Name Mode Size
..
AdditiveUnit-class.Rd 100644 1 kb
AdditiveUnit.Rd 100644 0 kb
AnnotationFunction-class.Rd 100644 1 kb
AnnotationFunction.Rd 100644 5 kb
ColorMapping-class.Rd 100644 1 kb
ColorMapping.Rd 100644 1 kb
ComplexHeatmap-package.Rd 100644 1 kb
Extract.AnnotationFunction.Rd 100644 1 kb
Extract.Heatmap.Rd 100644 1 kb
Extract.HeatmapAnnotation.Rd 100644 1 kb
Extract.HeatmapList.Rd 100644 1 kb
Extract.SingleAnnotation.Rd 100644 1 kb
Extract.comb_mat.Rd 100644 1 kb
Extract.gridtext.Rd 100644 0 kb
Heatmap-class.Rd 100644 1 kb
Heatmap.Rd 100644 14 kb
Heatmap3D.Rd 100644 1 kb
HeatmapAnnotation-class.Rd 100644 1 kb
HeatmapAnnotation.Rd 100644 5 kb
HeatmapList-class.Rd 100644 1 kb
HeatmapList.Rd 100644 0 kb
Legend.Rd 100644 5 kb
Legends-class.Rd 100644 0 kb
Legends.Rd 100644 0 kb
SingleAnnotation-class.Rd 100644 1 kb
SingleAnnotation.Rd 100644 6 kb
UpSet.Rd 100644 5 kb
add.AdditiveUnit.Rd 100644 1 kb
add_heatmap-Heatmap-method.Rd 100644 1 kb
add_heatmap-HeatmapAnnotation-method.Rd 100644 1 kb
add_heatmap-HeatmapList-method.Rd 100644 1 kb
add_heatmap-dispatch.Rd 100644 1 kb
adjust_dend_by_x.Rd 100644 1 kb
adjust_heatmap_list-HeatmapList-method.Rd 100644 1 kb
alter_graphic.Rd 100644 1 kb
anno_barplot.Rd 100644 3 kb
anno_block.Rd 100644 4 kb
anno_boxplot.Rd 100644 2 kb
anno_customize.Rd 100644 2 kb
anno_density.Rd 100644 3 kb
anno_empty.Rd 100644 2 kb
anno_histogram.Rd 100644 2 kb
anno_horizon.Rd 100644 3 kb
anno_image.Rd 100644 2 kb
anno_joyplot.Rd 100644 2 kb
anno_lines.Rd 100644 3 kb
anno_link.Rd 100644 0 kb
anno_mark.Rd 100644 2 kb
anno_numeric.Rd 100644 2 kb
anno_oncoprint_barplot.Rd 100644 1 kb
anno_points.Rd 100644 2 kb
anno_simple.Rd 100644 3 kb
anno_summary.Rd 100644 3 kb
anno_text.Rd 100644 2 kb
anno_textbox.Rd 100644 2 kb
anno_zoom.Rd 100644 4 kb
annotation_axis_grob.Rd 100644 5 kb
annotation_legend_size-HeatmapList-method.Rd 100644 1 kb
attach_annotation-Heatmap-method.Rd 100644 1 kb
bar3D.Rd 100644 1 kb
bin_genome.Rd 100644 1 kb
c.ColorMapping.Rd 100644 1 kb
c.HeatmapAnnotation.Rd 100644 1 kb
cluster_between_groups.Rd 100644 1 kb
cluster_within_group.Rd 100644 1 kb
color_mapping_legend-ColorMapping-method.Rd 100644 3 kb
columnAnnotation.Rd 100644 0 kb
column_dend-Heatmap-method.Rd 100644 1 kb
column_dend-HeatmapList-method.Rd 100644 1 kb
column_dend-dispatch.Rd 100644 0 kb
column_order-Heatmap-method.Rd 100644 1 kb
column_order-HeatmapList-method.Rd 100644 1 kb
column_order-dispatch.Rd 100644 0 kb
comb_degree.Rd 100644 1 kb
comb_name.Rd 100644 1 kb
comb_size.Rd 100644 1 kb
compare_heatmap.2.Rd 100644 1 kb
compare_heatmap.Rd 100644 1 kb
compare_pheatmap.Rd 100644 1 kb
complement_size.Rd 100644 0 kb
component_height-Heatmap-method.Rd 100644 1 kb
component_height-HeatmapList-method.Rd 100644 1 kb
component_height-dispatch.Rd 100644 0 kb
component_width-Heatmap-method.Rd 100644 1 kb
component_width-HeatmapList-method.Rd 100644 1 kb
component_width-dispatch.Rd 100644 0 kb
copy_all-AnnotationFunction-method.Rd 100644 1 kb
copy_all-SingleAnnotation-method.Rd 100644 1 kb
copy_all-dispatch.Rd 100644 0 kb
decorate_annotation.Rd 100644 1 kb
decorate_column_dend.Rd 100644 1 kb
decorate_column_names.Rd 100644 1 kb
decorate_column_title.Rd 100644 1 kb
decorate_dend.Rd 100644 1 kb
decorate_dimnames.Rd 100644 1 kb
decorate_heatmap_body.Rd 100644 1 kb
decorate_row_dend.Rd 100644 1 kb
decorate_row_names.Rd 100644 1 kb
decorate_row_title.Rd 100644 1 kb
decorate_title.Rd 100644 1 kb
default_axis_param.Rd 100644 1 kb
default_get_type.Rd 100644 0 kb
dend_heights.Rd 100644 0 kb
dend_xy.Rd 100644 1 kb
dendrogramGrob.Rd 100644 1 kb
densityHeatmap.Rd 100644 4 kb
dim.Heatmap.Rd 100644 0 kb
dist2.Rd 100644 1 kb
draw-AnnotationFunction-method.Rd 100644 1 kb
draw-Heatmap-method.Rd 100644 1 kb
draw-HeatmapAnnotation-method.Rd 100644 1 kb
draw-HeatmapList-method.Rd 100644 11 kb
draw-Legends-method.Rd 100644 1 kb
draw-SingleAnnotation-method.Rd 100644 1 kb
draw-dispatch.Rd 100644 1 kb
draw_annotation-Heatmap-method.Rd 100644 1 kb
draw_annotation_legend-HeatmapList-method.Rd 100644 1 kb
draw_dend-Heatmap-method.Rd 100644 1 kb
draw_dimnames-Heatmap-method.Rd 100644 1 kb
draw_heatmap_body-Heatmap-method.Rd 100644 1 kb
draw_heatmap_legend-HeatmapList-method.Rd 100644 1 kb
draw_heatmap_list-HeatmapList-method.Rd 100644 1 kb
draw_title-Heatmap-method.Rd 100644 1 kb
draw_title-HeatmapList-method.Rd 100644 1 kb
draw_title-dispatch.Rd 100644 0 kb
extract_comb.Rd 100644 1 kb
frequencyHeatmap.Rd 100644 2 kb
full_comb_code.Rd 100644 0 kb
getXY_in_parent_vp.Rd 100644 1 kb
get_color_mapping_list-HeatmapAnnotation-method.Rd 100644 1 kb
get_legend_param_list-HeatmapAnnotation-method.Rd 100644 1 kb
grid.annotation_axis.Rd 100644 1 kb
grid.boxplot.Rd 100644 1 kb
grid.dendrogram.Rd 100644 1 kb
grid.draw.Legends.Rd 100644 1 kb
grid.textbox.Rd 100644 1 kb
gt_render.Rd 100644 2 kb
heatmap_legend_size-HeatmapList-method.Rd 100644 1 kb
height.AnnotationFunction.Rd 100644 0 kb
height.Heatmap.Rd 100644 0 kb
height.HeatmapAnnotation.Rd 100644 0 kb
height.HeatmapList.Rd 100644 0 kb
height.Legends.Rd 100644 0 kb
height.SingleAnnotation.Rd 100644 0 kb
heightAssign.AnnotationFunction.Rd 100644 1 kb
heightAssign.HeatmapAnnotation.Rd 100644 1 kb
heightAssign.SingleAnnotation.Rd 100644 1 kb
heightDetails.annotation_axis.Rd 100644 0 kb
heightDetails.legend.Rd 100644 0 kb
heightDetails.legend_body.Rd 100644 0 kb
heightDetails.packed_legends.Rd 100644 0 kb
heightDetails.textbox.Rd 100644 0 kb
ht_global_opt.Rd 100644 1 kb
ht_opt.Rd 100644 4 kb
ht_size.Rd 100644 0 kb
is_abs_unit.Rd 100644 1 kb
length.HeatmapAnnotation.Rd 100644 0 kb
length.HeatmapList.Rd 100644 0 kb
list_components.Rd 100644 0 kb
list_to_matrix.Rd 100644 1 kb
make_column_cluster-Heatmap-method.Rd 100644 1 kb
make_comb_mat.Rd 100644 4 kb
make_layout-Heatmap-method.Rd 100644 1 kb
make_layout-HeatmapList-method.Rd 100644 8 kb
make_layout-dispatch.Rd 100644 0 kb
make_row_cluster-Heatmap-method.Rd 100644 1 kb
map_to_colors-ColorMapping-method.Rd 100644 1 kb
max_text_height.Rd 100644 1 kb
max_text_width.Rd 100644 1 kb
merge_dendrogram.Rd 100644 1 kb
names.HeatmapAnnotation.Rd 100644 0 kb
names.HeatmapList.Rd 100644 0 kb
namesAssign.HeatmapAnnotation.Rd 100644 0 kb
ncol.Heatmap.Rd 100644 0 kb
nobs.AnnotationFunction.Rd 100644 0 kb
nobs.HeatmapAnnotation.Rd 100644 0 kb
nobs.SingleAnnotation.Rd 100644 0 kb
normalize_comb_mat.Rd 100644 1 kb
normalize_genomic_signals_to_bins.Rd 100644 6 kb
nrow.Heatmap.Rd 100644 0 kb
oncoPrint.Rd 100644 5 kb
order.comb_mat.Rd 100644 1 kb
packLegend.Rd 100644 2 kb
pct_v_pct.Rd 100644 1 kb
pheatmap.Rd 100644 7 kb
pindex.Rd 100644 1 kb
plot.Heatmap.Rd 100644 0 kb
plot.HeatmapAnnotation.Rd 100644 0 kb
plot.HeatmapList.Rd 100644 0 kb
prepare-Heatmap-method.Rd 100644 1 kb
print.comb_mat.Rd 100644 0 kb
re_size-HeatmapAnnotation-method.Rd 100644 2 kb
restore_matrix.Rd 100644 3 kb
rowAnnotation.Rd 100644 0 kb
row_anno_barplot.Rd 100644 1 kb
row_anno_boxplot.Rd 100644 1 kb
row_anno_density.Rd 100644 1 kb
row_anno_histogram.Rd 100644 1 kb
row_anno_points.Rd 100644 1 kb
row_anno_text.Rd 100644 0 kb
row_dend-Heatmap-method.Rd 100644 1 kb
row_dend-HeatmapList-method.Rd 100644 1 kb
row_dend-dispatch.Rd 100644 0 kb
row_order-Heatmap-method.Rd 100644 1 kb
row_order-HeatmapList-method.Rd 100644 1 kb
row_order-dispatch.Rd 100644 0 kb
set_component_height-Heatmap-method.Rd 100644 1 kb
set_component_width-Heatmap-method.Rd 100644 1 kb
set_name.Rd 100644 0 kb
set_nameAssign.Rd 100644 0 kb
set_size.Rd 100644 0 kb
show-AnnotationFunction-method.Rd 100644 0 kb
show-ColorMapping-method.Rd 100644 0 kb
show-Heatmap-method.Rd 100644 1 kb
show-HeatmapAnnotation-method.Rd 100644 0 kb
show-HeatmapList-method.Rd 100644 1 kb
show-SingleAnnotation-method.Rd 100644 0 kb
show-dispatch.Rd 100644 1 kb
size.AnnotationFunction.Rd 100644 1 kb
size.HeatmapAnnotation.Rd 100644 0 kb
size.SingleAnnotation.Rd 100644 0 kb
sizeAssign.AnnotationFunction.Rd 100644 1 kb
sizeAssign.HeatmapAnnotation.Rd 100644 1 kb
sizeAssign.SingleAnnotation.Rd 100644 1 kb
smartAlign2.Rd 100644 1 kb
str.comb_mat.Rd 100644 0 kb
subset_gp.Rd 100644 0 kb
subset_matrix_by_row.Rd 100644 0 kb
subset_no.Rd 100644 0 kb
subset_vector.Rd 100644 0 kb
summary.Heatmap.Rd 100644 0 kb
summary.HeatmapList.Rd 100644 0 kb
t.comb_mat.Rd 100644 0 kb
test_alter_fun.Rd 100644 1 kb
textbox_grob.Rd 100644 3 kb
unify_mat_list.Rd 100644 1 kb
upset_left_annotation.Rd 100644 1 kb
upset_right_annotation.Rd 100644 2 kb
upset_top_annotation.Rd 100644 2 kb
width.AnnotationFunction.Rd 100644 0 kb
width.Heatmap.Rd 100644 0 kb
width.HeatmapAnnotation.Rd 100644 0 kb
width.HeatmapList.Rd 100644 0 kb
width.Legends.Rd 100644 0 kb
width.SingleAnnotation.Rd 100644 0 kb
widthAssign.AnnotationFunction.Rd 100644 1 kb
widthAssign.HeatmapAnnotation.Rd 100644 1 kb
widthAssign.SingleAnnotation.Rd 100644 1 kb
widthDetails.annotation_axis.Rd 100644 0 kb
widthDetails.legend.Rd 100644 0 kb
widthDetails.legend_body.Rd 100644 0 kb
widthDetails.packed_legends.Rd 100644 0 kb
widthDetails.textbox.Rd 100644 0 kb
README.md
# Make Complex Heatmaps <a href="https://jokergoo.github.io/ComplexHeatmap-reference/book/"><img src="https://jokergoo.github.io/ComplexHeatmap-reference/book/complexheatmap-cover.jpg" width=240 align="right" style="border:2px solid black;" ></a> [![R-CMD-check](https://github.com/jokergoo/ComplexHeatmap/workflows/R-CMD-check/badge.svg)](https://github.com/jokergoo/ComplexHeatmap/actions) [![codecov](https://img.shields.io/codecov/c/github/jokergoo/ComplexHeatmap.svg)](https://codecov.io/github/jokergoo/ComplexHeatmap) [![bioc](http://www.bioconductor.org/shields/downloads/devel/ComplexHeatmap.svg)](https://bioconductor.org/packages/stats/bioc/ComplexHeatmap/) [![bioc](http://www.bioconductor.org/shields/years-in-bioc/ComplexHeatmap.svg)](http://bioconductor.org/packages/devel/bioc/html/ComplexHeatmap.html) <img src="http://jokergoo.github.io/complexheatmap_logo.svg" width="550"> Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the **ComplexHeatmap** package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics. The [**InteractiveComplexHeatmap**](https://github.com/jokergoo/InteractiveComplexHeatmap) package can directly export static complex heatmaps into an interactive Shiny app. Have a try! ## Citation Zuguang Gu, et al., [Complex heatmaps reveal patterns and correlations in multidimensional genomic data](http://bioinformatics.oxfordjournals.org/content/early/2016/05/20/bioinformatics.btw313.abstract), Bioinformatics, 2016 ## Install `ComplexHeatmap` is available on [Bioconductor](http://www.bioconductor.org/packages/devel/bioc/html/ComplexHeatmap.html), you can install it by: ```r if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("ComplexHeatmap") ``` If you want the latest version, install it directly from GitHub: ```r library(devtools) install_github("jokergoo/ComplexHeatmap") ``` ## Usage Make a single heatmap: ```r Heatmap(mat, ...) ``` A single Heatmap with column annotations: ```r ha = HeatmapAnnotation(df = anno1, anno_fun = anno2, ...) Heatmap(mat, ..., top_annotation = ha) ``` Make a list of heatmaps: ```r Heatmap(mat1, ...) + Heatmap(mat2, ...) ``` Make a list of heatmaps and row annotations: ```r ha = HeatmapAnnotation(df = anno1, anno_fun = anno2, ..., which = "row") Heatmap(mat1, ...) + Heatmap(mat2, ...) + ha ``` ## Documentation The full documentations are available at https://jokergoo.github.io/ComplexHeatmap-reference/book/ and the website is at https://jokergoo.github.io/ComplexHeatmap. ## Blog posts There are following blog posts focusing on specific topics: - [Make 3D heatmap](https://jokergoo.github.io/2021/03/24/3d-heatmap/) - [Translate from pheatmap to ComplexHeatmap](https://jokergoo.github.io/2020/05/06/translate-from-pheatmap-to-complexheatmap/) - [Set cell width/height in the heatmap](https://jokergoo.github.io/2020/05/11/set-cell-width/height-in-the-heatmap/) - [Interactive ComplexHeatmap](https://jokergoo.github.io/2020/05/15/interactive-complexheatmap/) - [Word cloud as heatmap annotation](https://jokergoo.github.io/2020/05/31/word-cloud-as-heatmap-annotation/) - [Which heatmap function is faster?](https://jokergoo.github.io/2020/06/19/which-heatmap-function-is-faster/) - [Rasterization in ComplexHeatmap](https://jokergoo.github.io/2020/06/30/rasterization-in-complexheatmap/) - [Block annotation over several slices](https://jokergoo.github.io/2020/07/06/block-annotation-over-several-slices/) - [Integrate ComplexHeatmap with cowplot package](https://jokergoo.github.io/2020/07/14/integrate-complexheatmap-with-cowplot-package/) ## Examples ### Visualize Methylation Profile with Complex Annotations ![complexheatmap_example4](https://user-images.githubusercontent.com/449218/47718635-2ec22980-dc49-11e8-9f01-37becb19e0d5.png) ### Correlations between methylation, expression and other genomic features ![complexheatmap_example3](https://user-images.githubusercontent.com/449218/47718636-2ec22980-dc49-11e8-8db0-1659c27dcf40.png) ### Visualize Cell Heterogeneity from Single Cell RNASeq ![complexheatmap_example2](https://user-images.githubusercontent.com/449218/47718637-2ec22980-dc49-11e8-925e-955c16cfa982.png) ### Making Enhanced OncoPrint ![complexheatmap_example1](https://user-images.githubusercontent.com/449218/47718638-2ec22980-dc49-11e8-845e-21e51d3b8e73.png) ### UpSet plot <img src="https://user-images.githubusercontent.com/449218/102615477-48c76a80-4136-11eb-98d9-3c528844fbe8.png" width=500 /> ### 3D heatmap ![image](https://user-images.githubusercontent.com/449218/112284448-8c77c600-8c89-11eb-8d38-c5538900df20.png) ## License MIT @ Zuguang Gu