Reference

All functions

N52

Example data set N52

add_annotation()

add_annotation

add_attr()

Add attribute to abject

add_bar() add_bar()

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_point()

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`

annot_to_list()

annot_to_list

annotation_bar()

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_point()

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`

as_ComplexHeatmap()

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() 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_up()

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_diamond()

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_square()

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_text()

Adds a layers of texts above the heatmap tiles to a `InputHeatmap`, that on evaluation creates a `ComplexHeatmap`

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(<Heatmap>)

save_pdf

save_pdf(<InputHeatmap>)

save_pdf

save_pdf()

Save plot on PDF file

scale_design()

Scale design matrix

scale_robust()

Scale counts in a robust way against sd == 0

select_closest_pairs()

Sub function of remove_redundancy_elements_though_reduced_dimensions

split_rows() split_columns()

Split the heatmap row-wise depending on the biggest branches in the cladogram.

wrap_heatmap()

Wrap tidyHeatmap (ComplexHeatmap) in a patchwork-compliant patch