Files in jokergoo/ComplexHeatmap

Make Complex Heatmaps

.Rbuildignore

.github/.gitignore

.github/ISSUE_TEMPLATE/getting-help.md

.github/workflows/R-CMD-check.yaml

.gitignore

CODE_OF_CONDUCT.md

DESCRIPTION

LICENSE

NAMESPACE

NEWS

R/00_S4_generic_methods.R R/00_size.R R/3d.R R/AdditiveUnit-class.R R/AnnotationFunction-class.R R/AnnotationFunction-function.R R/ColorMapping-class.R R/Heatmap-class.R R/Heatmap-draw_component.R R/Heatmap-layout.R R/Heatmap-utils.R R/HeatmapAnnotation-class.R R/HeatmapList-class.R R/HeatmapList-draw_component.R R/HeatmapList-get_order.R R/HeatmapList-layout.R R/HeatmapList-legends.R R/SingleAnnotation-class.R R/Upset.R R/anno_textbox.R R/annotation_axis.R R/box_align.R R/decorate.R R/densityHeatmap.R R/genomic.R R/global.R R/grid.Legend.R R/grid.dendrogram.R R/gridtext.R R/is_abs_unit.R R/oncoPrint.R R/other_translation.R R/overview.R R/pheatmap_translate.R R/stacked_plot.R R/temp.R R/utils.R R/zzz.R README.md

_pkgdown.yml

build_pkg_site.R

docs/404.html

docs/LICENSE-text.html

docs/articles/complex_heatmap.html

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docs/reference/test_alter_fun-1.png

docs/reference/test_alter_fun.html

docs/reference/test_alter_fun.rd

docs/reference/unify_mat_list.html

docs/reference/unify_mat_list.rd

docs/reference/upset_right_annotation.html

docs/reference/upset_right_annotation.rd

docs/reference/upset_top_annotation.html

docs/reference/upset_top_annotation.rd

docs/reference/width.AnnotationFunction.html

docs/reference/width.AnnotationFunction.rd

docs/reference/width.Heatmap.html

docs/reference/width.Heatmap.rd

docs/reference/width.HeatmapAnnotation.html

docs/reference/width.HeatmapAnnotation.rd

docs/reference/width.HeatmapList.html

docs/reference/width.HeatmapList.rd

docs/reference/width.Legends.html

docs/reference/width.Legends.rd

docs/reference/width.SingleAnnotation.html

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docs/reference/widthAssign.AnnotationFunction.html

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docs/reference/widthAssign.HeatmapAnnotation.html

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docs/reference/widthAssign.SingleAnnotation.html

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docs/reference/widthDetails.annotation_axis.html

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docs/reference/widthDetails.legend_body.html

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docs/reference/widthDetails.packed_legends.html

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inst/CITATION

inst/extdata/dmr_summary.rds

inst/extdata/gene_expression.rds

inst/extdata/generate_random_dataset.R

inst/extdata/gr.rds

inst/extdata/measles.rds

inst/extdata/meth.rds

inst/extdata/rand_mat.rds

inst/extdata/random_meth_expr_data.RData

inst/extdata/sample_order.txt

inst/extdata/tcga_lung_adenocarcinoma_provisional_ras_raf_mek_jnk_signalling.rds

inst/extdata/tcga_lung_adenocarcinoma_provisional_ras_raf_mek_jnk_signalling.txt

logo.R man/AdditiveUnit-class.Rd man/AdditiveUnit.Rd man/AnnotationFunction-class.Rd man/AnnotationFunction.Rd man/ColorMapping-class.Rd man/ColorMapping.Rd man/ComplexHeatmap-package.Rd man/Extract.AnnotationFunction.Rd man/Extract.Heatmap.Rd man/Extract.HeatmapAnnotation.Rd man/Extract.HeatmapList.Rd man/Extract.SingleAnnotation.Rd man/Extract.comb_mat.Rd man/Extract.gridtext.Rd man/Heatmap-class.Rd man/Heatmap.Rd man/Heatmap3D.Rd man/HeatmapAnnotation-class.Rd man/HeatmapAnnotation.Rd man/HeatmapList-class.Rd man/HeatmapList.Rd man/Legend.Rd man/Legends-class.Rd man/Legends.Rd man/SingleAnnotation-class.Rd man/SingleAnnotation.Rd man/UpSet.Rd man/add.AdditiveUnit.Rd man/add_heatmap-Heatmap-method.Rd man/add_heatmap-HeatmapAnnotation-method.Rd man/add_heatmap-HeatmapList-method.Rd man/add_heatmap-dispatch.Rd man/adjust_dend_by_x.Rd man/adjust_heatmap_list-HeatmapList-method.Rd man/alter_graphic.Rd man/anno_barplot.Rd man/anno_block.Rd man/anno_boxplot.Rd man/anno_customize.Rd man/anno_density.Rd man/anno_empty.Rd man/anno_histogram.Rd man/anno_horizon.Rd man/anno_image.Rd man/anno_joyplot.Rd man/anno_lines.Rd man/anno_link.Rd man/anno_mark.Rd man/anno_numeric.Rd man/anno_oncoprint_barplot.Rd man/anno_points.Rd man/anno_simple.Rd man/anno_summary.Rd man/anno_text.Rd man/anno_textbox.Rd man/anno_zoom.Rd man/annotation_axis_grob.Rd man/annotation_legend_size-HeatmapList-method.Rd man/attach_annotation-Heatmap-method.Rd man/bar3D.Rd man/bin_genome.Rd man/c.ColorMapping.Rd man/c.HeatmapAnnotation.Rd man/cluster_between_groups.Rd man/cluster_within_group.Rd man/color_mapping_legend-ColorMapping-method.Rd man/columnAnnotation.Rd man/column_dend-Heatmap-method.Rd man/column_dend-HeatmapList-method.Rd man/column_dend-dispatch.Rd man/column_order-Heatmap-method.Rd man/column_order-HeatmapList-method.Rd man/column_order-dispatch.Rd man/comb_degree.Rd man/comb_name.Rd man/comb_size.Rd man/compare_heatmap.2.Rd man/compare_heatmap.Rd man/compare_pheatmap.Rd man/complement_size.Rd man/component_height-Heatmap-method.Rd man/component_height-HeatmapList-method.Rd man/component_height-dispatch.Rd man/component_width-Heatmap-method.Rd man/component_width-HeatmapList-method.Rd man/component_width-dispatch.Rd man/copy_all-AnnotationFunction-method.Rd man/copy_all-SingleAnnotation-method.Rd man/copy_all-dispatch.Rd man/decorate_annotation.Rd man/decorate_column_dend.Rd man/decorate_column_names.Rd man/decorate_column_title.Rd man/decorate_dend.Rd man/decorate_dimnames.Rd man/decorate_heatmap_body.Rd man/decorate_row_dend.Rd man/decorate_row_names.Rd man/decorate_row_title.Rd man/decorate_title.Rd man/default_axis_param.Rd man/default_get_type.Rd man/dend_heights.Rd man/dend_xy.Rd man/dendrogramGrob.Rd man/densityHeatmap.Rd man/dim.Heatmap.Rd man/dist2.Rd man/draw-AnnotationFunction-method.Rd man/draw-Heatmap-method.Rd man/draw-HeatmapAnnotation-method.Rd man/draw-HeatmapList-method.Rd man/draw-Legends-method.Rd man/draw-SingleAnnotation-method.Rd man/draw-dispatch.Rd man/draw_annotation-Heatmap-method.Rd man/draw_annotation_legend-HeatmapList-method.Rd man/draw_dend-Heatmap-method.Rd man/draw_dimnames-Heatmap-method.Rd man/draw_heatmap_body-Heatmap-method.Rd man/draw_heatmap_legend-HeatmapList-method.Rd man/draw_heatmap_list-HeatmapList-method.Rd man/draw_title-Heatmap-method.Rd man/draw_title-HeatmapList-method.Rd man/draw_title-dispatch.Rd man/extract_comb.Rd man/frequencyHeatmap.Rd man/full_comb_code.Rd man/getXY_in_parent_vp.Rd man/get_color_mapping_list-HeatmapAnnotation-method.Rd man/get_legend_param_list-HeatmapAnnotation-method.Rd man/grid.annotation_axis.Rd man/grid.boxplot.Rd man/grid.dendrogram.Rd man/grid.draw.Legends.Rd man/grid.textbox.Rd man/gt_render.Rd man/heatmap_legend_size-HeatmapList-method.Rd man/height.AnnotationFunction.Rd man/height.Heatmap.Rd man/height.HeatmapAnnotation.Rd man/height.HeatmapList.Rd man/height.Legends.Rd man/height.SingleAnnotation.Rd man/heightAssign.AnnotationFunction.Rd man/heightAssign.HeatmapAnnotation.Rd man/heightAssign.SingleAnnotation.Rd man/heightDetails.annotation_axis.Rd man/heightDetails.legend.Rd man/heightDetails.legend_body.Rd man/heightDetails.packed_legends.Rd man/heightDetails.textbox.Rd man/ht_global_opt.Rd man/ht_opt.Rd man/ht_size.Rd man/is_abs_unit.Rd man/length.HeatmapAnnotation.Rd man/length.HeatmapList.Rd man/list_components.Rd man/list_to_matrix.Rd man/make_column_cluster-Heatmap-method.Rd man/make_comb_mat.Rd man/make_layout-Heatmap-method.Rd man/make_layout-HeatmapList-method.Rd man/make_layout-dispatch.Rd man/make_row_cluster-Heatmap-method.Rd man/map_to_colors-ColorMapping-method.Rd man/max_text_height.Rd man/max_text_width.Rd man/merge_dendrogram.Rd man/names.HeatmapAnnotation.Rd man/names.HeatmapList.Rd man/namesAssign.HeatmapAnnotation.Rd man/ncol.Heatmap.Rd man/nobs.AnnotationFunction.Rd man/nobs.HeatmapAnnotation.Rd man/nobs.SingleAnnotation.Rd man/normalize_comb_mat.Rd man/normalize_genomic_signals_to_bins.Rd man/nrow.Heatmap.Rd man/oncoPrint.Rd man/order.comb_mat.Rd man/packLegend.Rd man/pct_v_pct.Rd man/pheatmap.Rd man/pindex.Rd man/plot.Heatmap.Rd man/plot.HeatmapAnnotation.Rd man/plot.HeatmapList.Rd man/prepare-Heatmap-method.Rd man/print.comb_mat.Rd man/re_size-HeatmapAnnotation-method.Rd man/restore_matrix.Rd man/rowAnnotation.Rd man/row_anno_barplot.Rd man/row_anno_boxplot.Rd man/row_anno_density.Rd man/row_anno_histogram.Rd man/row_anno_points.Rd man/row_anno_text.Rd man/row_dend-Heatmap-method.Rd man/row_dend-HeatmapList-method.Rd man/row_dend-dispatch.Rd man/row_order-Heatmap-method.Rd man/row_order-HeatmapList-method.Rd man/row_order-dispatch.Rd man/set_component_height-Heatmap-method.Rd man/set_component_width-Heatmap-method.Rd man/set_name.Rd man/set_nameAssign.Rd man/set_size.Rd man/show-AnnotationFunction-method.Rd man/show-ColorMapping-method.Rd man/show-Heatmap-method.Rd man/show-HeatmapAnnotation-method.Rd man/show-HeatmapList-method.Rd man/show-SingleAnnotation-method.Rd man/show-dispatch.Rd man/size.AnnotationFunction.Rd man/size.HeatmapAnnotation.Rd man/size.SingleAnnotation.Rd man/sizeAssign.AnnotationFunction.Rd man/sizeAssign.HeatmapAnnotation.Rd man/sizeAssign.SingleAnnotation.Rd man/smartAlign2.Rd man/str.comb_mat.Rd man/subset_gp.Rd man/subset_matrix_by_row.Rd man/subset_no.Rd man/subset_vector.Rd man/summary.Heatmap.Rd man/summary.HeatmapList.Rd man/t.comb_mat.Rd man/test_alter_fun.Rd man/textbox_grob.Rd man/unify_mat_list.Rd man/upset_left_annotation.Rd man/upset_right_annotation.Rd man/upset_top_annotation.Rd man/width.AnnotationFunction.Rd man/width.Heatmap.Rd man/width.HeatmapAnnotation.Rd man/width.HeatmapList.Rd man/width.Legends.Rd man/width.SingleAnnotation.Rd man/widthAssign.AnnotationFunction.Rd man/widthAssign.HeatmapAnnotation.Rd man/widthAssign.SingleAnnotation.Rd man/widthDetails.annotation_axis.Rd man/widthDetails.legend.Rd man/widthDetails.legend_body.Rd man/widthDetails.packed_legends.Rd man/widthDetails.textbox.Rd

tests/.directory

tests/test-AnnotationFunction.R tests/test-ColorMapping-class.R tests/test-Heatmap-class.R tests/test-Heatmap-cluster.R tests/test-HeatmapAnnotation.R tests/test-HeatmapList-class.R tests/test-Legend.R tests/test-SingleAnnotation.R tests/test-annotation_axis.R tests/test-dendrogram.R tests/test-gridtext.R tests/test-interactive.R tests/test-multiple-page.R tests/test-oncoPrint.R tests/test-pheatmap.R tests/test-textbox.R tests/test-upset.R tests/test-utils.R tests/testthat-all.R tests/testthat/testhat-utiles.R tests/testthat/testthat-ColorMapping.R tests/testthat/testthat-HeatmapAnnotation-size.R tests/testthat/testthat-UpSet.R vignettes/complex_heatmap.rmd

vignettes/custom.css

vignettes/most_probably_asked_questions.Rmd

jokergoo/ComplexHeatmap documentation built on Nov. 17, 2023, 11:27 a.m.