S3method("+", "AdditiveUnit")
export("+.AdditiveUnit")
S3method("[", "AnnotationFunction")
export("[.AnnotationFunction")
S3method("[", "Heatmap")
export("[.Heatmap")
S3method("[", "HeatmapAnnotation")
export("[.HeatmapAnnotation")
S3method("[", "HeatmapList")
export("[.HeatmapList")
S3method("[", "SingleAnnotation")
export("[.SingleAnnotation")
S3method("[", "comb_mat")
export("[.comb_mat")
S3method("[", "gridtext")
export("[.gridtext")
S3method("c", "ColorMapping")
export("c.ColorMapping")
S3method("c", "HeatmapAnnotation")
export("c.HeatmapAnnotation")
S3method("dim", "Heatmap")
export("dim.Heatmap")
S3method("grid.draw", "Legends")
export("grid.draw.Legends")
S3method("height", "AnnotationFunction")
export("height.AnnotationFunction")
S3method("height", "Heatmap")
export("height.Heatmap")
S3method("height", "HeatmapAnnotation")
export("height.HeatmapAnnotation")
S3method("height", "HeatmapList")
export("height.HeatmapList")
S3method("height", "Legends")
export("height.Legends")
S3method("height", "SingleAnnotation")
export("height.SingleAnnotation")
S3method("height<-", "AnnotationFunction")
export("height<-.AnnotationFunction")
S3method("height<-", "HeatmapAnnotation")
export("height<-.HeatmapAnnotation")
S3method("height<-", "SingleAnnotation")
export("height<-.SingleAnnotation")
S3method("heightDetails", "annotation_axis")
export("heightDetails.annotation_axis")
S3method("heightDetails", "legend")
export("heightDetails.legend")
S3method("heightDetails", "legend_body")
export("heightDetails.legend_body")
S3method("heightDetails", "packed_legends")
export("heightDetails.packed_legends")
S3method("heightDetails", "textbox")
export("heightDetails.textbox")
S3method("length", "HeatmapAnnotation")
export("length.HeatmapAnnotation")
S3method("length", "HeatmapList")
export("length.HeatmapList")
S3method("names", "HeatmapAnnotation")
export("names.HeatmapAnnotation")
S3method("names", "HeatmapList")
export("names.HeatmapList")
S3method("names<-", "HeatmapAnnotation")
export("names<-.HeatmapAnnotation")
S3method("ncol", "Heatmap")
export("ncol.Heatmap")
S3method("nobs", "AnnotationFunction")
export("nobs.AnnotationFunction")
S3method("nobs", "HeatmapAnnotation")
export("nobs.HeatmapAnnotation")
S3method("nobs", "SingleAnnotation")
export("nobs.SingleAnnotation")
S3method("nrow", "Heatmap")
export("nrow.Heatmap")
S3method("plot", "Heatmap")
export("plot.Heatmap")
S3method("plot", "HeatmapAnnotation")
export("plot.HeatmapAnnotation")
S3method("plot", "HeatmapList")
export("plot.HeatmapList")
S3method("print", "comb_mat")
export("print.comb_mat")
S3method("size", "AnnotationFunction")
export("size.AnnotationFunction")
S3method("size", "HeatmapAnnotation")
export("size.HeatmapAnnotation")
S3method("size", "SingleAnnotation")
export("size.SingleAnnotation")
S3method("size<-", "AnnotationFunction")
export("size<-.AnnotationFunction")
S3method("size<-", "HeatmapAnnotation")
export("size<-.HeatmapAnnotation")
S3method("size<-", "SingleAnnotation")
export("size<-.SingleAnnotation")
S3method("str", "comb_mat")
export("str.comb_mat")
S3method("summary", "Heatmap")
export("summary.Heatmap")
S3method("summary", "HeatmapList")
export("summary.HeatmapList")
S3method("t", "comb_mat")
export("t.comb_mat")
S3method("width", "AnnotationFunction")
export("width.AnnotationFunction")
S3method("width", "Heatmap")
export("width.Heatmap")
S3method("width", "HeatmapAnnotation")
export("width.HeatmapAnnotation")
S3method("width", "HeatmapList")
export("width.HeatmapList")
S3method("width", "Legends")
export("width.Legends")
S3method("width", "SingleAnnotation")
export("width.SingleAnnotation")
S3method("width<-", "AnnotationFunction")
export("width<-.AnnotationFunction")
S3method("width<-", "HeatmapAnnotation")
export("width<-.HeatmapAnnotation")
S3method("width<-", "SingleAnnotation")
export("width<-.SingleAnnotation")
S3method("widthDetails", "annotation_axis")
export("widthDetails.annotation_axis")
S3method("widthDetails", "legend")
export("widthDetails.legend")
S3method("widthDetails", "legend_body")
export("widthDetails.legend_body")
S3method("widthDetails", "packed_legends")
export("widthDetails.packed_legends")
S3method("widthDetails", "textbox")
export("widthDetails.textbox")
export("%v%")
export("AdditiveUnit")
export("AnnotationFunction")
export("ColorMapping")
export("Heatmap")
export("Heatmap3D")
export("HeatmapAnnotation")
export("HeatmapList")
export("Legend")
export("Legends")
export("SingleAnnotation")
export("UpSet")
export("adjust_dend_by_x")
export("alter_graphic")
export("anno_barplot")
export("anno_block")
export("anno_boxplot")
export("anno_customize")
export("anno_density")
export("anno_empty")
export("anno_histogram")
export("anno_horizon")
export("anno_image")
export("anno_joyplot")
export("anno_lines")
export("anno_link")
export("anno_mark")
export("anno_numeric")
export("anno_oncoprint_barplot")
export("anno_points")
export("anno_simple")
export("anno_summary")
export("anno_text")
export("anno_textbox")
export("anno_zoom")
export("annotation_axis_grob")
export("bar3D")
export("bin_genome")
export("cluster_between_groups")
export("cluster_within_group")
export("columnAnnotation")
export("comb_degree")
export("comb_name")
export("comb_size")
export("compare_heatmap")
export("compare_heatmap.2")
export("compare_pheatmap")
export("complement_size")
export("decorate_annotation")
export("decorate_column_dend")
export("decorate_column_names")
export("decorate_column_title")
export("decorate_dend")
export("decorate_dimnames")
export("decorate_heatmap_body")
export("decorate_row_dend")
export("decorate_row_names")
export("decorate_row_title")
export("decorate_title")
export("default_axis_param")
export("default_get_type")
export("dend_heights")
export("dend_xy")
export("dendrogramGrob")
export("densityHeatmap")
export("dist2")
export("extract_comb")
export("frequencyHeatmap")
export("full_comb_code")
export("getXY_in_parent_vp")
export("grid.annotation_axis")
export("grid.boxplot")
export("grid.dendrogram")
export("grid.textbox")
export("gt_render")
export("ht_global_opt")
export("ht_opt")
export("ht_size")
export("is_abs_unit")
export("list_components")
export("list_to_matrix")
export("make_comb_mat")
export("max_text_height")
export("max_text_width")
export("merge_dendrogram")
export("normalize_comb_mat")
export("normalize_genomic_signals_to_bins")
export("oncoPrint")
export("order.comb_mat")
export("packLegend")
export("pheatmap")
export("pindex")
export("restore_matrix")
export("rowAnnotation")
export("row_anno_barplot")
export("row_anno_boxplot")
export("row_anno_density")
export("row_anno_histogram")
export("row_anno_points")
export("row_anno_text")
export("set_name")
export("set_name<-")
export("set_size")
export("smartAlign2")
export("subset_gp")
export("subset_matrix_by_row")
export("subset_no")
export("subset_vector")
export("test_alter_fun")
export("textbox_grob")
export("unify_mat_list")
export("upset_left_annotation")
export("upset_right_annotation")
export("upset_top_annotation")
exportClasses("AdditiveUnit")
export("AdditiveUnit")
exportClasses("AnnotationFunction")
export("AnnotationFunction")
exportClasses("ColorMapping")
export("ColorMapping")
exportClasses("Heatmap")
export("Heatmap")
exportClasses("HeatmapAnnotation")
export("HeatmapAnnotation")
exportClasses("HeatmapList")
export("HeatmapList")
exportClasses("Legends")
export("Legends")
exportClasses("SingleAnnotation")
export("SingleAnnotation")
exportMethods("add_heatmap")
exportMethods("adjust_heatmap_list")
exportMethods("annotation_legend_size")
exportMethods("attach_annotation")
exportMethods("color_mapping_legend")
exportMethods("column_dend")
exportMethods("column_order")
exportMethods("component_height")
exportMethods("component_width")
exportMethods("copy_all")
exportMethods("draw")
exportMethods("draw_annotation")
exportMethods("draw_annotation_legend")
exportMethods("draw_dend")
exportMethods("draw_dimnames")
exportMethods("draw_heatmap_body")
exportMethods("draw_heatmap_legend")
exportMethods("draw_heatmap_list")
exportMethods("draw_title")
exportMethods("get_color_mapping_list")
exportMethods("get_legend_param_list")
exportMethods("heatmap_legend_size")
exportMethods("make_column_cluster")
exportMethods("make_layout")
exportMethods("make_row_cluster")
exportMethods("map_to_colors")
exportMethods("prepare")
exportMethods("re_size")
exportMethods("row_dend")
exportMethods("row_order")
exportMethods("set_component_height")
exportMethods("set_component_width")

import(digest)
import(doParallel)
import(foreach)
import(grDevices)
import(graphics)
import(grid)
import(matrixStats)
import(methods)
import(parallel)
import(png)
import(stats)
importFrom("GetoptLong", qq)
importFrom("GetoptLong", qq.options)
importFrom("GetoptLong", qqcat)
importFrom("GlobalOptions", setGlobalOptions)
importFrom("IRanges", "IntegerList")
importFrom("RColorBrewer", brewer.pal)
importFrom("circlize", add_transparency)
importFrom("circlize", colorRamp2)
importFrom("circlize", rand_color)
importFrom("circlize", smartAlign)
importFrom("clue", as.cl_hard_partition)
importFrom("clue", cl_class_ids)
importFrom("clue", cl_consensus)
importFrom("clue", cl_ensemble)
importFrom("codetools", "findGlobals")
importFrom("colorspace", RGB)
importFrom("colorspace", coords)
importFrom("colorspace", diverge_hcl)
importFrom("colorspace", rainbow_hcl)
importFrom("colorspace", sequential_hcl)
importFrom("utils", "combn")
importFrom("utils", "getFromNamespace")
importFrom("utils", "packageDescription")
importFrom("utils", "str")

