Package: tidyHeatmap 1.10.5

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]

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tidyHeatmap.pdf |tidyHeatmap.html✨
tidyHeatmap/json (API)

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

Peer review:

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

Datasets:
  • N52 - Example data set N52
  • pasilla - Example data set Pasilla

On CRAN:

assaydomaininfrastructurebrewercomplexheatmapcustom-palettedplyrgraphvizheatmapmtcarsplottingrstudioscaletibbletidytidy-data-frametidybulktidyverseviridis

9.63 score 319 stars 1 packages 182 scripts 1.2k downloads 2 mentions 23 exports 59 dependencies

Last updated 15 days agofrom:694f9b0d39. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winOKOct 31 2024
R-4.5-linuxOKOct 31 2024
R-4.4-winOKOct 31 2024
R-4.4-macOKOct 31 2024
R-4.3-winOKOct 31 2024
R-4.3-macOKOct 31 2024

Exports:add_baradd_lineadd_pointadd_tileannotation_barannotation_lineannotation_pointannotation_tileas_ComplexHeatmapheatmaplayer_arrow_downlayer_arrow_uplayer_asterisklayer_diamondlayer_pointlayer_squarelayer_starlayer_textsave_pdfscale_robustsplit_columnssplit_rowswrap_heatmap

Dependencies:BiocGenericscirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayondendextenddigestdoParalleldplyrfansifarverforeachgenericsGetoptLongggplot2GlobalOptionsgluegridExtragtableIRangesisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmatrixStatsmgcvmunsellnlmepatchworkpillarpkgconfigpngpurrrR6RColorBrewerrjsonrlangS4Vectorsscalesshapestringistringrtibbletidyrtidyselectutf8vctrsviridisviridisLitewithr

Overview of the tidyHeatmap package

Stefano Mangiola

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2021-11-19
Started: 2020-01-13

Readme and manuals

Help Manual

Help pageTopics
add_annotationadd_annotation
Add attribute to abjectadd_attr
DEPRECATED. Adds a bar annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`add_bar add_bar,InputHeatmap-method
Add class to abjectadd_class
DEPRECATED. Adds a line annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`add_line add_line,InputHeatmap-method
DEPRECATED. Adds a point annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`add_point add_point,InputHeatmap-method
DEPRECATED. Adds a tile annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`add_tile add_tile,InputHeatmap-method
annot_to_listannot_to_list
Adds a bar annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`annotation_bar annotation_bar,InputHeatmap-method
Adds a line annotation layer to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`annotation_line annotation_line,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 tibbleas_matrix
Check whether there are NA countscheck_if_counts_is_na
Check whether there are duplicated genes/transcriptscheck_if_duplicated_genes
Check whether there are NA countscheck_if_wrong_input
Remove class to abjectdrop_class
Check whether a numeric vector has been log transformederror_if_log_transformed
Get column names either from user or from attributesget_abundance_norm_if_exists
Get column names either from user or from attributesget_elements
Get column names either from user or from attributesget_elements_features
Get column names either from user or from attributesget_elements_features_abundance
Get column names either from user or from attributesget_sample_counts
Get column names either from user or from attributesget_sample_transcript
Get column names either from user or from attributesget_sample_transcript_counts
get_x_y_annotation_columnsget_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 objectsifelse_pipe
This is a generalisation of ifelse that accepts an object and return an objectsifelse2_pipe
input_heatmapinput_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 N52N52
.formula parserparse_formula
Example data set Pasillapasilla
From rlang deprecatedprepend
Convert array of quosure (e.g. c(col_a, col_b)) into character vectorquo_names
Save plot on PDF filesave_pdf
save_pdfsave_pdf,Heatmap-method
save_pdfsave_pdf,InputHeatmap-method
Scale design matrixscale_design
Scale counts in a robust way against sd == 0scale_robust
Sub function of remove_redundancy_elements_though_reduced_dimensionsselect_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 patchwrap_heatmap wrap_heatmap,InputHeatmap-method