Package: tidyHeatmap 1.13.2

tidyHeatmap: A Tidy Implementation of Heatmap

This is a tidy implementation for heatmap. At the moment it is based on the (great) package 'ComplexHeatmap'. The goal of this package is to interface a tidy data frame with this powerful tool. Some of the advantages are: Row and/or columns colour annotations are easy to integrate just specifying one parameter (column names). Custom grouping of rows is easy to specify providing a grouped tbl. For example: df %>% group_by(...). Labels size adjusted by row and column total number. Default use of Brewer and Viridis palettes.

Authors:Stefano Mangiola [aut, cre], Anthony Papenfuss [ctb]

tidyHeatmap_1.13.2.tar.gz
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tidyHeatmap_1.13.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
tidyHeatmap/json (API)

# Install 'tidyHeatmap' in R:

install.packages('tidyHeatmap', repos = c('https://stemangiola.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/stemangiola/tidyheatmap/issues

Datasets:

N52 - Example data set N52
pasilla - Example data set Pasilla

On CRAN:

assaydomain infrastructure brewer complexheatmap custom-palette dplyr graphviz heatmap mtcars plotting rstudio scale tibble tidy tidy-data-frame tidybulk tidyverse viridis

10.18 score 360 stars 1 packages 351 scripts 1.1k downloads 22 exports 53 dependencies

Last updated from:6075f30967. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	225
source / vignettes	OK	257
linux-release-x86_64	OK	237
macos-release-arm64	OK	174
macos-oldrel-arm64	OK	183
windows-devel	OK	205
windows-release	OK	191
windows-oldrel	OK	191
wasm-release	OK	130

Exports:annotation_bar annotation_group annotation_line annotation_numeric annotation_point annotation_tile as_ComplexHeatmap get_heatmap_data heatmap layer_arrow_down layer_arrow_up layer_asterisk layer_diamond layer_point layer_square layer_star layer_text save_pdf scale_robust split_columns split_rows wrap_heatmap

Dependencies:BiocGenerics circlize cli clue cluster codetools colorspace ComplexHeatmap cpp11 crayon dendextend digest doParallel dplyr farver foreach generics GetoptLong ggplot2 GlobalOptions glue gridExtra gtable IRanges isoband iterators labeling lifecycle magrittr matrixStats patchwork pillar pkgconfig png purrr R6 RColorBrewer rjson rlang S4Vectors S7 scales shape stringi stringr tibble tidyr tidyselect utf8 vctrs viridis viridisLite withr

Overview of the tidyHeatmap package

Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2025-10-27
Started: 2020-01-13

Help page	Topics
Add two tidyHeatmap objects together	+.InputHeatmap
add_annotation	add_annotation
Add attribute to abject	add_attr
Add class to abject	add_class
annot_to_list	annot_to_list
Adds a bar annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`	annotation_bar annotation_bar,InputHeatmap-method
Add group annotation strips to a tidyHeatmap	annotation_group annotation_group,InputHeatmap-method
Adds a line annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`	annotation_line annotation_line,InputHeatmap-method
Adds a numeric annotation layer to an `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`	annotation_numeric annotation_numeric,InputHeatmap-method
Adds a point annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`	annotation_point annotation_point,InputHeatmap-method
Adds a tile annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`	annotation_tile annotation_tile,InputHeatmap-method
Creates a `ComplexHeatmap` object for less standard plot manipulation (e.g. changing legend position)	as_ComplexHeatmap as_ComplexHeatmap,InputHeatmap-method
Get matrix from tibble	as_matrix
Check whether there are duplicated genes/transcripts	check_if_duplicated_genes
Check whether there are NA counts	check_if_wrong_input
Remove class to abject	drop_class
Check whether a numeric vector has been log transformed	error_if_log_transformed
Get column names either from user or from attributes	get_abundance_norm_if_exists
Get column names either from user or from attributes	get_elements
Get column names either from user or from attributes	get_elements_features
Get column names either from user or from attributes	get_elements_features_abundance
Retrieve heatmap data and dendrograms as plotted	get_heatmap_data get_heatmap_data,InputHeatmap-method
Get column names either from user or from attributes	get_sample_counts
Get column names either from user or from attributes	get_sample_transcript
Get column names either from user or from attributes	get_sample_transcript_counts
get_x_y_annotation_columns	get_x_y_annotation_columns
Creates a `InputHeatmap` object from `tbl_df` on evaluation creates a `ComplexHeatmap`	heatmap heatmap,tbl-method heatmap,tbl_df-method heatmap_
This is a generalisation of ifelse that accepts an object and return an objects	ifelse_pipe
This is a generalisation of ifelse that accepts an object and return an objects	ifelse2_pipe
input_heatmap	input_heatmap
Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`	layer_arrow_down layer_arrow_down,InputHeatmap-method
Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`	layer_arrow_up layer_arrow_up,InputHeatmap-method
Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`	layer_asterisk layer_asterisk,InputHeatmap-method
Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`	layer_diamond layer_diamond,InputHeatmap-method
Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`	layer_point layer_point,InputHeatmap-method
Adds a layers of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`	layer_square layer_square,InputHeatmap-method
Adds a layer of symbols above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`	layer_star layer_star,InputHeatmap-method
Adds a layers of texts above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`	layer_text layer_text,InputHeatmap-method
Example data set N52	N52
.formula parser	parse_formula
Example data set Pasilla	pasilla
From rlang deprecated	prepend
Convert array of quosure (e.g. c(col_a, col_b)) into character vector	quo_names
Save plot on PDF file	save_pdf
save_pdf	save_pdf,Heatmap-method
save_pdf	save_pdf,InputHeatmap-method
Scale counts in a robust way against sd == 0	scale_robust
Sub function of remove_redundancy_elements_though_reduced_dimensions	select_closest_pairs
Split the heatmap row-wise depending on the biggest branches in the cladogram.	split_columns split_columns,InputHeatmap-method split_rows split_rows,InputHeatmap-method
Wrap tidyHeatmap (ComplexHeatmap) in a patchwork-compliant patch	wrap_heatmap wrap_heatmap,InputHeatmap-method

Package: tidyHeatmap 1.13.2

tidyHeatmap: A Tidy Implementation of Heatmap

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