Title: Heatmaps from Tidy Data
Version: 0.2.1
Description: The goal of 'tidyheatmaps' is to simplify the generation of publication-ready heatmaps from tidy data. By offering an interface to the powerful 'pheatmap' package, it allows for the effortless creation of intricate heatmaps with minimal code.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.1
Imports: dplyr, pheatmap, rlang, grDevices, tidyr, tibble, RColorBrewer
Suggests: testthat (≥ 2.1.0), knitr, rmarkdown
URL: https://github.com/jbengler/tidyheatmaps, https://jbengler.github.io/tidyheatmaps/
BugReports: https://github.com/jbengler/tidyheatmaps/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-02-28 12:54:41 UTC; janbroderengler
Author: Jan Broder Engler ORCID iD [aut, cre, cph]
Maintainer: Jan Broder Engler <broder.engler@gmail.com>
Repository: CRAN
Date/Publication: 2024-02-29 13:00:02 UTC

Expression data from RNA-Seq study

Description

This data was taken form a RNA-Seq study investigating the regulation of genes in response to central nervous system inflammation.

Usage

data_exprs

Format

A data frame with 800 rows and 9 variables:

ensembl_gene_id

Ensembl gene id

external_gene_name

Gene symbol

sample

Sample name

expression

Normalized RNA-Seq expression value

group

Experimental group

sample_type

Sample type. Either input or IP.

condition

Condition of sampling. Either healthy or EAE.

is_immune_gene

Gene is annotated as immune cell gene. Either yes or no.

direction

Direction of regulation. Either up or down.

Source

data_exprs represents just a small subset of the data aquired in the study.

More details about the study can be found here

The complete raw data can be downloaded here

Create heatmap from tidy data

Description

A tidyverse-style interface to the powerful heatmap package pheatmap. It enables the convenient generation of complex heatmaps from tidy data.

Usage

tidyheatmap(
  df,
  rows,
  columns,
  values,
  colors = NA,
  color_legend_n = 15,
  color_legend_min = NA,
  color_legend_max = NA,
  color_na = "#DDDDDD",
  annotation_row = NULL,
  annotation_col = NULL,
  gaps_row = NULL,
  gaps_col = NULL,
  show_selected_row_labels = NULL,
  show_selected_col_labels = NULL,
  filename = NA,
  scale = "none",
  fontsize = 7,
  cellwidth = NA,
  cellheight = NA,
  cluster_rows = FALSE,
  cluster_cols = FALSE,
  border_color = NA,
  kmeans_k = NA,
  clustering_distance_rows = "euclidean",
  clustering_distance_cols = "euclidean",
  clustering_method = "complete",
  clustering_callback = function(x, ...) {
     return(x)
 },
  cutree_rows = NA,
  cutree_cols = NA,
  treeheight_row = ifelse((class(cluster_rows) == "hclust") || cluster_rows, 50, 0),
  treeheight_col = ifelse((class(cluster_cols) == "hclust") || cluster_cols, 50, 0),
  legend = TRUE,
  legend_breaks = NA,
  legend_labels = NA,
  annotation_colors = NA,
  annotation_legend = TRUE,
  annotation_names_row = TRUE,
  annotation_names_col = TRUE,
  drop_levels = TRUE,
  show_rownames = TRUE,
  show_colnames = TRUE,
  main = NA,
  fontsize_row = fontsize,
  fontsize_col = fontsize,
  angle_col = c("270", "0", "45", "90", "315"),
  display_numbers = FALSE,
  number_format = "%.2f",
  number_color = "grey30",
  fontsize_number = 0.8 * fontsize,
  width = NA,
  height = NA,
  silent = FALSE
)

Arguments

df

A tidy dataframe in long format.

rows, columns

Column in the dataframe to use for heatmap rows and columns.

values

Column in the dataframe containing the values to be color coded in the heatmap cells.

colors

Vector of colors used for the color legend.

color_legend_n

Number of colors in the color legend.

color_legend_min, color_legend_max

Min and max value of the color legend. Values smaller then the color_legend_min will have the lowest color, values bigger than the color_legend_max will get the highest color.

color_na

Color to use for NAs in values.

annotation_row, annotation_col

Column(s) in the dataframe to use for row and column annotation. To use multiple columns for annotation combine then by c(column1, column2).

gaps_row, gaps_col

Column in the dataframe to use for use for row and column gaps.

show_selected_row_labels, show_selected_col_labels

Only display a subset of selected labels for rows and columns. Provide selected labels as c("label1", "label2").

filename

file path where to save the picture. Filetype is decided by the extension in the path. Currently following formats are supported: png, pdf, tiff, bmp, jpeg. Even if the plot does not fit into the plotting window, the file size is calculated so that the plot would fit there, unless specified otherwise.

scale

character indicating if the values should be centered and scaled in either the row direction or the column direction, or none. Corresponding values are "row", "column" and "none"

fontsize

base fontsize for the plot

cellwidth

individual cell width in points. If left as NA, then the values depend on the size of plotting window.

cellheight

individual cell height in points. If left as NA, then the values depend on the size of plotting window.

cluster_rows

boolean values determining if rows should be clustered or hclust object,

cluster_cols

boolean values determining if columns should be clustered or hclust object.

border_color

color of cell borders on heatmap, use NA if no border should be drawn.

kmeans_k

the number of kmeans clusters to make, if we want to aggregate the rows before drawing heatmap. If NA then the rows are not aggregated.

clustering_distance_rows

distance measure used in clustering rows. Possible values are "correlation" for Pearson correlation and all the distances supported by dist, such as "euclidean", etc. If the value is none of the above it is assumed that a distance matrix is provided.

clustering_distance_cols

distance measure used in clustering columns. Possible values the same as for clustering_distance_rows.

clustering_method

clustering method used. Accepts the same values as hclust.

clustering_callback

callback function to modify the clustering. Is called with two parameters: original hclust object and the matrix used for clustering. Must return a hclust object.

cutree_rows

number of clusters the rows are divided into, based on the hierarchical clustering (using cutree), if rows are not clustered, the argument is ignored

cutree_cols

similar to cutree_rows, but for columns

treeheight_row

the height of a tree for rows, if these are clustered. Default value 50 points.

treeheight_col

the height of a tree for columns, if these are clustered. Default value 50 points.

legend

logical to determine if legend should be drawn or not.

legend_breaks

vector of breakpoints for the legend.

legend_labels

vector of labels for the legend_breaks.

annotation_colors

list for specifying annotation_row and annotation_col track colors manually. It is possible to define the colors for only some of the features. Check examples for details.

annotation_legend

boolean value showing if the legend for annotation tracks should be drawn.

annotation_names_row

boolean value showing if the names for row annotation tracks should be drawn.

annotation_names_col

boolean value showing if the names for column annotation tracks should be drawn.

drop_levels

logical to determine if unused levels are also shown in the legend

show_rownames

boolean specifying if column names are be shown.

show_colnames

boolean specifying if column names are be shown.

main

the title of the plot

fontsize_row

fontsize for rownames (Default: fontsize)

fontsize_col

fontsize for colnames (Default: fontsize)

angle_col

angle of the column labels, right now one can choose only from few predefined options (0, 45, 90, 270 and 315)

display_numbers

logical determining if the numeric values are also printed to the cells. If this is a matrix (with same dimensions as original matrix), the contents of the matrix are shown instead of original values.

number_format

format strings (C printf style) of the numbers shown in cells. For example "%.2f" shows 2 decimal places and "%.1e" shows exponential notation (see more in sprintf).

number_color

color of the text

fontsize_number

fontsize of the numbers displayed in cells

width

manual option for determining the output file width in inches.

height

manual option for determining the output file height in inches.

silent

do not draw the plot (useful when using the gtable output)

Value

Invisibly a pheatmap object that is a list with components

Examples

# Basic example
tidyheatmap(data_exprs,
            rows = external_gene_name,
            columns = sample,
            values = expression,
            scale = "row"
)

# Change number of colors in color lengend
tidyheatmap(data_exprs,
            rows = external_gene_name,
            columns = sample,
            values = expression,
            scale = "row",
            color_legend_n = 5
)

# Change color in color legend
tidyheatmap(data_exprs,
            rows = external_gene_name,
            columns = sample,
            values = expression,
            scale = "row",
            colors = c("#145afc","#ffffff","#ee4445")
)

# Add row and column annotation
tidyheatmap(data_exprs,
            rows = external_gene_name,
            columns = sample,
            values = expression,
            scale = "row",
            annotation_col = c(sample_type, condition, group),
            annotation_row = c(is_immune_gene, direction)
)

# Add gaps between rows and columns
tidyheatmap(data_exprs,
            rows = external_gene_name,
            columns = sample,
            values = expression,
            scale = "row",
            annotation_col = c(sample_type, condition, group),
            annotation_row = c(is_immune_gene, direction),
            gaps_row = direction,
            gaps_col = group
)