├── .Rbuildignore ├── .coveralls.yml ├── .github └── workflows │ └── rworkflows.yml ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── NAMESPACE ├── R ├── classes.R ├── data.R ├── deprecated_framework.R ├── functions.R ├── ggsave.R ├── methods.R ├── patchwork.R ├── subset.R ├── tidyHeatmap-package.R ├── utilities.R ├── validation.R └── zzz.R ├── README.md ├── codecov.yml ├── data ├── N52.rda └── pasilla.rda ├── doc ├── introduction.R └── introduction.Rmd ├── docs └── .txt ├── inst ├── .gitignore ├── CITATION ├── NEWS.rd ├── Thumbs.db └── WORDLIST ├── man ├── .gitignore ├── N52.Rd ├── add_annotation.Rd ├── add_attr.Rd ├── add_class.Rd ├── annot_to_list.Rd ├── annotation_bar-method.Rd ├── annotation_group.Rd ├── annotation_line-method.Rd ├── annotation_numeric-method.Rd ├── annotation_point-method.Rd ├── annotation_tile-method.Rd ├── as_ComplexHeatmap-method.Rd ├── as_matrix.Rd ├── check_if_duplicated_genes.Rd ├── check_if_wrong_input.Rd ├── drop_class.Rd ├── error_if_log_transformed.Rd ├── figures │ ├── example_plot.png │ ├── lifecycle-archived.svg │ ├── lifecycle-defunct.svg │ ├── lifecycle-deprecated.svg │ ├── lifecycle-experimental.svg │ ├── lifecycle-maturing.svg │ ├── lifecycle-questioning.svg │ ├── lifecycle-retired.svg │ ├── lifecycle-soft-deprecated.svg │ ├── lifecycle-stable.svg │ └── unnamed-chunk-17-1.png ├── get_abundance_norm_if_exists.Rd ├── get_elements.Rd ├── get_elements_features.Rd ├── get_elements_features_abundance.Rd ├── get_heatmap_data-method.Rd ├── get_sample_counts.Rd ├── get_sample_transcript.Rd ├── get_sample_transcript_counts.Rd ├── get_x_y_annotation_columns.Rd ├── heatmap-method.Rd ├── ifelse2_pipe.Rd ├── ifelse_pipe.Rd ├── input_heatmap.Rd ├── layer_arrow_down-method.Rd ├── layer_arrow_up-method.Rd ├── layer_asterisk-method.Rd ├── layer_diamond-method.Rd ├── layer_point-method.Rd ├── layer_square-method.Rd ├── layer_star-method.Rd ├── layer_text-method.Rd ├── parse_formula.Rd ├── pasilla.Rd ├── plus-.InputHeatmap.Rd ├── prepend.Rd ├── quo_names.Rd ├── save_pdf-Heatmap-method.Rd ├── save_pdf-InputHeatmap-method.Rd ├── save_pdf-methods.Rd ├── scale_robust.Rd ├── select_closest_pairs.Rd ├── split-methods.Rd └── wrap_heatmap-method.Rd ├── paper ├── .gitignore ├── paper.bib ├── paper.md ├── paper.pdf ├── paper_tables_and_figures.Rmd ├── paper_tables_and_figures.md └── paper_tables_and_figures_files │ └── figure-gfm │ └── example_figure-1.png ├── tests ├── testthat.R └── testthat │ ├── .gitignore │ ├── Rplots.pdf │ ├── _snaps │ ├── color-functionality │ │ ├── color-size-columns-text.svg │ │ ├── color-size-columns.svg │ │ ├── layer-arrow-down-color.svg │ │ ├── layer-arrow-up-color.svg │ │ ├── layer-asterisk-color.svg │ │ ├── layer-diamond-color.svg │ │ ├── layer-point-color-column.svg │ │ ├── layer-point-color.svg │ │ ├── layer-square-color.svg │ │ ├── layer-star-color.svg │ │ ├── layer-symbol-color-column.svg │ │ ├── layer-symbol-default-color.svg │ │ ├── layer-symbol-direct-color.svg │ │ ├── layer-text-color-column.svg │ │ ├── layer-text-default-color.svg │ │ ├── layer-text-direct-color.svg │ │ └── multiple-layers-colors.svg │ └── tests │ │ ├── annotated-heatmap-1.svg │ │ ├── annotated-heatmap-2.svg │ │ ├── annotation-ordering.svg │ │ ├── base.svg │ │ ├── colorramp2.svg │ │ ├── group-ordering-2.svg │ │ ├── group-ordering.svg │ │ ├── grouped-annotated-heatmap-1.svg │ │ ├── grouped-annotated-heatmap-2.svg │ │ ├── grouped-custom-color-both.svg │ │ ├── grouped.svg │ │ ├── layer-symbol.svg │ │ ├── legend.svg │ │ ├── multi-type.svg │ │ ├── numeric-right.svg │ │ ├── patchwork-padding.svg │ │ ├── plot-annotation-group.svg │ │ ├── plus-operator.svg │ │ ├── scale-both.svg │ │ ├── scale-column.svg │ │ ├── scale-none.svg │ │ ├── scale-row.svg │ │ ├── show-heatmap-legend.svg │ │ ├── size-annotation.svg │ │ ├── sparse-matrix.svg │ │ ├── sparse.svg │ │ ├── split.svg │ │ ├── text-base.svg │ │ ├── text-complex.svg │ │ ├── text-multiple.svg │ │ ├── text-with-size-column.svg │ │ ├── text-with-size.svg │ │ ├── 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