| ... | ... |
@@ -1,100 +1,96 @@ |
| 1 |
-export(column_anno_histogram) |
|
| 2 |
-export(anno_boxplot) |
|
| 3 |
-exportMethods(column_order) |
|
| 1 |
+export('+.AdditiveUnit')
|
|
| 2 |
+export(AdditiveUnit) |
|
| 4 | 3 |
export(ColorMapping) |
| 4 |
+export(Heatmap) |
|
| 5 | 5 |
export(HeatmapAnnotation) |
| 6 |
+export(HeatmapList) |
|
| 7 |
+export(Legend) |
|
| 8 |
+export(SingleAnnotation) |
|
| 9 |
+export(anno_barplot) |
|
| 10 |
+export(anno_boxplot) |
|
| 11 |
+export(anno_density) |
|
| 12 |
+export(anno_histogram) |
|
| 13 |
+export(anno_link) |
|
| 14 |
+export(anno_points) |
|
| 15 |
+export(anno_text) |
|
| 16 |
+export(columnAnnotation) |
|
| 17 |
+export(column_anno_barplot) |
|
| 6 | 18 |
export(column_anno_boxplot) |
| 7 |
-export(selectArea) |
|
| 8 |
-export(row_anno_barplot) |
|
| 9 |
-export(Heatmap) |
|
| 10 |
-export(row_anno_points) |
|
| 19 |
+export(column_anno_density) |
|
| 20 |
+export(column_anno_histogram) |
|
| 21 |
+export(column_anno_link) |
|
| 22 |
+export(column_anno_points) |
|
| 11 | 23 |
export(column_anno_text) |
| 12 |
-export(decorate_row_dend) |
|
| 13 |
-export(decorate_column_dend) |
|
| 14 |
-exportMethods(draw) |
|
| 15 |
-export(unify_mat_list) |
|
| 16 |
-exportMethods(draw_heatmap_body) |
|
| 17 |
-exportMethods(color_mapping_legend) |
|
| 18 |
-exportMethods(prepare) |
|
| 19 | 24 |
export(decorate_annotation) |
| 20 |
-exportMethods(map_to_colors) |
|
| 25 |
+export(decorate_column_dend) |
|
| 26 |
+export(decorate_column_names) |
|
| 27 |
+export(decorate_column_title) |
|
| 28 |
+export(decorate_dend) |
|
| 21 | 29 |
export(decorate_dimnames) |
| 22 |
-export(column_anno_points) |
|
| 23 |
-exportMethods(component_height) |
|
| 24 |
-export(row_anno_text) |
|
| 25 |
-exportClasses(SingleAnnotation) |
|
| 26 |
-export(SingleAnnotation) |
|
| 27 |
-export(oncoPrint) |
|
| 28 |
-exportClasses(AdditiveUnit) |
|
| 29 |
-export(AdditiveUnit) |
|
| 30 |
-export(max_text_height) |
|
| 30 |
+export(decorate_heatmap_body) |
|
| 31 |
+export(decorate_row_dend) |
|
| 32 |
+export(decorate_row_names) |
|
| 33 |
+export(decorate_row_title) |
|
| 34 |
+export(decorate_title) |
|
| 35 |
+export(densityHeatmap) |
|
| 36 |
+export(dist2) |
|
| 31 | 37 |
export(enhanced_basicplot) |
| 32 |
-exportMethods(annotation_legend_size) |
|
| 33 |
-exportMethods(row_order) |
|
| 34 |
-export(Legend) |
|
| 35 |
-export(AdditiveUnit) |
|
| 36 |
-exportMethods(draw_heatmap_list) |
|
| 37 |
-export(row_anno_density) |
|
| 38 |
+export(grid.dendrogram) |
|
| 39 |
+export(ht_global_opt) |
|
| 38 | 40 |
export(is_abs_unit) |
| 39 |
-export(dist2) |
|
| 40 |
-export(decorate_heatmap_body) |
|
| 41 |
-exportMethods(draw_heatmap_legend) |
|
| 42 |
-exportMethods(add_heatmap) |
|
| 43 |
-export(anno_barplot) |
|
| 44 |
-exportMethods(row_dend) |
|
| 45 |
-export(row_anno_boxplot) |
|
| 41 |
+export(max_text_height) |
|
| 46 | 42 |
export(max_text_width) |
| 47 |
-export(anno_link) |
|
| 48 |
-exportMethods(make_layout) |
|
| 49 |
-export(decorate_row_title) |
|
| 50 |
-export(anno_histogram) |
|
| 43 |
+export(oncoPrint) |
|
| 51 | 44 |
export(plotDataFrame) |
| 52 |
-exportMethods(draw_dimnames) |
|
| 45 |
+export(rowAnnotation) |
|
| 46 |
+export(row_anno_barplot) |
|
| 47 |
+export(row_anno_boxplot) |
|
| 48 |
+export(row_anno_density) |
|
| 49 |
+export(row_anno_histogram) |
|
| 50 |
+export(row_anno_link) |
|
| 51 |
+export(row_anno_points) |
|
| 52 |
+export(row_anno_text) |
|
| 53 |
+export(selectArea) |
|
| 54 |
+export(unify_mat_list) |
|
| 55 |
+exportClasses(AdditiveUnit) |
|
| 56 |
+export(AdditiveUnit) |
|
| 53 | 57 |
exportClasses(ColorMapping) |
| 54 | 58 |
export(ColorMapping) |
| 59 |
+exportClasses(Heatmap) |
|
| 60 |
+export(Heatmap) |
|
| 55 | 61 |
exportClasses(HeatmapAnnotation) |
| 56 | 62 |
export(HeatmapAnnotation) |
| 57 |
-export(anno_points) |
|
| 58 |
-exportMethods(draw_title) |
|
| 59 |
-export(ht_global_opt) |
|
| 60 |
-export('+.AdditiveUnit')
|
|
| 61 |
-export(decorate_column_names) |
|
| 62 |
-export(column_anno_barplot) |
|
| 63 |
-export(densityHeatmap) |
|
| 64 |
-exportMethods(heatmap_legend_size) |
|
| 65 | 63 |
exportClasses(HeatmapList) |
| 66 | 64 |
export(HeatmapList) |
| 67 |
-export(column_anno_density) |
|
| 68 |
-exportClasses(Heatmap) |
|
| 69 |
-export(Heatmap) |
|
| 70 |
-exportMethods(draw_annotation_legend) |
|
| 71 |
-exportMethods(column_dend) |
|
| 72 |
-exportMethods(set_component_height) |
|
| 73 |
-export(row_anno_link) |
|
| 74 |
-exportMethods(make_column_cluster) |
|
| 75 |
-export(HeatmapList) |
|
| 76 |
-exportMethods(draw_annotation) |
|
| 65 |
+exportClasses(SingleAnnotation) |
|
| 77 | 66 |
export(SingleAnnotation) |
| 78 |
-export(row_anno_histogram) |
|
| 79 |
-exportMethods(get_color_mapping_list) |
|
| 80 |
-exportMethods(make_row_cluster) |
|
| 67 |
+exportMethods(add_heatmap) |
|
| 68 |
+exportMethods(annotation_legend_size) |
|
| 69 |
+exportMethods(color_mapping_legend) |
|
| 70 |
+exportMethods(column_dend) |
|
| 71 |
+exportMethods(column_order) |
|
| 72 |
+exportMethods(component_height) |
|
| 81 | 73 |
exportMethods(component_width) |
| 82 |
-export(decorate_column_title) |
|
| 74 |
+exportMethods(draw) |
|
| 75 |
+exportMethods(draw_annotation) |
|
| 76 |
+exportMethods(draw_annotation_legend) |
|
| 83 | 77 |
exportMethods(draw_dend) |
| 78 |
+exportMethods(draw_dimnames) |
|
| 79 |
+exportMethods(draw_heatmap_body) |
|
| 80 |
+exportMethods(draw_heatmap_legend) |
|
| 81 |
+exportMethods(draw_heatmap_list) |
|
| 82 |
+exportMethods(draw_title) |
|
| 83 |
+exportMethods(get_color_mapping_list) |
|
| 84 | 84 |
exportMethods(get_color_mapping_param_list) |
| 85 |
-export(grid.dendrogram) |
|
| 86 |
-export(decorate_title) |
|
| 87 |
-export(decorate_dend) |
|
| 88 |
-export(rowAnnotation) |
|
| 89 |
-export(column_anno_link) |
|
| 90 |
-export(columnAnnotation) |
|
| 91 |
-export(decorate_row_names) |
|
| 92 |
-export(anno_text) |
|
| 93 |
-export(anno_density) |
|
| 94 |
- |
|
| 95 |
- |
|
| 96 |
- |
|
| 97 |
- |
|
| 85 |
+exportMethods(heatmap_legend_size) |
|
| 86 |
+exportMethods(make_column_cluster) |
|
| 87 |
+exportMethods(make_layout) |
|
| 88 |
+exportMethods(make_row_cluster) |
|
| 89 |
+exportMethods(map_to_colors) |
|
| 90 |
+exportMethods(prepare) |
|
| 91 |
+exportMethods(row_dend) |
|
| 92 |
+exportMethods(row_order) |
|
| 93 |
+exportMethods(set_component_height) |
|
| 98 | 94 |
|
| 99 | 95 |
import(grDevices) |
| 100 | 96 |
import(graphics) |
| ... | ... |
@@ -113,12 +109,9 @@ importFrom("colorspace", rainbow_hcl)
|
| 113 | 109 |
importFrom("dendextend", "labels<-")
|
| 114 | 110 |
importFrom("dendextend", get_branches_heights)
|
| 115 | 111 |
importFrom("dendextend", nnodes)
|
| 112 |
+importFrom("methods", "new", "show")
|
|
| 116 | 113 |
importFrom("methods", setClass)
|
| 117 | 114 |
importFrom("methods", setGeneric)
|
| 118 | 115 |
importFrom("methods", setMethod)
|
| 119 |
-importFrom("methods", "new", "show")
|
|
| 120 | 116 |
importFrom("utils", "getFromNamespace")
|
| 121 | 117 |
|
| 122 |
- |
|
| 123 |
- |
|
| 124 |
- |
| ... | ... |
@@ -25,10 +25,10 @@ setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
|
| 25 | 25 |
|
| 26 | 26 |
setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
|
| 27 | 27 |
|
| 28 |
-setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
|
|
| 29 |
- |
|
| 30 | 28 |
setGeneric('get_color_mapping_param_list', function(object, ...) standardGeneric('get_color_mapping_param_list'))
|
| 31 | 29 |
|
| 30 |
+setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
|
|
| 31 |
+ |
|
| 32 | 32 |
setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
|
| 33 | 33 |
|
| 34 | 34 |
setGeneric('draw', function(object, ...) standardGeneric('draw'))
|
| ... | ... |
@@ -52,6 +52,11 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",
|
| 52 | 52 |
# -width width of the whole heatmap annotations, only used for row annotation when appending to the list of heatmaps. |
| 53 | 53 |
# -gp graphic parameters for simple annotations. |
| 54 | 54 |
# -gap gap between each annotation |
| 55 |
+# -show_annotation_name whether show annotation names. For column annotation, annotation names are drawn either on the left |
|
| 56 |
+# or the right, and for row annotations, names are draw either on top to at bottom. The value can be a vector. |
|
| 57 |
+# -annotation_name_gp graphic parameters for anntation names. Graphic paramters can be vectors. |
|
| 58 |
+# -annotation_name_offset offset to the annotations, `grid::unit` object. The value can be a vector. |
|
| 59 |
+# -annotation_name_side side of the annotation names. |
|
| 55 | 60 |
# |
| 56 | 61 |
# == details |
| 57 | 62 |
# The simple annotations are defined by ``df`` and ``col`` arguments. Complex annotations are |
| ... | ... |
@@ -76,7 +81,11 @@ HeatmapAnnotation = function(df, name, col, na_col = "grey", |
| 76 | 81 |
height = calc_anno_size(), |
| 77 | 82 |
width = calc_anno_size(), |
| 78 | 83 |
gp = gpar(col = NA), |
| 79 |
- gap = unit(0, "mm")) {
|
|
| 84 |
+ gap = unit(0, "mm"), |
|
| 85 |
+ show_annotation_name = FALSE, |
|
| 86 |
+ annotation_name_gp = gpar(), |
|
| 87 |
+ annotation_name_offset = unit(2, "mm"), |
|
| 88 |
+ annotation_name_side = ifelse(which == "column", "right", "bottom")) {
|
|
| 80 | 89 |
|
| 81 | 90 |
.Object = new("HeatmapAnnotation")
|
| 82 | 91 |
|
| ... | ... |
@@ -94,7 +103,8 @@ HeatmapAnnotation = function(df, name, col, na_col = "grey", |
| 94 | 103 |
arg_list = as.list(match.call())[-1] |
| 95 | 104 |
called_args = names(arg_list) |
| 96 | 105 |
anno_args = setdiff(called_args, c("name", "col", "na_col", "annotation_legend_param", "show_legend", "which",
|
| 97 |
- "annotation_height", "annotation_width", "height", "width", "gp", "gap")) |
|
| 106 |
+ "annotation_height", "annotation_width", "height", "width", "gp", "gap", |
|
| 107 |
+ "show_annotation_name", "annotation_name_gp", "annotation_name_offset", "annotation_name_side")) |
|
| 98 | 108 |
if(any(anno_args == "")) stop("annotations should have names.")
|
| 99 | 109 |
if(any(duplicated(anno_args))) stop("names of annotations should be unique.")
|
| 100 | 110 |
anno_arg_list = list(...) |
| ... | ... |
@@ -143,7 +153,27 @@ HeatmapAnnotation = function(df, name, col, na_col = "grey", |
| 143 | 153 |
} |
| 144 | 154 |
} |
| 145 | 155 |
|
| 156 |
+ n_total_anno = 0 |
|
| 157 |
+ for(ag in anno_args) {
|
|
| 158 |
+ if(ag == "df") {
|
|
| 159 |
+ n_total_anno = n_total_anno + ncol(df) |
|
| 160 |
+ } else {
|
|
| 161 |
+ n_total_anno = n_total_anno + 1 |
|
| 162 |
+ } |
|
| 163 |
+ } |
|
| 164 |
+ if(length(show_annotation_name) == 1) {
|
|
| 165 |
+ show_annotation_name = rep(show_annotation_name, n_total_anno) |
|
| 166 |
+ } |
|
| 167 |
+ if(length(annotation_name_offset) == 1) {
|
|
| 168 |
+ annotation_name_offset = rep(annotation_name_offset, n_total_anno) |
|
| 169 |
+ } |
|
| 170 |
+ if(length(annotation_name_side) == 1) {
|
|
| 171 |
+ annotation_name_side = rep(annotation_name_side, n_total_anno) |
|
| 172 |
+ } |
|
| 173 |
+ annotation_name_gp = recycle_gp(annotation_name_gp, n_total_anno) |
|
| 174 |
+ |
|
| 146 | 175 |
i_simple = 0 |
| 176 |
+ i_anno = 0 |
|
| 147 | 177 |
simple_length = NULL |
| 148 | 178 |
for(ag in anno_args) {
|
| 149 | 179 |
if(ag == "df") {
|
| ... | ... |
@@ -161,21 +191,35 @@ HeatmapAnnotation = function(df, name, col, na_col = "grey", |
| 161 | 191 |
|
| 162 | 192 |
if(missing(col)) {
|
| 163 | 193 |
for(i in seq_len(n_anno)) {
|
| 164 |
- anno_list = c(anno_list, list(SingleAnnotation(name = anno_name[i], value = df[, i], na_col = na_col, which = which, show_legend = show_legend[i_simple + i], gp = gp, legend_param = annotation_legend_param[[i_simple + i]]))) |
|
| 194 |
+ i_anno = i_anno + 1 |
|
| 195 |
+ anno_list = c(anno_list, list(SingleAnnotation(name = anno_name[i], value = df[, i], na_col = na_col, which = which, |
|
| 196 |
+ show_legend = show_legend[i_simple + i], gp = gp, legend_param = annotation_legend_param[[i_simple + i]], |
|
| 197 |
+ show_name = show_annotation_name[i_anno], name_gp = subset_gp(annotation_name_gp, i_anno), |
|
| 198 |
+ name_offset = annotation_name_offset[i_anno], name_side = annotation_name_side[i_anno]))) |
|
| 165 | 199 |
} |
| 166 | 200 |
} else {
|
| 167 | 201 |
for(i in seq_len(n_anno)) {
|
| 202 |
+ i_anno = i_anno + 1 |
|
| 168 | 203 |
if(is.null(col[[ anno_name[i] ]])) { # if the color is not provided
|
| 169 |
- anno_list = c(anno_list, list(SingleAnnotation(name = anno_name[i], value = df[, i], na_col = na_col, which = which, show_legend = show_legend[i_simple + i], gp = gp, legend_param = annotation_legend_param[[i_simple + i]]))) |
|
| 204 |
+ anno_list = c(anno_list, list(SingleAnnotation(name = anno_name[i], value = df[, i], na_col = na_col, which = which, |
|
| 205 |
+ show_legend = show_legend[i_simple + i], gp = gp, legend_param = annotation_legend_param[[i_simple + i]], |
|
| 206 |
+ show_name = show_annotation_name[i_anno], name_gp = subset_gp(annotation_name_gp, i_anno), |
|
| 207 |
+ name_offset = annotation_name_offset[i_anno], name_side = annotation_name_side[i_anno]))) |
|
| 170 | 208 |
} else {
|
| 171 |
- anno_list = c(anno_list, list(SingleAnnotation(name = anno_name[i], value = df[, i], na_col = na_col, col = col[[ anno_name[i] ]], which = which, show_legend = show_legend[i_simple + i], gp = gp, legend_param = annotation_legend_param[[i_simple + i]]))) |
|
| 209 |
+ anno_list = c(anno_list, list(SingleAnnotation(name = anno_name[i], value = df[, i], na_col = na_col, col = col[[ anno_name[i] ]], |
|
| 210 |
+ which = which, show_legend = show_legend[i_simple + i], gp = gp, legend_param = annotation_legend_param[[i_simple + i]], |
|
| 211 |
+ show_name = show_annotation_name[i_anno], name_gp = subset_gp(annotation_name_gp, i_anno), |
|
| 212 |
+ name_offset = annotation_name_offset[i_anno], name_side = annotation_name_side[i_anno]))) |
|
| 172 | 213 |
} |
| 173 | 214 |
} |
| 174 | 215 |
} |
| 175 | 216 |
i_simple = i_simple + n_anno |
| 176 | 217 |
} else {
|
| 218 |
+ i_anno = i_anno + 1 |
|
| 177 | 219 |
if(inherits(anno_arg_list[[ag]], "function")) {
|
| 178 |
- anno_list = c(anno_list, list(SingleAnnotation(name = ag, fun = anno_arg_list[[ag]], which = which))) |
|
| 220 |
+ anno_list = c(anno_list, list(SingleAnnotation(name = ag, fun = anno_arg_list[[ag]], which = which, |
|
| 221 |
+ show_name = show_annotation_name[i_anno], name_gp = subset_gp(annotation_name_gp, i_anno), |
|
| 222 |
+ name_offset = annotation_name_offset[i_anno], name_side = annotation_name_side[i_anno]))) |
|
| 179 | 223 |
} else if(is.atomic(anno_arg_list[[ag]])) {
|
| 180 | 224 |
|
| 181 | 225 |
if(is.null(simple_length)) {
|
| ... | ... |
@@ -184,12 +228,21 @@ HeatmapAnnotation = function(df, name, col, na_col = "grey", |
| 184 | 228 |
stop("length of simple annotations differ.")
|
| 185 | 229 |
} |
| 186 | 230 |
if(missing(col)) {
|
| 187 |
- anno_list = c(anno_list, list(SingleAnnotation(name = ag, value = anno_arg_list[[ag]], na_col = na_col, which = which, show_legend = show_legend[i_simple + 1], gp = gp, legend_param = annotation_legend_param[[i_simple + 1]]))) |
|
| 231 |
+ anno_list = c(anno_list, list(SingleAnnotation(name = ag, value = anno_arg_list[[ag]], na_col = na_col, which = which, |
|
| 232 |
+ show_legend = show_legend[i_simple + 1], gp = gp, legend_param = annotation_legend_param[[i_simple + 1]], |
|
| 233 |
+ show_name = show_annotation_name[i_anno], name_gp = subset_gp(annotation_name_gp, i_anno), |
|
| 234 |
+ name_offset = annotation_name_offset[i_anno], name_side = annotation_name_side[i_anno]))) |
|
| 188 | 235 |
} else {
|
| 189 | 236 |
if(is.null(col[[ ag ]])) { # if the color is not provided
|
| 190 |
- anno_list = c(anno_list, list(SingleAnnotation(name = ag, value = anno_arg_list[[ag]], na_col = na_col, which = which, show_legend = show_legend[i_simple + 1], gp = gp, legend_param = annotation_legend_param[[i_simple + 1]]))) |
|
| 237 |
+ anno_list = c(anno_list, list(SingleAnnotation(name = ag, value = anno_arg_list[[ag]], na_col = na_col, which = which, |
|
| 238 |
+ show_legend = show_legend[i_simple + 1], gp = gp, legend_param = annotation_legend_param[[i_simple + 1]], |
|
| 239 |
+ show_name = show_annotation_name[i_anno], name_gp = subset_gp(annotation_name_gp, i_anno), |
|
| 240 |
+ name_offset = annotation_name_offset[i_anno], name_side = annotation_name_side[i_anno]))) |
|
| 191 | 241 |
} else {
|
| 192 |
- anno_list = c(anno_list, list(SingleAnnotation(name = ag, value = anno_arg_list[[ag]], na_col = na_col, col = col[[ ag ]], which = which, show_legend = show_legend[i_simple + 1], gp = gp, legend_param = annotation_legend_param[[i_simple + 1]]))) |
|
| 242 |
+ anno_list = c(anno_list, list(SingleAnnotation(name = ag, value = anno_arg_list[[ag]], na_col = na_col, col = col[[ ag ]], |
|
| 243 |
+ which = which, show_legend = show_legend[i_simple + 1], gp = gp, legend_param = annotation_legend_param[[i_simple + 1]], |
|
| 244 |
+ show_name = show_annotation_name[i_anno], name_gp = subset_gp(annotation_name_gp, i_anno), |
|
| 245 |
+ name_offset = annotation_name_offset[i_anno], name_side = annotation_name_side[i_anno]))) |
|
| 193 | 246 |
} |
| 194 | 247 |
} |
| 195 | 248 |
i_simple = i_simple + 1 |
| ... | ... |
@@ -199,19 +252,19 @@ HeatmapAnnotation = function(df, name, col, na_col = "grey", |
| 199 | 252 |
} |
| 200 | 253 |
} |
| 201 | 254 |
|
| 202 |
- n_anno = length(anno_list) |
|
| 255 |
+ n_total_anno = length(anno_list) |
|
| 203 | 256 |
|
| 204 | 257 |
if(is.null(gap)) gap = unit(0, "mm") |
| 205 | 258 |
|
| 206 | 259 |
# the nth gap does not really matter |
| 207 | 260 |
if(length(gap) == 1) {
|
| 208 |
- .Object@gap = rep(gap, n_anno) |
|
| 209 |
- } else if(length(gap) == n_anno - 1) {
|
|
| 261 |
+ .Object@gap = rep(gap, n_total_anno) |
|
| 262 |
+ } else if(length(gap) == n_total_anno - 1) {
|
|
| 210 | 263 |
.Object@gap = unit.c(gap, unit(0, "mm")) |
| 211 |
- } else if(length(gap) < n_anno - 1) {
|
|
| 264 |
+ } else if(length(gap) < n_total_anno - 1) {
|
|
| 212 | 265 |
stop("Length of `gap` is wrong.")
|
| 213 | 266 |
} else {
|
| 214 |
- gap[n_anno] = unit(0, "mm") |
|
| 267 |
+ gap[n_total_anno] = unit(0, "mm") |
|
| 215 | 268 |
.Object@gap = gap |
| 216 | 269 |
} |
| 217 | 270 |
|
| ... | ... |
@@ -221,7 +274,7 @@ HeatmapAnnotation = function(df, name, col, na_col = "grey", |
| 221 | 274 |
|
| 222 | 275 |
if(length(anno_size) == 1) {
|
| 223 | 276 |
if(!is.unit(anno_size)) {
|
| 224 |
- anno_size = rep(anno_size, n_anno) |
|
| 277 |
+ anno_size = rep(anno_size, n_total_anno) |
|
| 225 | 278 |
} |
| 226 | 279 |
} |
| 227 | 280 |
|
| ... | ... |
@@ -61,6 +61,10 @@ SingleAnnotation = setClass("SingleAnnotation",
|
| 61 | 61 |
# -show_legend if it is a simple annotation, whether show legend when making the complete heatmap. |
| 62 | 62 |
# -gp Since simple annotation is represented as a row of grids. This argument controls graphic parameters for the simple annotation. |
| 63 | 63 |
# -legend_param parameters for the legend. See `color_mapping_legend,ColorMapping-method` for options. |
| 64 |
+# -show_name whether show annotation name |
|
| 65 |
+# -name_gp graphic parameters for annotation name |
|
| 66 |
+# -name_offset offset to the annotation, a `grid::unit` object |
|
| 67 |
+# -name_side 'right' and 'left' for column annotations and 'top' and 'bottom' for row annotations |
|
| 64 | 68 |
# |
| 65 | 69 |
# == details |
| 66 | 70 |
# The most simple annotation is one row or one column grids in which different colors |
| ... | ... |
@@ -109,11 +109,18 @@ ht_global_opt = setGlobalOptions( |
| 109 | 109 |
.value = FALSE, |
| 110 | 110 |
.filter = function(x) {
|
| 111 | 111 |
if(x) {
|
| 112 |
- ComplexHeatmap:::hclust = fastcluster::hclust |
|
| 112 |
+ if(require(fastcluster)) {
|
|
| 113 |
+ assign("hclust", envir = topenv()) = getFromNamespace("hclust", "fastcluster")
|
|
| 114 |
+ } else {
|
|
| 115 |
+ stop("Cannot find fastcluster package.")
|
|
| 116 |
+ } |
|
| 113 | 117 |
} else {
|
| 114 |
- ComplexHeatmap:::hclust = stats::hclust |
|
| 118 |
+ assign("hclust", envir = topenv()) = getFromNamespace("hclust", "stats")
|
|
| 115 | 119 |
} |
| 116 | 120 |
x |
| 117 | 121 |
} |
| 118 | 122 |
) |
| 119 | 123 |
) |
| 124 |
+ |
|
| 125 |
+hclust = getFromNamespace("hclust", "stats")
|
|
| 126 |
+ |
| ... | ... |
@@ -39,8 +39,6 @@ increase_color_mapping_index = function() {
|
| 39 | 39 |
INDEX_ENV$I_COLOR_MAPPING = INDEX_ENV$I_COLOR_MAPPING + 1 |
| 40 | 40 |
} |
| 41 | 41 |
|
| 42 |
-hclust = stats::hclust |
|
| 43 |
- |
|
| 44 | 42 |
# default colors for matrix or annotations |
| 45 | 43 |
# this function should be improved later |
| 46 | 44 |
default_col = function(x, main_matrix = FALSE) {
|
| ... | ... |
@@ -17,7 +17,11 @@ HeatmapAnnotation(df, name, col, na_col = "grey", |
| 17 | 17 |
height = calc_anno_size(), |
| 18 | 18 |
width = calc_anno_size(), |
| 19 | 19 |
gp = gpar(col = NA), |
| 20 |
- gap = unit(0, "mm")) |
|
| 20 |
+ gap = unit(0, "mm"), |
|
| 21 |
+ show_annotation_name = FALSE, |
|
| 22 |
+ annotation_name_gp = gpar(), |
|
| 23 |
+ annotation_name_offset = unit(2, "mm"), |
|
| 24 |
+ annotation_name_side = ifelse(which == "column", "right", "bottom")) |
|
| 21 | 25 |
} |
| 22 | 26 |
\arguments{
|
| 23 | 27 |
|
| ... | ... |
@@ -35,6 +39,10 @@ HeatmapAnnotation(df, name, col, na_col = "grey", |
| 35 | 39 |
\item{width}{width of the whole heatmap annotations, only used for row annotation when appending to the list of heatmaps.}
|
| 36 | 40 |
\item{gp}{graphic parameters for simple annotations.}
|
| 37 | 41 |
\item{gap}{gap between each annotation}
|
| 42 |
+ \item{show_annotation_name}{whether show annotation names. For column annotation, annotation names are drawn either on the left or the right, and for row annotations, names are draw either on top to at bottom. The value can be a vector.}
|
|
| 43 |
+ \item{annotation_name_gp}{graphic parameters for anntation names. Graphic paramters can be vectors.}
|
|
| 44 |
+ \item{annotation_name_offset}{offset to the annotations, \code{\link[grid]{unit}} object. The value can be a vector.}
|
|
| 45 |
+ \item{annotation_name_side}{side of the annotation names.}
|
|
| 38 | 46 |
|
| 39 | 47 |
} |
| 40 | 48 |
\details{
|
| ... | ... |
@@ -12,7 +12,11 @@ SingleAnnotation(name, value, col, fun, |
| 12 | 12 |
which = c("column", "row"),
|
| 13 | 13 |
show_legend = TRUE, |
| 14 | 14 |
gp = gpar(col = NA), |
| 15 |
- legend_param = list()) |
|
| 15 |
+ legend_param = list(), |
|
| 16 |
+ show_name = TRUE, |
|
| 17 |
+ name_gp = gpar(fontsize = 12), |
|
| 18 |
+ name_offset = unit(2, "mm"), |
|
| 19 |
+ name_side = ifelse(which == "column", "right", "bottom")) |
|
| 16 | 20 |
} |
| 17 | 21 |
\arguments{
|
| 18 | 22 |
|
| ... | ... |
@@ -25,6 +29,10 @@ SingleAnnotation(name, value, col, fun, |
| 25 | 29 |
\item{show_legend}{if it is a simple annotation, whether show legend when making the complete heatmap.}
|
| 26 | 30 |
\item{gp}{Since simple annotation is represented as a row of grids. This argument controls graphic parameters for the simple annotation.}
|
| 27 | 31 |
\item{legend_param}{parameters for the legend. See \code{\link{color_mapping_legend,ColorMapping-method}} for options.}
|
| 32 |
+ \item{show_name}{whether show annotation name}
|
|
| 33 |
+ \item{name_gp}{graphic parameters for annotation name}
|
|
| 34 |
+ \item{name_offset}{offset to the annotation, a \code{\link[grid]{unit}} object}
|
|
| 35 |
+ \item{name_side}{'right' and 'left' for column annotations and 'top' and 'bottom' for row annotations}
|
|
| 28 | 36 |
|
| 29 | 37 |
} |
| 30 | 38 |
\details{
|
| ... | ... |
@@ -41,6 +41,7 @@ There are following parameters: |
| 41 | 41 |
\item{heatmap_legend_grid_width}{set \code{grid_width} element in \code{legend_param} in \code{\link{SingleAnnotation}}.}
|
| 42 | 42 |
\item{heatmap_legend_grid_height}{set \code{grid_height} element in \code{legend_param} in \code{\link{SingleAnnotation}}.}
|
| 43 | 43 |
\item{heatmap_legend_grid_border}{set \code{grid_border} element in \code{legend_param} in \code{\link{SingleAnnotation}}.}
|
| 44 |
+ \item{fast_hclust}{whether use \code{\link[fastcluster]{hclust}} to speed up clustering?}
|
|
| 44 | 45 |
} |
| 45 | 46 |
|
| 46 | 47 |
You can get or set option values by the traditional way (like \code{\link[base]{options}}) or by \code{$} operator:
|
