# A Tidy Implementation of Heatmap

## Documentation for package ‘tidyHeatmap’ version 1.11.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

add_annotation | add_annotation
add_attr | Add attribute to abject
add_bar | DEPRECATED. Adds a bar annotation layer to a 'InputHeatmap', that on evaluation creates a 'ComplexHeatmap'
add_bar-method | DEPRECATED. Adds a bar annotation layer to a 'InputHeatmap', that on evaluation creates a 'ComplexHeatmap'
add_class | Add class to abject
add_line | DEPRECATED. Adds a line annotation layer to a 'InputHeatmap', that on evaluation creates a 'ComplexHeatmap'
add_line-method | DEPRECATED. Adds a line annotation layer to a 'InputHeatmap', that on evaluation creates a 'ComplexHeatmap'
add_point | DEPRECATED. Adds a point annotation layer to a 'InputHeatmap', that on evaluation creates a 'ComplexHeatmap'
add_point-method | DEPRECATED. Adds a point annotation layer to a 'InputHeatmap', that on evaluation creates a 'ComplexHeatmap'
add_tile | DEPRECATED. Adds a tile annotation layer to a 'InputHeatmap', that on evaluation creates a 'ComplexHeatmap'
add_tile-method | DEPRECATED. Adds a tile annotation layer to a 'InputHeatmap', that on evaluation creates a 'ComplexHeatmap'
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_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_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