used for conversion of the dendrogram, anything not supported by as.ggdend() will not work (such as "nodes_bg" or "rect.dendrogram"). See examples and the clustering article for example usage.

Value

The heatmap as a ggplot object. If return_data is TRUE the output is a list containing the plot (named 'plot'), the plotting data ('plot_data', with factor columns 'row' and 'col' and a column 'value' containing the cell values), and the result of the clustering ('row_clustering' and/or 'col_clustering). If the layout is mixed, an extra factor column named 'layout' is included in 'plot_data', showing which triangle each cell belongs to.

Examples

library(ggplot2)

# Use part of the mtcars data (for visibility)
hm_in <- mtcars[1:15, ]

# Basic usage
gghm(hm_in)

# Different layout (using a symmetric matrix)
gghm(cor(mtcars), layout = "tl")

# Mixed layouts
gghm(cor(mtcars), layout = c("tr", "bl"),
     # Hide one of the legends
     legend_order = c(1, NA))

# With clustering
gghm(scale(hm_in), cluster_rows = TRUE, cluster_cols = TRUE)

# Adjusting cluster dendrograms using common and specific options
gghm(scale(hm_in), cluster_rows = TRUE, cluster_cols = TRUE,
     # Common options
     dend_lwd = 0.7, dend_col = "magenta",
     # Specific options
     dend_rows_params = list(height = 1), dend_cols_params = list(lty = 2))

# With annotation and specifying colour scales
set.seed(123)
annot_rows <- data.frame(.names = rownames(hm_in),
                         annot1 = rnorm(nrow(hm_in)),
                         annot2 = sample(letters[1:3], nrow(hm_in), TRUE))
# Specify colour scale for one of the annotations (viridis mako)
annot_fill <- list(annot1 = "G")

gghm(scale(hm_in),
     # Change colours of heatmap (Brewer Purples)
     col_scale = "Purples",
     annot_rows_df = annot_rows, annot_rows_col = annot_fill) +
     # Use ggplot2::theme to adjust margins to fit the annotation names
     theme(plot.margin = margin(30, 10, 60, 20))

# Using the dend_*_extend arguments
gghm(scale(hm_in), cluster_rows = TRUE, dend_rows_extend =
  list("set" = list("branches_lty", c(1, 2, 3)),
       # Empty list element (or NULL) if no arguments to be given
       "highlight_branches_col" = list()))

`gghm()` for long format data.

Description

gghm() for long format data.

Usage

gghm_tidy(
  x,
  rows,
  cols,
  values,
  labels = NULL,
  annot_rows = NULL,
  annot_cols = NULL,
  facet_rows = NULL,
  facet_cols = NULL,
  ...
)

Arguments

x

Data frame containing data to plot.

rows, cols, values

Columns to use as rows, columns, and cell values.

labels

Column to use for cell labels. NULL (default) for no labels.

annot_rows, annot_cols

Columns to use for row and column annotations.

facet_rows, facet_cols

Columns to use for row/column facet memberships.

...

Additional arguments for gghm().

Value

A ggplot2 object with the heatmap. If return_data is TRUE, plotting data is returned as well.

Examples

# Basic example
set.seed(123)
hm_in <- data.frame(row = rep(letters[1:10], each = 5),
                    col = rep(LETTERS[1:5], 10),
                    val = rnorm(50))
gghm_tidy(hm_in, row, col, val)

# Annotation and clustering
# Add annotation by giving names of columns in the data
hm_in$row_annot1 <- rep(1:10, each = 5)
hm_in$row_annot2 <- rep(10:1, each = 5)
hm_in$col_annot <- rep(letters[1:5], 10)
# Columns are given using 'tidy' selection
# so they can be unquoted, quoted, from variables (with !! notation) or indices
gghm_tidy(hm_in, row, col, val,
          annot_rows = c(row_annot1, row_annot2),
          annot_cols = col_annot,
          cluster_rows = TRUE,
          cluster_cols = TRUE)

# Add cell labels
hm_in$lab <- 1:50
gghm_tidy(hm_in, row, col, val,
          labels = lab, cell_label_col = "white")

Increment between 1 and 8.

Description

Increment between 1 and 8.

Usage

increment1to8(x)

Arguments

x

Integer to increment.

Value

Integer. x + 1 if x is between 1 and 7, 1 otherwise.

Layout heatmap data for plotting

Description

Layout heatmap data for plotting

Usage

layout_hm(x, layout = "f", na_remove = FALSE)

Arguments

x

Matrix to plot.

layout

Layout (full, triangular (topleft, topright, bottomleft, bottomright)).

na_remove

Logical indicating if NAs should be removed.

Value

Long format data for plotting.

Make vector for facetting

Description

Make vector for facetting

Usage

make_facet_vector(facet_in, len)

Arguments

facet_in

User input for facetting (split_rows, split_cols).

len

Length of output vector.

Value

Vector of facet memberships.

Make main heatmap part of plot for gghm.

Description

Make main heatmap part of plot for gghm.

Usage

make_heatmap(
  x_long,
  plt = NULL,
  mode = "heatmap",
  include_diag = TRUE,
  invisible_diag = FALSE,
  border_lwd = 0.1,
  border_col = "grey",
  border_lty = 1,
  show_names_diag = TRUE,
  show_names_x = FALSE,
  show_names_y = FALSE,
  names_x_side = "top",
  names_y_side = "left",
  col_scale = NULL,
  size_scale = NULL,
  cell_labels = FALSE,
  cell_label_col = "black",
  cell_label_size = 3,
  cell_label_digits = 2,
  cell_bg_col = "white",
  cell_bg_alpha = 0,
  split_rows_names = FALSE,
  split_cols_names = FALSE,
  split_rows_side = "right",
  split_cols_side = "bottom"
)

Arguments

x_long

Long format data.

plt

A ggplot object to build onto. If NULL, makes a new plot.

mode

Plotting mode.

include_diag

Logical indicating if diagonal should be included.

invisible_diag

Logical indicating if an invisible diagonal should be included.

border_lwd

Border linewidth.

border_col

Border colour.

border_lty

Border linetype.

show_names_diag

Logical indicating if names should be displayed on the diagonal.

show_names_x

Logical indicating if names should be displayed on the x axis.

show_names_y

Logical indicating if names should be displayed on the y axis.

names_x_side

X axis side.

names_y_side

Y axis side.

col_scale

Scale for colour/fill aesthetic.

size_scale

Scale for size aesthetic.

cell_labels

Data frame of text to write on cells (processed by check_cell_labels).

cell_label_col

Colour of cell labels.

cell_label_size

Size of cell labels.

cell_label_digits

Number of digits for cell labels if numeric.

cell_bg_col

Cell background colour (fill).

cell_bg_alpha

Cell background alpha.

split_rows_names, split_cols_names

Logicals indicating if the facet names should be shown (if plot is built from scratch).

split_rows_side, split_cols_side

Sides to put the facet strips.

Value

ggplot object with heatmap component.

Make legend order depending on what the plot will contain.

Description

Make legend order depending on what the plot will contain.

Usage

make_legend_order(
  mode,
  col_scale = NULL,
  size_scale = NULL,
  annot_rows_df = NULL,
  annot_cols_df = NULL,
  bins = NULL,
  limits = NULL,
  high = NULL,
  mid = NULL,
  low = NULL,
  na_col = "grey50",
  midpoint = 0,
  size_range = NULL,
  legend_order = NULL
)

Arguments

mode

Plotting modes.

col_scale

One or two colour scales (shared for fill and colour). NULL for default, string for Brewer or Viridis, or a scale.

size_scale

Size scales (NULL or ggplot2 scales).

annot_rows_df

Annotation data frame for rows.

annot_cols_df

Annotation data frame for columns.

bins

Numeric for number of bins to determine if multiple scales are needed (if multiple bins values).

limits

Limits of scale (list of limits if two scales).

high

Colours at high values (correlation heatmap).

mid

Colours at medium values (correlation heatmap).

low

Colours at low values (correlation heatmap).

na_col

Colour if NA.

midpoint

Midpoint of divergent scale (correlation heatmap).

size_range

Size range (list of ranges if two scales).

legend_order

Numeric vector with legend order. NULL for default.

Value

A list with aesthetics for the main plot and orders of all legends.

Move coordinates of dendrogram to edges of heatmap

Description

Move coordinates of dendrogram by calculating distance it has to move to end up at the desired edges of the heatmap

Usage

move_dendrogram(
  dend_seg,
  x_long,
  context = c("rows", "cols"),
  dend_side,
  dend_dist,
  annot_df,
  annot_side,
  annot_pos,
  annot_size
)

Arguments

dend_seg

Data frame containing dendrogram segments, attained from dendextend::as.ggdend()

x_long

Long format data frame with the values

context

Character specifying whether the dendrogram is linked to rows or columns in the heatmap

dend_side

Logical specifying dendrogram position. TRUE is left of the heatmap if row dendrogram, bottom of heatmap if column dendrogram

dend_dist

Distance from heatmap (or annotation) to dendrogram in cell size.

annot_df

Data frame with annotations for checking that annotations exist as well as their size

annot_side

Logical specifying annotation position, analogous to dend_side

annot_pos

Numeric vector of annotation coordinates (x coordinates for row annotations, y for column annotations)

annot_size

Numeric of length 1, the specified size (width or height) of annotation cells

Value

Data frame with updated dendrogram coordinates

Orient a dendrogram.

Description

Orient a dendrogram.

Usage

orient_dendrogram(dend, dim = c("rows", "cols"), full_plt, layout, dend_side)

Arguments

dend

Dendrogram segments or nodes data frame (containing x, y, xend, yend).

dim

String, rows or cols to know which dimensions dendrogram should be on.

full_plt

Logical indicating if it's for the full layout.

layout

The heatmap layout to take mixed layout into account.

dend_side

Logical indicating if the dendrogram should be placed on the left (if row dend) or bottom (if col dend).

Value

The input dendrogram data frame but rotated and mirrored to fit the plot.

Prepare annotation parameters and positions

Description

Prepare annotation parameters and positions

Usage

prepare_annotation(
  annot_df,
  annot_defaults,
  annot_params,
  annot_side,
  context = c("rows", "cols"),
  annot_names_size,
  annot_name_params,
  annot_names_side,
  data_size,
  x_long,
  annot_names_strategy = "geom"
)

Arguments

annot_df

Annotation data frame. Should contain the rownames or a column called '.names' with names, other columns are used for annotation

annot_defaults

Default parameters for annotation.

annot_params

Provided annotation parameters to update.

annot_side

String for annotation side.

context

String stating the context ("rows" or "cols").

annot_names_size

Size of annotation names.

annot_name_params

Annotation label (names next to annotations) parameters to update.

annot_names_side

Annotation label side.

data_size

Size of data (ncol if row annotations, nrow if column annotations).

x_long

Long format plotting data, to see if there are any facets to take into account.

annot_names_strategy

String stating how to draw names (geom, grid). To deal with deprecated argument.

Value

List with updated annotation parameters, calculated annotation positions, and updated annotation label parameters.

Prepare cell labels in ggcorrhm to pass to gghm

Description

Prepare cell labels in ggcorrhm to pass to gghm

Usage

prepare_cell_labels(
  mode,
  cell_labels,
  p_values,
  cell_label_p,
  cell_label_digits,
  p_thresholds = NULL,
  cor_mat_dat = NULL
)

Arguments

mode

Plotting mode.

cell_labels

Cell labels (TRUE, FALSE, matrix, data frame).

p_values

Logical indicating if p-values should be computed.

cell_label_p

Logical indicating if cell labels should be swapped for p-values.

cell_label_digits

Number of digits to display for cell labels.

p_thresholds

P-value thresholds.

cor_mat_dat

Correlation long format data from correlation tests.

Value

Object to use as cell_labels in gghm (containing a logical, a matrix/data frame, or a list of length 2 with those things).

Prepare dendrogram by transforming dendrogram segments.

Description

Prepare dendrogram by transforming dendrogram segments.

Usage

prepare_dendrogram(
  dendro_in,
  context = c("rows", "cols"),
  dend_side,
  dend_defaults,
  dend_params,
  full_plt,
  layout,
  x_long,
  annot_df,
  annot_side,
  annot_pos,
  annot_size
)

Arguments

dendro_in

Dendrogram object generated by some_matrix |> dist() |> hclust() |> as.dendrogram() |> dendextend::as.ggdend().

context

Dimension the dendrogram will be plotted against (rows or columns).

dend_side

String for dendrogram side.

dend_defaults

List with dendrogram default parameters.

dend_params

List with dendrogram parameters to overwrite defaults.

full_plt

Logical indicating if the whole heatmap is plotted or not.

layout

The heatmap layout (for reordering rows).

x_long

Data frame containing the values that will be plotted in the heatmap.

annot_df

Data frame containing annotations.

annot_side

Logical specifying which side the annotation will be drawn, analogous to 'dend_down' or 'dend_left' (use the one in the same dimension as the dendrogram).

annot_pos

Vector of the annotation positions along the opposite dimension.

annot_size

Size of annotation cells, specified in heatmap cells (1 being the size of one cell).

Value

Data frame with dendrogram segment and node parameters.

Prepare facetting columns in the plotting data.

Description

Prepare facetting columns in the plotting data.

Usage

prepare_facets(
  x_long,
  x,
  facet_in,
  layout,
  context = c("row", "col"),
  dendro = NULL
)

Arguments

x_long

Long format plotting data.

x

Wide format plotting data.

facet_in

Facetting user input (vector or data frame).

layout

Plot layout vector.

context

Context of facetting (row or col).

dendro

List containing clustering results (or NULL if no clustering).

Value

Long format plotting data with facetting column added.

Prepare facets for gghm_tidy

Description

Prepare facets for gghm_tidy

Usage

prepare_facets_tidy(x, id_col, facet_col, params, context = c("row", "column"))

Arguments

x

Input long format data frame.

id_col

Column containing IDs (rows or column names).

facet_col

Column containing facet memberships.

params

Input arguments for gghm (passed to ...).

context

Context for facets (row or column).

Value

Vector containing facet membersips.

Prepare parameters for mixed layouts.

Description

Prepare parameters for mixed layouts.

Usage

prepare_mixed_param(param, param_name)

Arguments

param

Parameter to prepare.

param_name

Parameter name (for error messages and handling special parameter).

Value

If length one, it is returned duplicated in a list for use in each triangle. If longer than 1 an error message is returned. In other cases, the input parameter is returned (length two input).

Prepare scales for heatmap.

Description

Prepare scales for heatmap.

Usage

prepare_scales(
  scale_order,
  context = c("gghm", "ggcorrhm"),
  layout,
  val_type,
  col_scale = NULL,
  col_name = "value",
  size_scale = NULL,
  size_name = "value",
  bins = NULL,
  limits = c(-1, 1),
  high = "sienna2",
  mid = "white",
  low = "skyblue2",
  midpoint = 0,
  size_range = NULL,
  na_col = "grey50"
)

Arguments

scale_order

List of necessary scales and their orders, as obtained make_legend_order.

context

Scale context (gghm or ggcorrhm) for deciding which defaults to use.

layout

Layout of plot to treat parameters depending on length.

val_type

String with type of value ('continuous' or 'discrete').

col_scale

Colour scales input.

col_name

Colour scale names.

size_scale

Size scales input.

size_name

Size scale names.

bins

Number of bins to divide scale into (only for ggcorrhm).

limits

Scale limits (for ggcorrhm).

high

Colour at higher end of scale (for ggcorrhm).

mid

Colour at middle point of scale (for ggcorrhm).

low

Colour at Lower end of scale (for ggcorrhm).

midpoint

Middle point of scale (for ggcorrhm).

size_range

Size range for size scale (for ggcorrhm).

na_col

Colour to use for NAs (for ggcorrhm).

Value

ggplot2 scales for the plot.

Prepare default colour scales for annotation.

Description

Prepares a brewer palette or viridis option for all annotations that don't have any colour scale specified by the user. There are eight options each for brewer (categorical) and viridis (continuous) and they are selected sequentially, going back to the beginning if there are more than eight annotations of each kind.

Usage

prepare_scales_annot(
  scale_order,
  annot_rows_df = NULL,
  annot_cols_df = NULL,
  annot_rows_col = NULL,
  annot_cols_col = NULL,
  na_col = "grey50"
)

Arguments

scale_order

List containing orders of scales as obtained from make_legend_order.

annot_rows_df

Data frame with annotation for rows.

annot_cols_df

Data frame with annotation for columns.

annot_rows_col

List with colour scales for rows.

annot_cols_col

List with colour scales for columns.

na_col

Colour of NA cells.

Value

List of length two containing lists of row annotation and column annotation.

Process dendrogram with customisation options

Description

Process dendrogram with customisation options

Usage

process_dendrogram(mat, dendro, dend_options)

Arguments

mat

Data that was used for clustering.

dendro

Dendrogram object.

dend_options

Dendrogram extension options (list or fseq or NULL).

Value

Processed dendrogram object.

Remove duplicate scales.

Description

If a mixed layout uses the same aesthetic for both triangles and only one (or no) colour or size scale has been specified, remove redundant scales.

Usage

remove_duplicate_scales(
  scale_vec,
  col_scale = NULL,
  size_scale = NULL,
  bins,
  limits,
  high,
  mid,
  low,
  na_col,
  midpoint,
  size_range
)

Arguments

scale_vec

Vector of scale aesthetics.

col_scale

Input colour scales (NULL, string or scale object).

size_scale

Input size scales.

bins

Numeric for number of bins to determine if multiple scales are needed (if multiple bins values).

limits

Limits of scale (list of limits if two scales).

high

Colours at high values (correlation heatmap).

mid

Colours at medium values (correlation heatmap).

low

Colours at low values (correlation heatmap).

na_col

Colour if NA.

midpoint

Midpoint of divergent scale (correlation heatmap).

size_range

Size range (list of ranges if two scales).

Value

Vector of aesthetics with duplicates removed if appropriate.

Remove triangle from symmetric matrix and return long format data.

Description

Remove triangle from symmetric matrix and return long format data.

Usage

remove_triangle(x, tri_remove = "upper", na_remove = FALSE)

Arguments

x

Matrix to remove triangle from (and make long).

tri_remove

Triangle to remove.

na_remove

If NAs should be removed.

Value

Matrix in long format with triangle removed.

Replace default elements in a named list with corresponding elements in a new list.

Description

Replace default elements in a named list with corresponding elements in a new list.

Usage

replace_default(
  default_param,
  new_param,
  add_new = FALSE,
  warning_context = NULL
)

Arguments

default_param

Named list with elements to potentially replace ("defaults").

new_param

Named list with elements to replace with.

add_new

Logical, if TRUE elements with names unique to new_param will be added to the output.

warning_context

String to add to the beginning of warning message if any unsupported parameters are detected (if add_new is FALSE). Default (NULL) produces no warning.

Value

A named list where overlapping elements with overlapping names are replaced.

Scale height of dendrogram.

Description

Scale height of dendrogram.

Usage

scale_dendrogram(dend_seg, context = c("rows", "cols"), dend_side, dend_height)

Arguments

dend_seg

Data frame containing dendrogram segments in format obtained from dendextend.

context

Dimension to draw dendrogram along (rows or columns).

dend_side

Logical indicating which side to draw dendrogram on. If row dendrogram TRUE is left. If column dendrogram TRUE is down.

dend_height

Scaling parameter for dendrogram height (1 is no scaling).

Value

Data frame containing coordinates for dendrogram segments (and any colour, linewidth, line type parameters)

Scale data rows or columns.

Description

Scale data rows or columns.

Usage

scale_mat(x, scl = NULL)

Arguments

x

Matrix to scale.

scl

String of dimension to scale ("row", "column", "none" (or NULL), or a substring of the beginning).

Value

Scaled (or not scaled) matrix.

Convert a matrix to long format using row names and column names.

Description

Convert a matrix to long format using row names and column names.

Usage

shape_mat_long(x, unique_pairs = FALSE, na_remove = FALSE)

Arguments

x

Matrix to convert to long format.

unique_pairs

Whether only unique combinations should be included in the output (for symmetric matrices).

na_remove

Logical indicating if NAs should be excluded (removes NaNs too).

Value

A data frame with the columns 'row', 'col' (indicating combinations), and 'value'.

Convert long format matrix to wide.

Description

Convert long format matrix to wide.

Usage

shape_mat_wide(x)

Arguments

x

Long format matrix as obtained from 'shape_mat_long' (contains columns named 'row', 'col', and 'value').

Value

Wide format version of x.

Calculate correlations and p-values between columns.

Description

Calculate correlations and p-values between columns.

Usage

test_cor(
  x,
  y = NULL,
  method = "pearson",
  use = "everything",
  p_adj_method = "none"
)

Arguments

x

Matrix or data frame with columns to correlate.

y

Matrix or data frame, if provided will be correlated with x.

method

Passed to stats::cor.

use

Passed to stats::cor.

p_adj_method

P-value adjustment method, passed to stats::p.adjust.

Value

Data frame in long format with correlation values and nominal and adjusted p-values.

ggcorrheatmap: Make Flexible 'ggplot2' Correlation Heatmaps

Description

Author(s)

See Also

Add annotations to ggplot heatmap

Description

Usage

Arguments

Value

Add dendrogram to ggplot object.

Description

Usage

Arguments

Value

Add diagonal names to heatmap.

Description

Usage

Arguments

Value

Add a layout column to long format data for mixed layouts.

Description

Usage

Arguments

Value

Examples

Successively apply dendextend functions to a dendrogram.

Description

Usage

Arguments

Value

Check names of annotation

Description

Usage

Arguments

Value

Check annotation name parameters for deprecated usage.

Description

Usage

Arguments

Value

Check cell labels if they are ok.

Description

Usage

Arguments

Value

Check that dendrograms are positioned correctly

Description

Usage

Arguments

Value

Check that layout and mode are correct

Description

Usage

Arguments

Value

Check (supposed) logical values.

Description

Usage

Arguments

Value

Check input numeric arguments for class and length.

Description

Usage

Arguments

Value

Cluster data using hierarchical clustering or use provided clustering.

Description

Usage

Arguments

Value

Make a correlation matrix from long format data.

Description

Usage

Arguments

Details

Value

Examples

Get default colour scale for non-correlation heatmaps.

Description

Usage

`ggcorrhm()` for long format data.

`gghm()` for long format data.