A Tidy Implementation of Heatmap

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Documentation for package ‘tidyHeatmap’ version 1.12.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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