Zuguang Gu authored on 31/08/2022 14:37:52 | ... | ... |
@@ -211,6 +211,9 @@ HeatmapAnnotation = function(..., |
| 211 | 211 |
if(length(show_legend) == 1) {
|
| 212 | 212 |
show_legend = recycle_param(show_legend, simple_anno_name, TRUE) |
| 213 | 213 |
} |
| 214 |
+ if(length(show_legend) < length(anno_value_list) && length(show_legend) > 1) {
|
|
| 215 |
+ show_legend = recycle_param(show_legend, simple_anno_name, TRUE) |
|
| 216 |
+ } |
|
| 214 | 217 |
# check length of show_legend |
| 215 | 218 |
if(length(show_legend) == length(anno_value_list) && !all(l_simple_anno)) {
|
| 216 | 219 |
show_legend = show_legend[l_simple_anno] |
Zuguang Gu authored on 23/03/2022 16:30:55 | ... | ... |
@@ -1051,6 +1051,9 @@ anno_type = function(ha) {
|
| 1051 | 1051 |
size(x2) = sum(x2@anno_size) + sum(x2@gap) - x2@gap[length(x2@gap)] |
| 1052 | 1052 |
|
| 1053 | 1053 |
} else if(nargs() == 2) { # ha[1:4]
|
| 1054 |
+ if(is.character(i) && all(i %in% names(x2@anno_list))) {
|
|
| 1055 |
+ warning_wrap("It seems you want to obtain a subset of annotations. You should set in a form of `anno[, names]`.")
|
|
| 1056 |
+ } |
|
| 1054 | 1057 |
x2 = x |
| 1055 | 1058 |
for(nm in names(x2@anno_list)) {
|
| 1056 | 1059 |
x2@anno_list[[nm]] = x2@anno_list[[nm]][i] |
Zuguang Gu authored on 18/02/2022 19:51:49 | ... | ... |
@@ -95,7 +95,7 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",
|
| 95 | 95 |
# Zuguang Gu <z.gu@dkfz.de> |
| 96 | 96 |
# |
| 97 | 97 |
HeatmapAnnotation = function(..., |
| 98 |
- df, name, col, na_col = "grey", |
|
| 98 |
+ df = NULL, name, col, na_col = "grey", |
|
| 99 | 99 |
annotation_legend_param = list(), |
| 100 | 100 |
show_legend = TRUE, |
| 101 | 101 |
which = c("column", "row"),
|
| ... | ... |
@@ -150,53 +150,8 @@ HeatmapAnnotation = function(..., |
| 150 | 150 |
.Object@name = name |
| 151 | 151 |
n_anno = 0 |
| 152 | 152 |
|
| 153 |
- #### check system calls #### |
|
| 154 |
- # HeatmapAnnotation is either called by `HeatmapAnnotation()` or by `rowAnnotation()`/`columnAnnotation()` |
|
| 155 |
- sc = sys.calls() |
|
| 156 |
- nsc = length(sc) |
|
| 157 |
- if(nsc == 1) { # HeatmapAnnotation(...)
|
|
| 158 |
- scl = as.list(sc[[1]]) |
|
| 159 |
- arg_list = scl[-1] |
|
| 160 |
- } else {
|
|
| 161 |
- |
|
| 162 |
- scl = as.list(sc[[nsc-1]]) |
|
| 163 |
- if(is.function(scl[[1]])) {
|
|
| 164 |
- if(identical(scl[[1]], pheatmap)) {
|
|
| 165 |
- scl = as.list(sc[[nsc]]) |
|
| 166 |
- arg_list = scl[-1] |
|
| 167 |
- } else if(identical(scl[[1]], heatmap)) {
|
|
| 168 |
- scl = as.list(sc[[nsc]]) |
|
| 169 |
- arg_list = scl[-1] |
|
| 170 |
- } else if(identical(scl[[1]], heatmap.2)) {
|
|
| 171 |
- scl = as.list(sc[[nsc]]) |
|
| 172 |
- arg_list = scl[-1] |
|
| 173 |
- } else {
|
|
| 174 |
- # do.call(rowAnnotation, list(...)) |
|
| 175 |
- # do.call(columnAnnotation, list(...)) |
|
| 176 |
- arg_list = scl[-1] |
|
| 177 |
- } |
|
| 178 |
- } else if(any(as.character(scl[[1]]) %in% c("HeatmapAnnotation", "rowAnnotation", "columnAnnotation"))) {
|
|
| 179 |
- # columnAnnotation(...), rowAnnotation(...) |
|
| 180 |
- # do.call("columnAnnotation", list(...))
|
|
| 181 |
- # do.call("rowAnnotation", list(...))
|
|
| 182 |
- arg_list = scl[-1] |
|
| 183 |
- } else {
|
|
| 184 |
- # do.call("HeatmapAnnotation", list(...))
|
|
| 185 |
- # do.call(HeatmapAnnotation, list(...)) |
|
| 186 |
- scl = as.list(sc[[nsc]]) |
|
| 187 |
- arg_list = scl[-1] |
|
| 188 |
- } |
|
| 189 |
- } |
|
| 190 |
- |
|
| 191 |
- called_args = names(arg_list) |
|
| 192 |
- anno_args = setdiff(called_args, fun_args) |
|
| 193 |
- if(any(anno_args == "")) stop_wrap("annotations should have names.")
|
|
| 194 |
- if(is.null(called_args)) {
|
|
| 195 |
- stop_wrap("It seems you are putting only one argument to the function. If it is a simple vector annotation or a function annotation (e.g. anno_*()), specify it as HeatmapAnnotation(name = value). If it is a data frame annotation, specify it as HeatmapAnnotation(df = value)")
|
|
| 196 |
- } |
|
| 197 |
- |
|
| 198 | 153 |
##### pull all annotation to `anno_value_list`#### |
| 199 |
- if("df" %in% called_args) {
|
|
| 154 |
+ if(!is.null(df)) {
|
|
| 200 | 155 |
if(is.matrix(df)) {
|
| 201 | 156 |
warning_wrap("`df` should be a data frame while not a matrix. Convert it to data frame.")
|
| 202 | 157 |
df = as.data.frame(df) |
| ... | ... |
@@ -209,23 +164,35 @@ HeatmapAnnotation = function(..., |
| 209 | 164 |
} |
| 210 | 165 |
|
| 211 | 166 |
anno_arg_list = list(...) |
| 212 |
- if("df" %in% called_args && length(anno_arg_list)) {
|
|
| 213 |
- if(any(duplicated(c(names(df), names(anno_arg_list))))) {
|
|
| 214 |
- stop_wrap("Annotation names are duplicated. Check the column names of `df`.")
|
|
| 167 |
+ anno_arg_names = names(anno_arg_list) |
|
| 168 |
+ if(any(anno_arg_names == "")) {
|
|
| 169 |
+ stop_wrap("Annotations should have names.")
|
|
| 170 |
+ } |
|
| 171 |
+ if(is.null(anno_arg_names)) {
|
|
| 172 |
+ if(length(anno_arg_list) == 1) {
|
|
| 173 |
+ stop_wrap("The annotation should be specified as name-value pairs or via argument `df` with a data frame.")
|
|
| 174 |
+ } |
|
| 175 |
+ if(length(anno_arg_list) > 1) {
|
|
| 176 |
+ stop_wrap("Annotations should have names.")
|
|
| 177 |
+ } |
|
| 178 |
+ } |
|
| 179 |
+ |
|
| 180 |
+ if(!is.null(df) && length(anno_arg_list)) {
|
|
| 181 |
+ if(any(duplicated(c(names(df), anno_arg_names)))) {
|
|
| 182 |
+ stop_wrap("Annotation names are duplicated to those in `df`. Check the column names of `df`.")
|
|
| 215 | 183 |
} |
| 216 | 184 |
} |
| 217 | 185 |
|
| 218 | 186 |
anno_value_list = list() |
| 219 |
- for(nm in called_args) {
|
|
| 220 |
- if(nm %in% names(anno_arg_list)) {
|
|
| 221 |
- anno_value_list[[nm]] = anno_arg_list[[nm]] |
|
| 222 |
- } else if(nm == "df") {
|
|
| 223 |
- for(nm2 in colnames(df)) {
|
|
| 224 |
- if(is.null(rownames(df))) {
|
|
| 225 |
- anno_value_list[[nm2]] = df[, nm2] |
|
| 226 |
- } else {
|
|
| 227 |
- anno_value_list[[nm2]] = structure(df[, nm2], names = rownames(df)) |
|
| 228 |
- } |
|
| 187 |
+ for(nm in anno_arg_names) {
|
|
| 188 |
+ anno_value_list[[nm]] = anno_arg_list[[nm]] |
|
| 189 |
+ } |
|
| 190 |
+ if(!is.null(df)) {
|
|
| 191 |
+ for(nm2 in colnames(df)) {
|
|
| 192 |
+ if(is.null(rownames(df))) {
|
|
| 193 |
+ anno_value_list[[nm2]] = df[, nm2] |
|
| 194 |
+ } else {
|
|
| 195 |
+ anno_value_list[[nm2]] = structure(df[, nm2], names = rownames(df)) |
|
| 229 | 196 |
} |
| 230 | 197 |
} |
| 231 | 198 |
} |
Zuguang Gu authored on 03/02/2022 09:53:48 | ... | ... |
@@ -25,7 +25,7 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",
|
| 25 | 25 |
width = "ANY", |
| 26 | 26 |
height = "ANY", |
| 27 | 27 |
gap = "ANY", |
| 28 |
- subsetable = "logical", |
|
| 28 |
+ subsettable = "logical", |
|
| 29 | 29 |
extended = "ANY", |
| 30 | 30 |
param = "list" |
| 31 | 31 |
), |
| ... | ... |
@@ -33,7 +33,7 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",
|
| 33 | 33 |
anno_list = list(), |
| 34 | 34 |
which = "column", |
| 35 | 35 |
gap = unit(0, "mm"), |
| 36 |
- subsetable = FALSE, |
|
| 36 |
+ subsettable = FALSE, |
|
| 37 | 37 |
extended = unit(c(0, 0, 0, 0), "mm"), |
| 38 | 38 |
param = list() |
| 39 | 39 |
), |
| ... | ... |
@@ -526,7 +526,7 @@ HeatmapAnnotation = function(..., |
| 526 | 526 |
.Object@width = width |
| 527 | 527 |
.Object@height = height |
| 528 | 528 |
|
| 529 |
- .Object@subsetable = all(sapply(anno_list, function(x) x@subsetable)) |
|
| 529 |
+ .Object@subsettable = all(sapply(anno_list, function(x) x@subsettable)) |
|
| 530 | 530 |
extended = unit(c(0, 0, 0, 0), "mm") |
| 531 | 531 |
for(i in 1:4) {
|
| 532 | 532 |
extended[i] = unit(max(sapply(anno_list, function(anno) {
|
| ... | ... |
@@ -795,7 +795,7 @@ setMethod(f = "show", |
| 795 | 795 |
cat(" items:", ifelse(length(len), len[1], "unknown"), "\n")
|
| 796 | 796 |
cat(" width:", as.character(object@width), "\n")
|
| 797 | 797 |
cat(" height:", as.character(object@height), "\n")
|
| 798 |
- cat(" this object is ", ifelse(object@subsetable, "", "not "), "subsetable\n", sep = "")
|
|
| 798 |
+ cat(" this object is ", ifelse(object@subsettable, "", "not "), "subsettable\n", sep = "")
|
|
| 799 | 799 |
dirt = c("bottom", "left", "top", "right")
|
| 800 | 800 |
for(i in 1:4) {
|
| 801 | 801 |
if(!identical(unit(0, "mm"), object@extended[i])) {
|
Zuguang Gu authored on 13/07/2021 15:43:05 | ... | ... |
@@ -220,8 +220,13 @@ HeatmapAnnotation = function(..., |
| 220 | 220 |
if(nm %in% names(anno_arg_list)) {
|
| 221 | 221 |
anno_value_list[[nm]] = anno_arg_list[[nm]] |
| 222 | 222 |
} else if(nm == "df") {
|
| 223 |
- for(nm2 in colnames(df)) |
|
| 224 |
- anno_value_list[[nm2]] = df[, nm2] |
|
| 223 |
+ for(nm2 in colnames(df)) {
|
|
| 224 |
+ if(is.null(rownames(df))) {
|
|
| 225 |
+ anno_value_list[[nm2]] = df[, nm2] |
|
| 226 |
+ } else {
|
|
| 227 |
+ anno_value_list[[nm2]] = structure(df[, nm2], names = rownames(df)) |
|
| 228 |
+ } |
|
| 229 |
+ } |
|
| 225 | 230 |
} |
| 226 | 231 |
} |
| 227 | 232 |
|
Zuguang authored on 16/04/2021 07:42:28 | ... | ... |
@@ -151,7 +151,6 @@ HeatmapAnnotation = function(..., |
| 151 | 151 |
n_anno = 0 |
| 152 | 152 |
|
| 153 | 153 |
#### check system calls #### |
| 154 |
- |
|
| 155 | 154 |
# HeatmapAnnotation is either called by `HeatmapAnnotation()` or by `rowAnnotation()`/`columnAnnotation()` |
| 156 | 155 |
sc = sys.calls() |
| 157 | 156 |
nsc = length(sc) |
| ... | ... |
@@ -159,11 +158,23 @@ HeatmapAnnotation = function(..., |
| 159 | 158 |
scl = as.list(sc[[1]]) |
| 160 | 159 |
arg_list = scl[-1] |
| 161 | 160 |
} else {
|
| 162 |
- # do.call(rowAnnotation, list(...)) |
|
| 163 |
- # do.call(columnAnnotation, list(...)) |
|
| 161 |
+ |
|
| 164 | 162 |
scl = as.list(sc[[nsc-1]]) |
| 165 | 163 |
if(is.function(scl[[1]])) {
|
| 166 |
- arg_list = scl[-1] |
|
| 164 |
+ if(identical(scl[[1]], pheatmap)) {
|
|
| 165 |
+ scl = as.list(sc[[nsc]]) |
|
| 166 |
+ arg_list = scl[-1] |
|
| 167 |
+ } else if(identical(scl[[1]], heatmap)) {
|
|
| 168 |
+ scl = as.list(sc[[nsc]]) |
|
| 169 |
+ arg_list = scl[-1] |
|
| 170 |
+ } else if(identical(scl[[1]], heatmap.2)) {
|
|
| 171 |
+ scl = as.list(sc[[nsc]]) |
|
| 172 |
+ arg_list = scl[-1] |
|
| 173 |
+ } else {
|
|
| 174 |
+ # do.call(rowAnnotation, list(...)) |
|
| 175 |
+ # do.call(columnAnnotation, list(...)) |
|
| 176 |
+ arg_list = scl[-1] |
|
| 177 |
+ } |
|
| 167 | 178 |
} else if(any(as.character(scl[[1]]) %in% c("HeatmapAnnotation", "rowAnnotation", "columnAnnotation"))) {
|
| 168 | 179 |
# columnAnnotation(...), rowAnnotation(...) |
| 169 | 180 |
# do.call("columnAnnotation", list(...))
|
Zuguang authored on 23/03/2021 09:09:02 | ... | ... |
@@ -155,17 +155,23 @@ HeatmapAnnotation = function(..., |
| 155 | 155 |
# HeatmapAnnotation is either called by `HeatmapAnnotation()` or by `rowAnnotation()`/`columnAnnotation()` |
| 156 | 156 |
sc = sys.calls() |
| 157 | 157 |
nsc = length(sc) |
| 158 |
- if(nsc == 1) {
|
|
| 158 |
+ if(nsc == 1) { # HeatmapAnnotation(...)
|
|
| 159 | 159 |
scl = as.list(sc[[1]]) |
| 160 | 160 |
arg_list = scl[-1] |
| 161 | 161 |
} else {
|
| 162 |
+ # do.call(rowAnnotation, list(...)) |
|
| 163 |
+ # do.call(columnAnnotation, list(...)) |
|
| 162 | 164 |
scl = as.list(sc[[nsc-1]]) |
| 163 | 165 |
if(is.function(scl[[1]])) {
|
| 164 |
- scl = as.list(sc[[nsc]]) |
|
| 165 | 166 |
arg_list = scl[-1] |
| 166 |
- } else if(any(as.character(scl[[1]]) %in% c("HeatmapAnnotation", "rowAnnotation", "columnAnnotation"))) {
|
|
| 167 |
+ } else if(any(as.character(scl[[1]]) %in% c("HeatmapAnnotation", "rowAnnotation", "columnAnnotation"))) {
|
|
| 168 |
+ # columnAnnotation(...), rowAnnotation(...) |
|
| 169 |
+ # do.call("columnAnnotation", list(...))
|
|
| 170 |
+ # do.call("rowAnnotation", list(...))
|
|
| 167 | 171 |
arg_list = scl[-1] |
| 168 | 172 |
} else {
|
| 173 |
+ # do.call("HeatmapAnnotation", list(...))
|
|
| 174 |
+ # do.call(HeatmapAnnotation, list(...)) |
|
| 169 | 175 |
scl = as.list(sc[[nsc]]) |
| 170 | 176 |
arg_list = scl[-1] |
| 171 | 177 |
} |
Zuguang Gu authored on 21/12/2020 16:03:30 | ... | ... |
@@ -1058,12 +1058,16 @@ anno_type = function(ha) {
|
| 1058 | 1058 |
for(nm in names(x2@anno_list)) {
|
| 1059 | 1059 |
x2@anno_list[[nm]] = x2@anno_list[[nm]][i] |
| 1060 | 1060 |
} |
| 1061 |
+ x2@anno_size = do.call(unit.c, lapply(x2@anno_list, size)) |
|
| 1062 |
+ size(x2) = sum(x2@anno_size) + sum(x2@gap) - x2@gap[length(x2@gap)] |
|
| 1061 | 1063 |
|
| 1062 | 1064 |
} else if(nargs() == 2) { # ha[1:4]
|
| 1063 | 1065 |
x2 = x |
| 1064 | 1066 |
for(nm in names(x2@anno_list)) {
|
| 1065 | 1067 |
x2@anno_list[[nm]] = x2@anno_list[[nm]][i] |
| 1066 | 1068 |
} |
| 1069 |
+ x2@anno_size = do.call(unit.c, lapply(x2@anno_list, size)) |
|
| 1070 |
+ size(x2) = sum(x2@anno_size) + sum(x2@gap) - x2@gap[length(x2@gap)] |
|
| 1067 | 1071 |
|
| 1068 | 1072 |
} else if (!missing(i) && !missing(j)) { # ha[1:4, "foo"]
|
| 1069 | 1073 |
x2 = x |
| ... | ... |
@@ -1075,6 +1079,7 @@ anno_type = function(ha) {
|
| 1075 | 1079 |
x2@gap = x@gap[j] |
| 1076 | 1080 |
x2@gap[length(x2@gap)] = unit(0, "mm") |
| 1077 | 1081 |
|
| 1082 |
+ x2@anno_size = do.call(unit.c, lapply(x2@anno_list, size)) |
|
| 1078 | 1083 |
size(x2) = sum(x2@anno_size) + sum(x2@gap) - x2@gap[length(x2@gap)] |
| 1079 | 1084 |
} |
| 1080 | 1085 |
|
Zuguang Gu authored on 27/10/2020 20:12:15 | ... | ... |
@@ -273,13 +273,17 @@ HeatmapAnnotation = function(..., |
| 273 | 273 |
} |
| 274 | 274 |
border = recycle_param(border, an, FALSE) |
| 275 | 275 |
annotation_name_gp = recycle_gp(annotation_name_gp, n_total_anno) |
| 276 |
- if(length(annotation_label) > 0) {
|
|
| 277 |
- if(length(annotation_label) != length(an)) {
|
|
| 278 |
- stop_wrap("Length of `annotation_label` should be the same as number of annotations.")
|
|
| 276 |
+ if(length(annotation_label)) {
|
|
| 277 |
+ if(inherits(annotation_label, "gridtext")) {
|
|
| 278 |
+ annotation_label = lapply(seq_along(annotation_label), function(i) annotation_label[i]) |
|
| 279 |
+ names(annotation_label) = an |
|
| 279 | 280 |
} |
| 280 |
- annotation_label = lapply(seq_along(annotation_label), function(i) annotation_label[i]) |
|
| 281 |
- names(annotation_label) == an |
|
| 282 | 281 |
} |
| 282 |
+ annotation_label = recycle_list(annotation_label, an, NULL) |
|
| 283 |
+ # if(length(annotation_label) > 0) {
|
|
| 284 |
+ # annotation_label = lapply(seq_along(annotation_label), function(i) annotation_label[i]) |
|
| 285 |
+ # names(annotation_label) == an |
|
| 286 |
+ # } |
|
| 283 | 287 |
|
| 284 | 288 |
if(!missing(col)) {
|
| 285 | 289 |
if(length(col) >= 1) {
|
| ... | ... |
@@ -328,7 +332,7 @@ HeatmapAnnotation = function(..., |
| 328 | 332 |
i_anno = i_anno + 1 |
| 329 | 333 |
arg_list = list(name = ag, which = which, |
| 330 | 334 |
label = annotation_label[[i_anno]], |
| 331 |
- show_name = show_annotation_name[i_anno], |
|
| 335 |
+ show_name = show_annotation_name[[i_anno]], |
|
| 332 | 336 |
name_gp = subset_gp(annotation_name_gp, i_anno), |
| 333 | 337 |
name_offset = annotation_name_offset[[i_anno]], |
| 334 | 338 |
name_side = annotation_name_side[i_anno], |
Zuguang Gu authored on 27/10/2020 14:22:45 | ... | ... |
@@ -273,8 +273,12 @@ HeatmapAnnotation = function(..., |
| 273 | 273 |
} |
| 274 | 274 |
border = recycle_param(border, an, FALSE) |
| 275 | 275 |
annotation_name_gp = recycle_gp(annotation_name_gp, n_total_anno) |
| 276 |
- if(length(annotation_label) != length(an)) {
|
|
| 277 |
- stop_wrap("Length of `annotation_label` should be the same as number of annotations.")
|
|
| 276 |
+ if(length(annotation_label) > 0) {
|
|
| 277 |
+ if(length(annotation_label) != length(an)) {
|
|
| 278 |
+ stop_wrap("Length of `annotation_label` should be the same as number of annotations.")
|
|
| 279 |
+ } |
|
| 280 |
+ annotation_label = lapply(seq_along(annotation_label), function(i) annotation_label[i]) |
|
| 281 |
+ names(annotation_label) == an |
|
| 278 | 282 |
} |
| 279 | 283 |
|
| 280 | 284 |
if(!missing(col)) {
|
| ... | ... |
@@ -323,7 +327,7 @@ HeatmapAnnotation = function(..., |
| 323 | 327 |
|
| 324 | 328 |
i_anno = i_anno + 1 |
| 325 | 329 |
arg_list = list(name = ag, which = which, |
| 326 |
- label = annotation_label[i_anno], |
|
| 330 |
+ label = annotation_label[[i_anno]], |
|
| 327 | 331 |
show_name = show_annotation_name[i_anno], |
| 328 | 332 |
name_gp = subset_gp(annotation_name_gp, i_anno), |
| 329 | 333 |
name_offset = annotation_name_offset[[i_anno]], |
Zuguang Gu authored on 27/10/2020 14:13:38 | ... | ... |
@@ -273,7 +273,9 @@ HeatmapAnnotation = function(..., |
| 273 | 273 |
} |
| 274 | 274 |
border = recycle_param(border, an, FALSE) |
| 275 | 275 |
annotation_name_gp = recycle_gp(annotation_name_gp, n_total_anno) |
| 276 |
- annotation_label = recycle_list(annotation_label, an, NULL) |
|
| 276 |
+ if(length(annotation_label) != length(an)) {
|
|
| 277 |
+ stop_wrap("Length of `annotation_label` should be the same as number of annotations.")
|
|
| 278 |
+ } |
|
| 277 | 279 |
|
| 278 | 280 |
if(!missing(col)) {
|
| 279 | 281 |
if(length(col) >= 1) {
|
| ... | ... |
@@ -321,7 +323,7 @@ HeatmapAnnotation = function(..., |
| 321 | 323 |
|
| 322 | 324 |
i_anno = i_anno + 1 |
| 323 | 325 |
arg_list = list(name = ag, which = which, |
| 324 |
- label = annotation_label[[i_anno]], |
|
| 326 |
+ label = annotation_label[i_anno], |
|
| 325 | 327 |
show_name = show_annotation_name[i_anno], |
| 326 | 328 |
name_gp = subset_gp(annotation_name_gp, i_anno), |
| 327 | 329 |
name_offset = annotation_name_offset[[i_anno]], |
Zuguang Gu authored on 26/10/2020 14:12:31 | ... | ... |
@@ -663,8 +663,8 @@ setMethod(f = "draw", |
| 663 | 663 |
|
| 664 | 664 |
if(test2) {
|
| 665 | 665 |
grid.newpage() |
| 666 |
- if(which == "column") pushViewport(viewport(width = unit(1, "npc") - unit(3, "cm"), height = object@height)) |
|
| 667 |
- if(which == "row") pushViewport(viewport(height = unit(1, "npc") - unit(3, "cm"), width = object@width)) |
|
| 666 |
+ if(which == "column") pushViewport(viewport(width = unit(1, "npc") - unit(3, "cm") - sum(object@extended[c(2,4)]), height = object@height)) |
|
| 667 |
+ if(which == "row") pushViewport(viewport(height = unit(1, "npc") - unit(3, "cm") - sum(object@extended[c(1,3)]), width = object@width)) |
|
| 668 | 668 |
} else {
|
| 669 | 669 |
pushViewport(do.call(viewport, vp_param)) |
| 670 | 670 |
} |
Zuguang Gu authored on 23/10/2020 16:02:23 | ... | ... |
@@ -63,7 +63,7 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",
|
| 63 | 63 |
# -annotation_name_gp Graphic parameters for anntation names. Graphic paramters can be vectors. |
| 64 | 64 |
# -annotation_name_offset Offset to the annotation names, a `grid::unit` object. The value can be a vector. |
| 65 | 65 |
# -annotation_name_side Side of the annotation names. |
| 66 |
-# -annotation_name_rot Rotation of the annotation names, it can only take values in ``c(00, 90, 180, 270)``. The value can be a vector. |
|
| 66 |
+# -annotation_name_rot Rotation of the annotation names. The value can be a vector. |
|
| 67 | 67 |
# -annotation_name_align Whether to align the annotation names. |
| 68 | 68 |
# -annotation_height Height of each annotation if annotations are column annotations. |
| 69 | 69 |
# -annotation_width Width of each annotation if annotations are row annotations. |
| ... | ... |
@@ -900,7 +900,7 @@ setMethod(f = "add_heatmap", |
| 900 | 900 |
# ha3 = HeatmapAnnotation(sth = cbind(1:10, 10:1)) |
| 901 | 901 |
# ha = c(ha1, ha2, ha3, gap = unit(c(1, 4), "mm")) |
| 902 | 902 |
# ha |
| 903 |
-c.HeatmapAnnotation = function(..., gap = unit(0, "mm")) {
|
|
| 903 |
+c.HeatmapAnnotation = function(..., gap = unit(1, "points")) {
|
|
| 904 | 904 |
anno_list = list(...) |
| 905 | 905 |
if(length(anno_list) == 1) {
|
| 906 | 906 |
return(anno_list[[1]]) |
| ... | ... |
@@ -1410,3 +1410,90 @@ has_zoomed_anno_empty = function(ha) {
|
| 1410 | 1410 |
} |
| 1411 | 1411 |
return(FALSE) |
| 1412 | 1412 |
} |
| 1413 |
+ |
|
| 1414 |
+# == title |
|
| 1415 |
+# Attach heatmap annotations to the heatmap |
|
| 1416 |
+# |
|
| 1417 |
+# == param |
|
| 1418 |
+# -object A `Heatmap-class` object. |
|
| 1419 |
+# -ha A `HeatmapAnnotation-class` object. |
|
| 1420 |
+# -side Which side of the heatmap. Value should be in "top", "bottom", "left", "right". |
|
| 1421 |
+# -gap Space between the two heatmap annotations. |
|
| 1422 |
+# |
|
| 1423 |
+# == example |
|
| 1424 |
+# m = matrix(rnorm(100), 10) |
|
| 1425 |
+# ht = Heatmap(m) |
|
| 1426 |
+# ha = HeatmapAnnotation(foo = 1:10) |
|
| 1427 |
+# ht = attach_annotation(ht, ha) |
|
| 1428 |
+# ht |
|
| 1429 |
+# ha2 = HeatmapAnnotation(bar = letters[1:10]) |
|
| 1430 |
+# ht = attach_annotation(ht, ha2) |
|
| 1431 |
+# ht |
|
| 1432 |
+setMethod(f = "attach_annotation", |
|
| 1433 |
+ signature = "Heatmap", |
|
| 1434 |
+ definition = function(object, ha, side = c("top", "bottom", "left", "right"),
|
|
| 1435 |
+ gap = unit(1, "points")) {
|
|
| 1436 |
+ |
|
| 1437 |
+ if(missing(side)) {
|
|
| 1438 |
+ side = ifelse(ha@which == "column", "top", "left") |
|
| 1439 |
+ } else {
|
|
| 1440 |
+ side = match.arg(side)[1] |
|
| 1441 |
+ } |
|
| 1442 |
+ ha_which = ha@which |
|
| 1443 |
+ if(ha_which == "column" && side %in% c("left", "right")) {
|
|
| 1444 |
+ stop_wrap("Column annotations can only be attached to the top/bottom side of the heatmap.")
|
|
| 1445 |
+ } else if(ha_which == "row" && side %in% c("top", "bottom")) {
|
|
| 1446 |
+ stop_wrap("Row annotations can only be attached to the left/right side of the heatmap.")
|
|
| 1447 |
+ } |
|
| 1448 |
+ |
|
| 1449 |
+ if(side == "top") {
|
|
| 1450 |
+ if(is.null(object@top_annotation)) {
|
|
| 1451 |
+ object@top_annotation = ha |
|
| 1452 |
+ h = height(ha) + ht_opt$COLUMN_ANNO_PADDING |
|
| 1453 |
+ h = convertHeight(h, "mm") |
|
| 1454 |
+ object@top_annotation_param = list(height = h) |
|
| 1455 |
+ } else {
|
|
| 1456 |
+ object@top_annotation = c(object@top_annotation, ha, gap = gap) |
|
| 1457 |
+ h = height(object@top_annotation) + height(ha) + gap |
|
| 1458 |
+ h = convertHeight(h, "mm") |
|
| 1459 |
+ object@top_annotation_param = list(height = h) |
|
| 1460 |
+ } |
|
| 1461 |
+ } else if(side == "bottom") {
|
|
| 1462 |
+ if(is.null(object@bottom_annotation)) {
|
|
| 1463 |
+ object@bottom_annotation = ha |
|
| 1464 |
+ h = height(ha) + ht_opt$COLUMN_ANNO_PADDING |
|
| 1465 |
+ h = convertHeight(h, "mm") |
|
| 1466 |
+ object@bottom_annotation_param = list(height = h) |
|
| 1467 |
+ } else {
|
|
| 1468 |
+ object@bottom_annotation = c(object@bottom_annotation, ha, gap = gap) |
|
| 1469 |
+ h = height(object@bottom_annotation) + height(ha) + gap |
|
| 1470 |
+ h = convertHeight(h, "mm") |
|
| 1471 |
+ object@bottom_annotation_param = list(height = h) |
|
| 1472 |
+ } |
|
| 1473 |
+ } else if(side == "left") {
|
|
| 1474 |
+ if(is.null(object@left_annotation)) {
|
|
| 1475 |
+ object@left_annotation = ha |
|
| 1476 |
+ w = width(ha) + ht_opt$ROW_ANNO_PADDING |
|
| 1477 |
+ w = convertWidth(w, "mm") |
|
| 1478 |
+ object@left_annotation_param = list(width = w) |
|
| 1479 |
+ } else {
|
|
| 1480 |
+ object@left_annotation = c(object@left_annotation, ha, gap = gap) |
|
| 1481 |
+ w = width(object@left_annotation) + width(ha) + gap |
|
| 1482 |
+ w = convertWidth(w, "mm") |
|
| 1483 |
+ object@left_annotation_param = list(width = w) |
|
| 1484 |
+ } |
|
| 1485 |
+ } else if(side == "right") {
|
|
| 1486 |
+ if(is.null(object@right_annotation)) {
|
|
| 1487 |
+ object@right_annotation = ha |
|
| 1488 |
+ w = width(ha) + ht_opt$ROW_ANNO_PADDING |
|
| 1489 |
+ w = convertWidth(w, "mm") |
|
| 1490 |
+ object@right_annotation_param = list(width = w) |
|
| 1491 |
+ } else {
|
|
| 1492 |
+ object@right_annotation = c(object@right_annotation, ha, gap = gap) |
|
| 1493 |
+ w = width(object@right_annotation) + width(ha) + gap |
|
| 1494 |
+ w = convertWidth(w, "mm") |
|
| 1495 |
+ object@right_annotation_param = list(height = w) |
|
| 1496 |
+ } |
|
| 1497 |
+ } |
|
| 1498 |
+ object |
|
| 1499 |
+}) |
Zuguang Gu authored on 22/10/2020 10:44:27 | ... | ... |
@@ -64,6 +64,7 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",
|
| 64 | 64 |
# -annotation_name_offset Offset to the annotation names, a `grid::unit` object. The value can be a vector. |
| 65 | 65 |
# -annotation_name_side Side of the annotation names. |
| 66 | 66 |
# -annotation_name_rot Rotation of the annotation names, it can only take values in ``c(00, 90, 180, 270)``. The value can be a vector. |
| 67 |
+# -annotation_name_align Whether to align the annotation names. |
|
| 67 | 68 |
# -annotation_height Height of each annotation if annotations are column annotations. |
| 68 | 69 |
# -annotation_width Width of each annotation if annotations are row annotations. |
| 69 | 70 |
# -height Height of the whole column annotations. |
| ... | ... |
@@ -108,6 +109,7 @@ HeatmapAnnotation = function(..., |
| 108 | 109 |
annotation_name_offset = NULL, |
| 109 | 110 |
annotation_name_side = ifelse(which == "column", "right", "bottom"), |
| 110 | 111 |
annotation_name_rot = NULL, |
| 112 |
+ annotation_name_align = FALSE, |
|
| 111 | 113 |
|
| 112 | 114 |
annotation_height = NULL, |
| 113 | 115 |
annotation_width = NULL, |
| ... | ... |
@@ -441,6 +443,51 @@ HeatmapAnnotation = function(..., |
| 441 | 443 |
anno_size = convertWidth(anno_size, "mm") |
| 442 | 444 |
|
| 443 | 445 |
names(anno_list) = sapply(anno_list, function(x) x@name) |
| 446 |
+ |
|
| 447 |
+ if(annotation_name_align) {
|
|
| 448 |
+ # adjust x, y, offset slot in SingleAnnotation objects |
|
| 449 |
+ l_bottom = sapply(anno_list, function(x) x@name_param$side == "bottom" & x@name_param$show & x@fun@fun_name != "anno_simple") |
|
| 450 |
+ if(sum(l_bottom) > 1) {
|
|
| 451 |
+ max_offset = unit(max(sapply(anno_list[l_bottom], function(anno) {
|
|
| 452 |
+ unit_to_numeric(anno@name_param$offset) |
|
| 453 |
+ })), "mm") |
|
| 454 |
+ for(i in which(l_bottom)) {
|
|
| 455 |
+ anno_list[[i]]@name_param$offset = max_offset |
|
| 456 |
+ anno_list[[i]]@name_param$y = unit(0, "npc") - max_offset |
|
| 457 |
+ } |
|
| 458 |
+ } |
|
| 459 |
+ l_top = sapply(anno_list, function(x) x@name_param$side == "top" & x@name_param$show & x@fun@fun_name != "anno_simple") |
|
| 460 |
+ if(sum(l_top) > 1) {
|
|
| 461 |
+ max_offset = unit(max(sapply(anno_list[l_top], function(anno) {
|
|
| 462 |
+ unit_to_numeric(anno@name_param$offset) |
|
| 463 |
+ })), "mm") |
|
| 464 |
+ for(i in which(l_bottom)) {
|
|
| 465 |
+ anno_list[[i]]@name_param$offset = max_offset |
|
| 466 |
+ anno_list[[i]]@name_param$y = unit(1, "npc") + max_offset |
|
| 467 |
+ } |
|
| 468 |
+ } |
|
| 469 |
+ l_left = sapply(anno_list, function(x) x@name_param$side == "left" & x@name_param$show & x@fun@fun_name != "anno_simple") |
|
| 470 |
+ if(sum(l_left) > 1) {
|
|
| 471 |
+ max_offset = unit(max(sapply(anno_list[l_left], function(anno) {
|
|
| 472 |
+ unit_to_numeric(anno@name_param$offset) |
|
| 473 |
+ })), "mm") |
|
| 474 |
+ for(i in which(l_left)) {
|
|
| 475 |
+ anno_list[[i]]@name_param$offset = max_offset |
|
| 476 |
+ anno_list[[i]]@name_param$x = unit(0, "npc") - max_offset |
|
| 477 |
+ } |
|
| 478 |
+ } |
|
| 479 |
+ l_right = sapply(anno_list, function(x) x@name_param$side == "right" & x@name_param$show & x@fun@fun_name != "anno_simple") |
|
| 480 |
+ if(sum(l_right) > 1) {
|
|
| 481 |
+ max_offset = unit(max(sapply(anno_list[l_right], function(anno) {
|
|
| 482 |
+ unit_to_numeric(anno@name_param$offset) |
|
| 483 |
+ })), "mm") |
|
| 484 |
+ for(i in which(l_right)) {
|
|
| 485 |
+ anno_list[[i]]@name_param$offset = max_offset |
|
| 486 |
+ anno_list[[i]]@name_param$x = unit(1, "npc") + max_offset |
|
| 487 |
+ } |
|
| 488 |
+ } |
|
| 489 |
+ } |
|
| 490 |
+ |
|
| 444 | 491 |
.Object@anno_list = anno_list |
| 445 | 492 |
.Object@anno_size = anno_size |
| 446 | 493 |
.Object@which = which |
| ... | ... |
@@ -455,6 +502,7 @@ HeatmapAnnotation = function(..., |
| 455 | 502 |
})), "mm") |
| 456 | 503 |
} |
| 457 | 504 |
.Object@extended = extended |
| 505 |
+ |
|
| 458 | 506 |
.Object@param = list( |
| 459 | 507 |
simple_anno_size = simple_anno_size, |
| 460 | 508 |
simple_anno_size_adjust = simple_anno_size_adjust, |
Zuguang Gu authored on 08/10/2020 08:44:52 | ... | ... |
@@ -281,6 +281,7 @@ HeatmapAnnotation = function(..., |
| 281 | 281 |
if(any(is.na(names(col)))) {
|
| 282 | 282 |
stop_wrap("`col` should be a named list.")
|
| 283 | 283 |
} |
| 284 |
+ col = col[intersect(simple_anno_name, names(col))] |
|
| 284 | 285 |
if(any(sapply(col, function(x) if(is.function(x)) FALSE else is.null(names(x))))) {
|
| 285 | 286 |
stop_wrap("elements in `col` should be named vectors.")
|
| 286 | 287 |
} |
simplifyEnrichment authored on 06/10/2020 12:07:17 | ... | ... |
@@ -158,7 +158,10 @@ HeatmapAnnotation = function(..., |
| 158 | 158 |
arg_list = scl[-1] |
| 159 | 159 |
} else {
|
| 160 | 160 |
scl = as.list(sc[[nsc-1]]) |
| 161 |
- if(any(as.character(scl[[1]]) %in% c("HeatmapAnnotation", "rowAnnotation", "columnAnnotation"))) {
|
|
| 161 |
+ if(is.function(scl[[1]])) {
|
|
| 162 |
+ scl = as.list(sc[[nsc]]) |
|
| 163 |
+ arg_list = scl[-1] |
|
| 164 |
+ } else if(any(as.character(scl[[1]]) %in% c("HeatmapAnnotation", "rowAnnotation", "columnAnnotation"))) {
|
|
| 162 | 165 |
arg_list = scl[-1] |
| 163 | 166 |
} else {
|
| 164 | 167 |
scl = as.list(sc[[nsc]]) |
Zuguang Gu authored on 09/09/2020 06:54:18 | ... | ... |
@@ -942,6 +942,9 @@ names.HeatmapAnnotation = function(x) {
|
| 942 | 942 |
names(x@anno_list) = value |
| 943 | 943 |
for(i in seq_along(value)) {
|
| 944 | 944 |
x@anno_list[[i]]@name = value[i] |
| 945 |
+ if(!is.null(x@anno_list[[i]]@color_mapping)) {
|
|
| 946 |
+ x@anno_list[[i]]@color_mapping@name = value[i] |
|
| 947 |
+ } |
|
| 945 | 948 |
} |
| 946 | 949 |
return(x) |
| 947 | 950 |
} |
Zuguang Gu authored on 06/05/2020 07:21:34 | ... | ... |
@@ -271,18 +271,20 @@ HeatmapAnnotation = function(..., |
| 271 | 271 |
annotation_label = recycle_list(annotation_label, an, NULL) |
| 272 | 272 |
|
| 273 | 273 |
if(!missing(col)) {
|
| 274 |
- if(is.null(names(col))) {
|
|
| 275 |
- stop_wrap("`col` should be a named list.")
|
|
| 276 |
- } |
|
| 277 |
- if(any(is.na(names(col)))) {
|
|
| 278 |
- stop_wrap("`col` should be a named list.")
|
|
| 279 |
- } |
|
| 280 |
- if(any(sapply(col, function(x) if(is.function(x)) FALSE else is.null(names(x))))) {
|
|
| 281 |
- stop_wrap("elements in `col` should be named vectors.")
|
|
| 282 |
- } |
|
| 283 |
- if(any(sapply(col, function(x) if(is.function(x)) FALSE else any(is.na(names(x)))))) {
|
|
| 284 |
- stop_wrap("elements in `col` should be named vectors.")
|
|
| 285 |
- } |
|
| 274 |
+ if(length(col) >= 1) {
|
|
| 275 |
+ if(is.null(names(col))) {
|
|
| 276 |
+ stop_wrap("`col` should be a named list.")
|
|
| 277 |
+ } |
|
| 278 |
+ if(any(is.na(names(col)))) {
|
|
| 279 |
+ stop_wrap("`col` should be a named list.")
|
|
| 280 |
+ } |
|
| 281 |
+ if(any(sapply(col, function(x) if(is.function(x)) FALSE else is.null(names(x))))) {
|
|
| 282 |
+ stop_wrap("elements in `col` should be named vectors.")
|
|
| 283 |
+ } |
|
| 284 |
+ if(any(sapply(col, function(x) if(is.function(x)) FALSE else any(is.na(names(x)))))) {
|
|
| 285 |
+ stop_wrap("elements in `col` should be named vectors.")
|
|
| 286 |
+ } |
|
| 287 |
+ } |
|
| 286 | 288 |
} |
| 287 | 289 |
|
| 288 | 290 |
### check the length of annotations |
Zuguang Gu authored on 06/04/2020 13:08:25 | ... | ... |
@@ -59,6 +59,7 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",
|
| 59 | 59 |
# -gap Gap between annotations. It can be a single value or a vector of `grid::unit` objects. |
| 60 | 60 |
# -show_annotation_name Whether show annotation names? For column annotation, annotation names are drawn either on the left |
| 61 | 61 |
# or the right, and for row annotations, names are draw either on top or at the bottom. The value can be a vector. |
| 62 |
+# -annotation_label Labels for the annotations. By default it is the same as individual annotation names. |
|
| 62 | 63 |
# -annotation_name_gp Graphic parameters for anntation names. Graphic paramters can be vectors. |
| 63 | 64 |
# -annotation_name_offset Offset to the annotation names, a `grid::unit` object. The value can be a vector. |
| 64 | 65 |
# -annotation_name_side Side of the annotation names. |
| ... | ... |
@@ -102,6 +103,7 @@ HeatmapAnnotation = function(..., |
| 102 | 103 |
gap = unit(1, "points"), |
| 103 | 104 |
|
| 104 | 105 |
show_annotation_name = TRUE, |
| 106 |
+ annotation_label = NULL, |
|
| 105 | 107 |
annotation_name_gp = gpar(), |
| 106 | 108 |
annotation_name_offset = NULL, |
| 107 | 109 |
annotation_name_side = ifelse(which == "column", "right", "bottom"), |
| ... | ... |
@@ -266,6 +268,7 @@ HeatmapAnnotation = function(..., |
| 266 | 268 |
} |
| 267 | 269 |
border = recycle_param(border, an, FALSE) |
| 268 | 270 |
annotation_name_gp = recycle_gp(annotation_name_gp, n_total_anno) |
| 271 |
+ annotation_label = recycle_list(annotation_label, an, NULL) |
|
| 269 | 272 |
|
| 270 | 273 |
if(!missing(col)) {
|
| 271 | 274 |
if(is.null(names(col))) {
|
| ... | ... |
@@ -310,6 +313,7 @@ HeatmapAnnotation = function(..., |
| 310 | 313 |
|
| 311 | 314 |
i_anno = i_anno + 1 |
| 312 | 315 |
arg_list = list(name = ag, which = which, |
| 316 |
+ label = annotation_label[[i_anno]], |
|
| 313 | 317 |
show_name = show_annotation_name[i_anno], |
| 314 | 318 |
name_gp = subset_gp(annotation_name_gp, i_anno), |
| 315 | 319 |
name_offset = annotation_name_offset[[i_anno]], |
Zuguang Gu authored on 20/03/2020 19:42:24 | ... | ... |
@@ -961,6 +961,7 @@ anno_type = function(ha) {
|
| 961 | 961 |
# ha[, 1:2] |
| 962 | 962 |
# ha[1:5, c("foo", "sth")]
|
| 963 | 963 |
"[.HeatmapAnnotation" = function(x, i, j) {
|
| 964 |
+ |
|
| 964 | 965 |
if(!missing(j)) {
|
| 965 | 966 |
if(is.character(j)) {
|
| 966 | 967 |
j = which(names(x@anno_list) %in% j) |
| ... | ... |
@@ -1004,7 +1005,6 @@ anno_type = function(ha) {
|
| 1004 | 1005 |
x2@gap[length(x2@gap)] = unit(0, "mm") |
| 1005 | 1006 |
|
| 1006 | 1007 |
size(x2) = sum(x2@anno_size) + sum(x2@gap) - x2@gap[length(x2@gap)] |
| 1007 |
- |
|
| 1008 | 1008 |
} |
| 1009 | 1009 |
|
| 1010 | 1010 |
extended = unit(c(0, 0, 0, 0), "mm") |
Zuguang Gu authored on 05/03/2020 22:22:45 | ... | ... |
@@ -1237,7 +1237,7 @@ setMethod(f = "re_size", |
| 1237 | 1237 |
if(is_size_set) {
|
| 1238 | 1238 |
if(is_abs_unit(size_adjusted)) {
|
| 1239 | 1239 |
rel_num = sapply(which(l_rel_unit), function(i) {
|
| 1240 |
- if(identical(class(annotation_size_adjusted[i]), "unit")) {
|
|
| 1240 |
+ if(inherits(annotation_size_adjusted[i], "unit")) {
|
|
| 1241 | 1241 |
if(unitType(annotation_size_adjusted[i]) != "null") {
|
| 1242 | 1242 |
stop_wrap("relative unit should be defined as `unit(..., 'null')")
|
| 1243 | 1243 |
} |
Zuguang Gu authored on 05/03/2020 22:12:49 | ... | ... |
@@ -1238,7 +1238,7 @@ setMethod(f = "re_size", |
| 1238 | 1238 |
if(is_abs_unit(size_adjusted)) {
|
| 1239 | 1239 |
rel_num = sapply(which(l_rel_unit), function(i) {
|
| 1240 | 1240 |
if(identical(class(annotation_size_adjusted[i]), "unit")) {
|
| 1241 |
- if(attr(annotation_size_adjusted[i], "unit") != "null") {
|
|
| 1241 |
+ if(unitType(annotation_size_adjusted[i]) != "null") {
|
|
| 1242 | 1242 |
stop_wrap("relative unit should be defined as `unit(..., 'null')")
|
| 1243 | 1243 |
} |
| 1244 | 1244 |
} else {
|
jokergoo authored on 05/03/2020 14:31:53 | ... | ... |
@@ -440,9 +440,9 @@ HeatmapAnnotation = function(..., |
| 440 | 440 |
.Object@subsetable = all(sapply(anno_list, function(x) x@subsetable)) |
| 441 | 441 |
extended = unit(c(0, 0, 0, 0), "mm") |
| 442 | 442 |
for(i in 1:4) {
|
| 443 |
- extended[[i]] = max(sapply(anno_list, function(anno) {
|
|
| 444 |
- anno@extended[[i]] |
|
| 445 |
- })) |
|
| 443 |
+ extended[i] = unit(max(sapply(anno_list, function(anno) {
|
|
| 444 |
+ unit_to_numeric(anno@extended[i]) |
|
| 445 |
+ })), "mm") |
|
| 446 | 446 |
} |
| 447 | 447 |
.Object@extended = extended |
| 448 | 448 |
.Object@param = list( |
| ... | ... |
@@ -893,9 +893,9 @@ c.HeatmapAnnotation = function(..., gap = unit(0, "mm")) {
|
| 893 | 893 |
|
| 894 | 894 |
extended = unit(c(0, 0, 0, 0), "mm") |
| 895 | 895 |
for(i in 1:4) {
|
| 896 |
- extended[[i]] = max(sapply(x@anno_list, function(anno) {
|
|
| 897 |
- anno@extended[[i]] |
|
| 898 |
- })) |
|
| 896 |
+ extended[i] = unit(max(sapply(x@anno_list, function(anno) {
|
|
| 897 |
+ unit_to_numeric(anno@extended[i]) |
|
| 898 |
+ })), "mm") |
|
| 899 | 899 |
} |
| 900 | 900 |
x@extended = extended |
| 901 | 901 |
|
| ... | ... |
@@ -1009,9 +1009,9 @@ anno_type = function(ha) {
|
| 1009 | 1009 |
|
| 1010 | 1010 |
extended = unit(c(0, 0, 0, 0), "mm") |
| 1011 | 1011 |
for(i in 1:4) {
|
| 1012 |
- extended[[i]] = max(sapply(x2@anno_list, function(anno) {
|
|
| 1013 |
- anno@extended[[i]] |
|
| 1014 |
- })) |
|
| 1012 |
+ extended[[i]] = unit(max(sapply(x2@anno_list, function(anno) {
|
|
| 1013 |
+ unit_to_numeric(anno@extended[i]) |
|
| 1014 |
+ })), "mm") |
|
| 1015 | 1015 |
} |
| 1016 | 1016 |
x2@extended = extended |
| 1017 | 1017 |
|
| ... | ... |
@@ -1202,7 +1202,11 @@ setMethod(f = "re_size", |
| 1202 | 1202 |
anno_size = object@anno_size |
| 1203 | 1203 |
size = slot(object, size_name) |
| 1204 | 1204 |
gap = object@gap |
| 1205 |
- gap = gap[-length(gap)] |
|
| 1205 |
+ if(length(gap) == 1) {
|
|
| 1206 |
+ gap = unit(0, "mm") |
|
| 1207 |
+ } else {
|
|
| 1208 |
+ gap = gap[-length(gap)] |
|
| 1209 |
+ } |
|
| 1206 | 1210 |
n = length(object@anno_list) |
| 1207 | 1211 |
|
| 1208 | 1212 |
# the basic rule is |
| ... | ... |
@@ -1240,7 +1244,7 @@ setMethod(f = "re_size", |
| 1240 | 1244 |
} else {
|
| 1241 | 1245 |
stop_wrap("relative unit should be defined as `unit(..., 'null')")
|
| 1242 | 1246 |
} |
| 1243 |
- annotation_size_adjusted[i][[1]] |
|
| 1247 |
+ unit_to_numeric(annotation_size_adjusted[i][[1]]) |
|
| 1244 | 1248 |
}) |
| 1245 | 1249 |
rel_num = rel_num/sum(rel_num) |
| 1246 | 1250 |
if(any(!l_rel_unit)) {
|
Zuguang Gu authored on 26/03/2019 14:25:36 | ... | ... |
@@ -52,7 +52,7 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",
|
| 52 | 52 |
# See `SingleAnnotation` for how to set colors. |
| 53 | 53 |
# -na_col Color for ``NA`` values in simple annotations. |
| 54 | 54 |
# -annotation_legend_param A list which contains parameters for annotation legends. See `color_mapping_legend,ColorMapping-method` for all possible options. |
| 55 |
-# -show_legend Whether show annotation legends. The value can be one single value or a vector which corresponds to simple annotations. |
|
| 55 |
+# -show_legend Whether show annotation legends. The value can be one single value or a vector. |
|
| 56 | 56 |
# -which Are these row annotations or column annotations? |
| 57 | 57 |
# -gp Graphic parameters for simple annotations (with ``fill`` parameter ignored). |
| 58 | 58 |
# -border border of single annotations. |
| ... | ... |
@@ -215,6 +215,10 @@ HeatmapAnnotation = function(..., |
| 215 | 215 |
if(length(show_legend) == 1) {
|
| 216 | 216 |
show_legend = recycle_param(show_legend, simple_anno_name, TRUE) |
| 217 | 217 |
} |
| 218 |
+ # check length of show_legend |
|
| 219 |
+ if(length(show_legend) == length(anno_value_list) && !all(l_simple_anno)) {
|
|
| 220 |
+ show_legend = show_legend[l_simple_anno] |
|
| 221 |
+ } |
|
| 218 | 222 |
|
| 219 | 223 |
###### normalize `heatmap_legend_param` ####### |
| 220 | 224 |
if(length(annotation_legend_param) == 0) {
|
jokergoo authored on 15/03/2019 13:47:43 | ... | ... |
@@ -26,14 +26,16 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",
|
| 26 | 26 |
height = "ANY", |
| 27 | 27 |
gap = "ANY", |
| 28 | 28 |
subsetable = "logical", |
| 29 |
- extended = "ANY" |
|
| 29 |
+ extended = "ANY", |
|
| 30 |
+ param = "list" |
|
| 30 | 31 |
), |
| 31 | 32 |
prototype = list( |
| 32 | 33 |
anno_list = list(), |
| 33 | 34 |
which = "column", |
| 34 | 35 |
gap = unit(0, "mm"), |
| 35 | 36 |
subsetable = FALSE, |
| 36 |
- extended = unit(c(0, 0, 0, 0), "mm") |
|
| 37 |
+ extended = unit(c(0, 0, 0, 0), "mm"), |
|
| 38 |
+ param = list() |
|
| 37 | 39 |
), |
| 38 | 40 |
contains = "AdditiveUnit" |
| 39 | 41 |
) |
| ... | ... |
@@ -65,7 +67,7 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",
|
| 65 | 67 |
# -annotation_width Width of each annotation if annotations are row annotations. |
| 66 | 68 |
# -height Height of the whole column annotations. |
| 67 | 69 |
# -width Width of the whole heatmap annotations. |
| 68 |
-# -anno_simple_size Size of the simple annotation. |
|
| 70 |
+# -simple_anno_size Size of the simple annotation. |
|
| 69 | 71 |
# -simple_anno_size_adjust Whether also adjust the size of simple annotations when adjusting the whole heatmap annotation. |
| 70 | 72 |
# |
| 71 | 73 |
# == details |
| ... | ... |
@@ -109,12 +111,17 @@ HeatmapAnnotation = function(..., |
| 109 | 111 |
annotation_width = NULL, |
| 110 | 112 |
height = NULL, |
| 111 | 113 |
width = NULL, |
| 112 |
- anno_simple_size = ht_opt$anno_simple_size, |
|
| 114 |
+ simple_anno_size = ht_opt$simple_anno_size, |
|
| 113 | 115 |
simple_anno_size_adjust = FALSE |
| 114 | 116 |
) {
|
| 115 | 117 |
|
| 116 | 118 |
dev.null() |
| 117 | 119 |
|
| 120 |
+ is_height_set = !missing(height) |
|
| 121 |
+ is_width_set = !missing(width) |
|
| 122 |
+ is_annotation_height_set = !missing(annotation_height) |
|
| 123 |
+ is_annotation_width_set = !missing(annotation_width) |
|
| 124 |
+ |
|
| 118 | 125 |
.ENV$current_annotation_which = NULL |
| 119 | 126 |
which = match.arg(which)[1] |
| 120 | 127 |
.ENV$current_annotation_which = which |
| ... | ... |
@@ -198,6 +205,10 @@ HeatmapAnnotation = function(..., |
| 198 | 205 |
n_simple_anno = sum(l_simple_anno) |
| 199 | 206 |
simple_anno_name = names(anno_value_list[l_simple_anno]) |
| 200 | 207 |
|
| 208 |
+ if("anno_simple_size" %in% names(anno_value_list)) {
|
|
| 209 |
+ stop_wrap("Please use `simple_anno_size` as the argument.")
|
|
| 210 |
+ } |
|
| 211 |
+ |
|
| 201 | 212 |
if(verbose) qqcat("in total there are @{length(anno_value_list)} annotations (@{n_simple_anno} simple annotations)\n")
|
| 202 | 213 |
|
| 203 | 214 |
# normalize `show_legend` |
| ... | ... |
@@ -318,7 +329,7 @@ HeatmapAnnotation = function(..., |
| 318 | 329 |
arg_list$legend_param = annotation_legend_param[[i_simple + 1]] |
| 319 | 330 |
arg_list$value = anno_value_list[[ag]] |
| 320 | 331 |
arg_list$na_col = na_col |
| 321 |
- # arg_list$anno_simple_size = anno_simple_size |
|
| 332 |
+ arg_list$simple_anno_size = simple_anno_size |
|
| 322 | 333 |
if(missing(col)) {
|
| 323 | 334 |
anno_list[[ag]] = do.call(SingleAnnotation, arg_list) |
| 324 | 335 |
} else {
|
| ... | ... |
@@ -361,6 +372,8 @@ HeatmapAnnotation = function(..., |
| 361 | 372 |
|
| 362 | 373 |
|
| 363 | 374 |
if(is.null(gap)) gap = unit(0, "mm") |
| 375 |
+ if(identical(gap, 0)) gap = unit(0, "mm") |
|
| 376 |
+ if(!inherits(gap, "unit")) stop_wrap("`gap` needs to be a unit object.")
|
|
| 364 | 377 |
|
| 365 | 378 |
# the nth gap does not really matter |
| 366 | 379 |
if(length(gap) == 1) {
|
| ... | ... |
@@ -428,14 +441,20 @@ HeatmapAnnotation = function(..., |
| 428 | 441 |
})) |
| 429 | 442 |
} |
| 430 | 443 |
.Object@extended = extended |
| 444 |
+ .Object@param = list( |
|
| 445 |
+ simple_anno_size = simple_anno_size, |
|
| 446 |
+ simple_anno_size_adjust = simple_anno_size_adjust, |
|
| 447 |
+ is_height_set = is_height_set, |
|
| 448 |
+ is_width_set = is_width_set, |
|
| 449 |
+ is_annotation_height_set = is_annotation_height_set, |
|
| 450 |
+ is_annotation_width_set = is_annotation_width_set |
|
| 451 |
+ ) |
|
| 431 | 452 |
|
| 432 | 453 |
## adjust height/width if `width`/`annotation_width` is set |
| 433 | 454 |
if(which == "column") {
|
| 434 |
- .Object = re_size(.Object, height = height, annotation_height = annotation_height, |
|
| 435 |
- anno_simple_size = anno_simple_size, simple_anno_size_adjust = simple_anno_size_adjust) |
|
| 455 |
+ .Object = re_size(.Object, height = height, annotation_height = annotation_height) |
|
| 436 | 456 |
} else {
|
| 437 |
- .Object = re_size(.Object, width = width, annotation_width = annotation_width, |
|
| 438 |
- anno_simple_size = anno_simple_size, simple_anno_size_adjust = simple_anno_size_adjust) |
|
| 457 |
+ .Object = re_size(.Object, width = width, annotation_width = annotation_width) |
|
| 439 | 458 |
} |
| 440 | 459 |
|
| 441 | 460 |
return(.Object) |
| ... | ... |
@@ -1015,7 +1034,7 @@ length.HeatmapAnnotation = function(x) {
|
| 1015 | 1034 |
# -annotation_width A vector of of annotation widths in `grid::unit` class. |
| 1016 | 1035 |
# -height The height of the complete heatmap annotation. |
| 1017 | 1036 |
# -width The width of the complete heatmap annotation. |
| 1018 |
-# -anno_simple_size The size of one line of the simple annotation. |
|
| 1037 |
+# -simple_anno_size The size of one line of the simple annotation. |
|
| 1019 | 1038 |
# -simple_anno_size_adjust Whether adjust the size of the simple annotation? |
| 1020 | 1039 |
# |
| 1021 | 1040 |
# == details |
| ... | ... |
@@ -1027,10 +1046,10 @@ length.HeatmapAnnotation = function(x) {
|
| 1027 | 1046 |
# ``annotation_height`` are absolute units, ``height`` is ignored. |
| 1028 | 1047 |
# 2. If ``annotation_height`` contains non-absolute units, ``height`` also need to be set and the |
| 1029 | 1048 |
# non-absolute units should be set in a simple form such as 1:10 or ``unit(1, "null")``. |
| 1030 |
-# 3. ``anno_simple_size`` is only used when ``annotation_height`` is NULL. |
|
| 1049 |
+# 3. ``simple_anno_size`` is only used when ``annotation_height`` is NULL. |
|
| 1031 | 1050 |
# 4. If only ``height`` is set, non-simple annotation is adjusted while keeps simple anntation unchanged. |
| 1032 | 1051 |
# 5. If only ``height`` is set and all annotations are simple annotations, all anntations are adjusted, |
| 1033 |
-# and ``anno_simple_size`` is disabled. |
|
| 1052 |
+# and ``simple_anno_size`` is disabled. |
|
| 1034 | 1053 |
# 6. If ``simple_anno_size_adjust`` is ``FALSE``, the size of the simple annotations will not change. |
| 1035 | 1054 |
# |
| 1036 | 1055 |
setMethod(f = "re_size", |
| ... | ... |
@@ -1040,17 +1059,17 @@ setMethod(f = "re_size", |
| 1040 | 1059 |
annotation_width = NULL, |
| 1041 | 1060 |
height = NULL, |
| 1042 | 1061 |
width = NULL, |
| 1043 |
- anno_simple_size = ht_opt$anno_simple_size, |
|
| 1044 |
- simple_anno_size_adjust = NULL) {
|
|
| 1062 |
+ simple_anno_size = object@param$simple_anno_size, |
|
| 1063 |
+ simple_anno_size_adjust = object@param$simple_anno_size_adjust) {
|
|
| 1045 | 1064 |
|
| 1046 | 1065 |
if(object@which == "column") {
|
| 1047 | 1066 |
if(!missing(width) || !missing(annotation_width)) {
|
| 1048 |
- stop_wrap("Please use ComplexHeatmap:::width() directly")
|
|
| 1067 |
+ stop_wrap("You cannot set the width of the column annotations.")
|
|
| 1049 | 1068 |
} |
| 1050 | 1069 |
} |
| 1051 | 1070 |
if(object@which == "colrowumn") {
|
| 1052 | 1071 |
if(!missing(height) || !missing(annotation_height)) {
|
| 1053 |
- stop_wrap("Please use ComplexHeatmap:::height() directly")
|
|
| 1072 |
+ stop_wrap("You cannot set the height of the row annotations.")
|
|
| 1054 | 1073 |
} |
| 1055 | 1074 |
} |
| 1056 | 1075 |
|
| ... | ... |
@@ -1078,7 +1097,6 @@ setMethod(f = "re_size", |
| 1078 | 1097 |
return(object) |
| 1079 | 1098 |
} |
| 1080 | 1099 |
} |
| 1081 |
- |
|
| 1082 | 1100 |
if(which == "column") {
|
| 1083 | 1101 |
if(is.null(height)) {
|
| 1084 | 1102 |
is_size_set = FALSE |
| ... | ... |
@@ -1106,7 +1124,7 @@ setMethod(f = "re_size", |
| 1106 | 1124 |
if(length(object@anno_list) == 1 && !inherits(annotation_height, "unit")) {
|
| 1107 | 1125 |
stop_wrap("When there is only one annotation, `annotation_height` should be set as a unit object.")
|
| 1108 | 1126 |
} |
| 1109 |
- if(!inherits(height, "unit")) {
|
|
| 1127 |
+ if(!inherits(height, "unit") || !object@param$is_height_set) {
|
|
| 1110 | 1128 |
height = annotation_height[1] |
| 1111 | 1129 |
} |
| 1112 | 1130 |
if(!inherits(height, "unit")) {
|
| ... | ... |
@@ -1151,7 +1169,7 @@ setMethod(f = "re_size", |
| 1151 | 1169 |
if(length(object@anno_list) == 1 && !inherits(annotation_width, "unit")) {
|
| 1152 | 1170 |
stop_wrap("When there is only one annotation, `annotation_width` should be set as a unit object.")
|
| 1153 | 1171 |
} |
| 1154 |
- if(!inherits(width, "unit")) {
|
|
| 1172 |
+ if(!inherits(width, "unit") || !object@param$is_width_set) {
|
|
| 1155 | 1173 |
width = annotation_width[1] |
| 1156 | 1174 |
} |
| 1157 | 1175 |
if(!inherits(width, "unit")) {
|
| ... | ... |
@@ -1260,10 +1278,14 @@ setMethod(f = "re_size", |
| 1260 | 1278 |
} else {
|
| 1261 | 1279 |
size = convertUnitFun(size, "mm", valueOnly = TRUE) |
| 1262 | 1280 |
anno_size = convertUnitFun(anno_size, "mm", valueOnly = TRUE) |
| 1263 |
- |
|
| 1264 |
- l_simple_anno = sapply(seq_len(n), function(i) {
|
|
| 1265 |
- !is.null(object@anno_list[[i]]@color_mapping) |
|
| 1266 |
- }) |
|
| 1281 |
+ |
|
| 1282 |
+ if(simple_anno_size_adjust) {
|
|
| 1283 |
+ l_simple_anno = rep(FALSE, n) |
|
| 1284 |
+ } else {
|
|
| 1285 |
+ l_simple_anno = sapply(seq_len(n), function(i) {
|
|
| 1286 |
+ !is.null(object@anno_list[[i]]@color_mapping) |
|
| 1287 |
+ }) |
|
| 1288 |
+ } |
|
| 1267 | 1289 |
|
| 1268 | 1290 |
if(all(l_simple_anno)) {
|
| 1269 | 1291 |
anno_size2 = anno_size/sum(anno_size) * (size_adjusted - sum(gap)) |
| ... | ... |
@@ -1273,22 +1295,21 @@ setMethod(f = "re_size", |
| 1273 | 1295 |
|
| 1274 | 1296 |
anno_size2 = anno_size |
| 1275 | 1297 |
# size_adjusted = convertUnitFun(size_adjusted, "mm", valueOnly = TRUE) |
| 1276 |
- if(is.null(anno_simple_size)) {
|
|
| 1277 |
- anno_simple_size = 5 |
|
| 1298 |
+ if(is.null(simple_anno_size)) {
|
|
| 1299 |
+ simple_anno_size = 5 |
|
| 1278 | 1300 |
} else {
|
| 1279 |
- anno_simple_size = convertUnitFun(anno_simple_size, "mm", valueOnly = TRUE) |
|
| 1301 |
+ simple_anno_size = convertUnitFun(simple_anno_size, "mm", valueOnly = TRUE) |
|
| 1280 | 1302 |
} |
| 1281 | 1303 |
if(size_adjusted <= sum(gap)) {
|
| 1282 | 1304 |
stop_wrap(paste0(size_name, " you set is smaller than sum of gaps.")) |
| 1283 | 1305 |
} |
| 1284 | 1306 |
|
| 1285 | 1307 |
## fix the size of simple annotation and zoom function annotations |
| 1286 |
- ts = size_adjusted - sum(gap) - sum(anno_size[l_simple_anno]*anno_simple_size/5) |
|
| 1308 |
+ ts = size_adjusted - sum(gap) - sum(anno_size[l_simple_anno]) # total size excluding simple annotations and gap |
|
| 1287 | 1309 |
if(ts < 0) {
|
| 1288 | 1310 |
stop_wrap(paste0(size_name, " you set is too small.")) |
| 1289 | 1311 |
} |
| 1290 | 1312 |
anno_size2[!l_simple_anno] = anno_size[!l_simple_anno]/sum(anno_size[!l_simple_anno]) * ts |
| 1291 |
- anno_size2[l_simple_anno] = anno_size[l_simple_anno]*anno_simple_size/5 |
|
| 1292 | 1313 |
|
| 1293 | 1314 |
size_adjusted = unit(size_adjusted, "mm") |
| 1294 | 1315 |
anno_size2 = unit(anno_size2, "mm") |
Zuguang Gu authored on 12/02/2019 08:33:38 | ... | ... |
@@ -1041,7 +1041,7 @@ setMethod(f = "re_size", |
| 1041 | 1041 |
height = NULL, |
| 1042 | 1042 |
width = NULL, |
| 1043 | 1043 |
anno_simple_size = ht_opt$anno_simple_size, |
| 1044 |
- simple_anno_size_adjust = FALSE) {
|
|
| 1044 |
+ simple_anno_size_adjust = NULL) {
|
|
| 1045 | 1045 |
|
| 1046 | 1046 |
if(object@which == "column") {
|
| 1047 | 1047 |
if(!missing(width) || !missing(annotation_width)) {
|
| ... | ... |
@@ -1054,9 +1054,17 @@ setMethod(f = "re_size", |
| 1054 | 1054 |
} |
| 1055 | 1055 |
} |
| 1056 | 1056 |
|
| 1057 |
+ all_simple_annotation = all(sapply(object@anno_list, function(x) is_simple_annotation(x) || is_matrix_annotation(x))) |
|
| 1058 |
+ if(is.null(simple_anno_size_adjust)) {
|
|
| 1059 |
+ if(all_simple_annotation) {
|
|
| 1060 |
+ simple_anno_size_adjust = TRUE |
|
| 1061 |
+ } else {
|
|
| 1062 |
+ simple_anno_size_adjust = FALSE |
|
| 1063 |
+ } |
|
| 1064 |
+ } |
|
| 1057 | 1065 |
which = object@which |
| 1058 | 1066 |
if(!simple_anno_size_adjust) {
|
| 1059 |
- if(all(sapply(object@anno_list, function(x) is_simple_annotation(x) || is_matrix_annotation(x)))) {
|
|
| 1067 |
+ if(all_simple_annotation) {
|
|
| 1060 | 1068 |
if(which == "column") {
|
| 1061 | 1069 |
height = sum(object@anno_size) + sum(object@gap) - object@gap[length(object@gap)] |
| 1062 | 1070 |
object@height = convertHeight(height, "mm") |
| ... | ... |
@@ -1064,6 +1072,9 @@ setMethod(f = "re_size", |
| 1064 | 1072 |
width = sum(object@anno_size) + sum(object@gap) - object@gap[length(object@gap)] |
| 1065 | 1073 |
object@width = convertWidth(width, "mm") |
| 1066 | 1074 |
} |
| 1075 |
+ if(ht_opt$verbose) {
|
|
| 1076 |
+ message_wrap("`simple_anno_size_adjust` is set to FALSE and all annotations are simple annotations or matrix annotations, the heights of all annotations are not adjusted.")
|
|
| 1077 |
+ } |
|
| 1067 | 1078 |
return(object) |
| 1068 | 1079 |
} |
| 1069 | 1080 |
} |
| ... | ... |
@@ -1083,6 +1094,11 @@ setMethod(f = "re_size", |
| 1083 | 1094 |
if(is.null(annotation_height)) {
|
| 1084 | 1095 |
is_annotation_size_set = FALSE |
| 1085 | 1096 |
} else {
|
| 1097 |
+ if(length(annotation_height) == 1) {
|
|
| 1098 |
+ if(!inherits(annotation_height, "unit")) {
|
|
| 1099 |
+ annotation_height = rep(annotation_height, length(object@anno_list)) |
|
| 1100 |
+ } |
|
| 1101 |
+ } |
|
| 1086 | 1102 |
if(length(annotation_height) == 1) {
|
| 1087 | 1103 |
if(length(object@anno_list) > 1) {
|
| 1088 | 1104 |
warning_wrap("`annotation_height` is set with length of one while with multiple annotations, `annotation_height` is treated as `height`.")
|
| ... | ... |
@@ -1090,7 +1106,9 @@ setMethod(f = "re_size", |
| 1090 | 1106 |
if(length(object@anno_list) == 1 && !inherits(annotation_height, "unit")) {
|
| 1091 | 1107 |
stop_wrap("When there is only one annotation, `annotation_height` should be set as a unit object.")
|
| 1092 | 1108 |
} |
| 1093 |
- height = annotation_height[1] |
|
| 1109 |
+ if(!inherits(height, "unit")) {
|
|
| 1110 |
+ height = annotation_height[1] |
|
| 1111 |
+ } |
|
| 1094 | 1112 |
if(!inherits(height, "unit")) {
|
| 1095 | 1113 |
stop_wrap("`height` should be a `unit` object")
|
| 1096 | 1114 |
} |
| ... | ... |
@@ -1121,6 +1139,11 @@ setMethod(f = "re_size", |
| 1121 | 1139 |
if(is.null(annotation_width)) {
|
| 1122 | 1140 |
is_annotation_size_set = FALSE |
| 1123 | 1141 |
} else {
|
| 1142 |
+ if(length(annotation_width) == 1) {
|
|
| 1143 |
+ if(!inherits(annotation_width, "unit")) {
|
|
| 1144 |
+ annotation_width = rep(annotation_width, length(object@anno_list)) |
|
| 1145 |
+ } |
|
| 1146 |
+ } |
|
| 1124 | 1147 |
if(length(annotation_width) == 1) {
|
| 1125 | 1148 |
if(length(object@anno_list) > 1) {
|
| 1126 | 1149 |
warning_wrap("`annotation_width` is set with length of one while with multiple annotations, `annotation_width` is treated as `width`.")
|
| ... | ... |
@@ -1128,7 +1151,9 @@ setMethod(f = "re_size", |
| 1128 | 1151 |
if(length(object@anno_list) == 1 && !inherits(annotation_width, "unit")) {
|
| 1129 | 1152 |
stop_wrap("When there is only one annotation, `annotation_width` should be set as a unit object.")
|
| 1130 | 1153 |
} |
| 1131 |
- width = annotation_width[1] |
|
| 1154 |
+ if(!inherits(width, "unit")) {
|
|
| 1155 |
+ width = annotation_width[1] |
|
| 1156 |
+ } |
|
| 1132 | 1157 |
if(!inherits(width, "unit")) {
|
| 1133 | 1158 |
stop_wrap("`width` should be a `unit` object")
|
| 1134 | 1159 |
} |
Zuguang Gu authored on 29/12/2018 15:24:39 | ... | ... |
@@ -58,7 +58,7 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",
|
| 58 | 58 |
# -show_annotation_name Whether show annotation names? For column annotation, annotation names are drawn either on the left |
| 59 | 59 |
# or the right, and for row annotations, names are draw either on top or at the bottom. The value can be a vector. |
| 60 | 60 |
# -annotation_name_gp Graphic parameters for anntation names. Graphic paramters can be vectors. |
| 61 |
-# -annotation_name_offset Offset to the annotations, `grid::unit` object. The value can be a vector. |
|
| 61 |
+# -annotation_name_offset Offset to the annotation names, a `grid::unit` object. The value can be a vector. |
|
| 62 | 62 |
# -annotation_name_side Side of the annotation names. |
| 63 | 63 |
# -annotation_name_rot Rotation of the annotation names, it can only take values in ``c(00, 90, 180, 270)``. The value can be a vector. |
| 64 | 64 |
# -annotation_height Height of each annotation if annotations are column annotations. |
Zuguang Gu authored on 10/12/2018 10:01:04 | ... | ... |
@@ -1085,7 +1085,10 @@ setMethod(f = "re_size", |
| 1085 | 1085 |
} else {
|
| 1086 | 1086 |
if(length(annotation_height) == 1) {
|
| 1087 | 1087 |
if(length(object@anno_list) > 1) {
|
| 1088 |
- warning_wrap("`annotation_height` is set with length of one while with multiplt annotations, `annotation_height` is treated as `height`.")
|
|
| 1088 |
+ warning_wrap("`annotation_height` is set with length of one while with multiple annotations, `annotation_height` is treated as `height`.")
|
|
| 1089 |
+ } |
|
| 1090 |
+ if(length(object@anno_list) == 1 && !inherits(annotation_height, "unit")) {
|
|
| 1091 |
+ stop_wrap("When there is only one annotation, `annotation_height` should be set as a unit object.")
|
|
| 1089 | 1092 |
} |
| 1090 | 1093 |
height = annotation_height[1] |
| 1091 | 1094 |
if(!inherits(height, "unit")) {
|
| ... | ... |
@@ -1120,7 +1123,10 @@ setMethod(f = "re_size", |
| 1120 | 1123 |
} else {
|
| 1121 | 1124 |
if(length(annotation_width) == 1) {
|
| 1122 | 1125 |
if(length(object@anno_list) > 1) {
|
| 1123 |
- warning_wrap("`annotation_width` is set with length of one while with multiplt annotations, `annotation_width` is treated as `width`.")
|
|
| 1126 |
+ warning_wrap("`annotation_width` is set with length of one while with multiple annotations, `annotation_width` is treated as `width`.")
|
|
| 1127 |
+ } |
|
| 1128 |
+ if(length(object@anno_list) == 1 && !inherits(annotation_width, "unit")) {
|
|
| 1129 |
+ stop_wrap("When there is only one annotation, `annotation_width` should be set as a unit object.")
|
|
| 1124 | 1130 |
} |
| 1125 | 1131 |
width = annotation_width[1] |
| 1126 | 1132 |
if(!inherits(width, "unit")) {
|
Zuguang Gu authored on 07/12/2018 14:41:15 | ... | ... |
@@ -553,6 +553,8 @@ setMethod(f = "get_legend_param_list", |
| 553 | 553 |
# -n Total number of slices. |
| 554 | 554 |
# -... Pass to `grid::viewport` which contains all the annotations. |
| 555 | 555 |
# -test Is it in test mode? The value can be logical or a text which is plotted as the title of plot. |
| 556 |
+# -anno_mark_param It contains specific parameters for drawing `anno_mark` and pass to the |
|
| 557 |
+# `draw,SingleAnnotation-method`. |
|
| 556 | 558 |
# |
| 557 | 559 |
# == value |
| 558 | 560 |
# No value is returned. |
| ... | ... |
@@ -563,7 +565,7 @@ setMethod(f = "get_legend_param_list", |
| 563 | 565 |
setMethod(f = "draw", |
| 564 | 566 |
signature = "HeatmapAnnotation", |
| 565 | 567 |
definition = function(object, index, k = 1, n = 1, ..., |
| 566 |
- test = FALSE) {
|
|
| 568 |
+ test = FALSE, anno_mark_param = list()) {
|
|
| 567 | 569 |
|
| 568 | 570 |
which = object@which |
| 569 | 571 |
n_anno = length(object@anno_list) |
| ... | ... |
@@ -609,21 +611,23 @@ setMethod(f = "draw", |
| 609 | 611 |
for(i in seq_len(n_anno)) {
|
| 610 | 612 |
pushViewport(viewport(y = sum(anno_size[seq(i, n_anno)]) + sum(gap[seq(i, n_anno)]) - gap[n_anno], |
| 611 | 613 |
height = anno_size[i], just = c("center", "top")))
|
| 612 |
- oe = try(draw(object@anno_list[[i]], index, k, n)) |
|
| 613 |
- if(inherits(oe, "try-error")) {
|
|
| 614 |
- cat("Error when drawing annotation '", object@anno_list[[i]]@name, "'\n", sep = "")
|
|
| 615 |
- stop_wrap(oe) |
|
| 616 |
- } |
|
| 614 |
+ draw(object@anno_list[[i]], index, k, n, anno_mark_param = anno_mark_param) |
|
| 615 |
+ # oe = try(draw(object@anno_list[[i]], index, k, n)) |
|
| 616 |
+ # if(inherits(oe, "try-error")) {
|
|
| 617 |
+ # cat("Error when drawing annotation '", object@anno_list[[i]]@name, "'\n", sep = "")
|
|
| 618 |
+ # stop_wrap(oe) |
|
| 619 |
+ # } |
|
| 617 | 620 |
upViewport() |
| 618 | 621 |
} |
| 619 | 622 |
} else if(which == "row") {
|
| 620 | 623 |
for(i in seq_len(n_anno)) {
|
| 621 | 624 |
pushViewport(viewport(x = sum(anno_size[seq_len(i)]) + sum(gap[seq_len(i)]) - gap[i], width = anno_size[i], just = c("right", "center")))
|
| 622 |
- oe = try(draw(object@anno_list[[i]], index, k, n)) |
|
| 623 |
- if(inherits(oe, "try-error")) {
|
|
| 624 |
- cat("Error when drawing annotation '", object@anno_list[[i]]@name, "'\n", sep = "")
|
|
| 625 |
- stop_wrap(oe) |
|
| 626 |
- } |
|
| 625 |
+ draw(object@anno_list[[i]], index, k, n, anno_mark_param = anno_mark_param) |
|
| 626 |
+ # oe = try(draw(object@anno_list[[i]], index, k, n)) |
|
| 627 |
+ # if(inherits(oe, "try-error")) {
|
|
| 628 |
+ # cat("Error when drawing annotation '", object@anno_list[[i]]@name, "'\n", sep = "")
|
|
| 629 |
+ # stop_wrap(oe) |
|
| 630 |
+ # } |
|
| 627 | 631 |
upViewport() |
| 628 | 632 |
} |
| 629 | 633 |
} |
| ... | ... |
@@ -913,6 +917,10 @@ names.HeatmapAnnotation = function(x) {
|
| 913 | 917 |
return(x) |
| 914 | 918 |
} |
| 915 | 919 |
|
| 920 |
+anno_type = function(ha) {
|
|
| 921 |
+ sapply(ha@anno_list, function(x) x@fun@fun_name) |
|
| 922 |
+} |
|
| 923 |
+ |
|
| 916 | 924 |
|
| 917 | 925 |
# == title |
| 918 | 926 |
# Subset the HeatmapAnnotation object |
Zuguang Gu authored on 24/11/2018 07:57:48 | ... | ... |
@@ -1075,8 +1075,23 @@ setMethod(f = "re_size", |
| 1075 | 1075 |
if(is.null(annotation_height)) {
|
| 1076 | 1076 |
is_annotation_size_set = FALSE |
| 1077 | 1077 |
} else {
|
| 1078 |
- is_annotation_size_set = TRUE |
|
| 1079 |
- annotation_size_adjusted = annotation_height |
|
| 1078 |
+ if(length(annotation_height) == 1) {
|
|
| 1079 |
+ if(length(object@anno_list) > 1) {
|
|
| 1080 |
+ warning_wrap("`annotation_height` is set with length of one while with multiplt annotations, `annotation_height` is treated as `height`.")
|
|
| 1081 |
+ } |
|
| 1082 |
+ height = annotation_height[1] |
|
| 1083 |
+ if(!inherits(height, "unit")) {
|
|
| 1084 |
+ stop_wrap("`height` should be a `unit` object")
|
|
| 1085 |
+ } |
|
| 1086 |
+ if(!is_abs_unit(height)) {
|
|
| 1087 |
+ stop_wrap("`height` should be an absolute unit.")
|
|
| 1088 |
+ } |
|
| 1089 |
+ is_size_set = TRUE |
|
| 1090 |
+ is_annotation_size_set = FALSE |
|
| 1091 |
+ } else {
|
|
| 1092 |
+ is_annotation_size_set = TRUE |
|
| 1093 |
+ annotation_size_adjusted = annotation_height |
|
| 1094 |
+ } |
|
| 1080 | 1095 |
} |
| 1081 | 1096 |
size_adjusted = height |
| 1082 | 1097 |
size_name = "height" |
| ... | ... |
@@ -1095,8 +1110,23 @@ setMethod(f = "re_size", |
| 1095 | 1110 |
if(is.null(annotation_width)) {
|
| 1096 | 1111 |
is_annotation_size_set = FALSE |
| 1097 | 1112 |
} else {
|
| 1098 |
- is_annotation_size_set = TRUE |
|
| 1099 |
- annotation_size_adjusted = annotation_width |
|
| 1113 |
+ if(length(annotation_width) == 1) {
|
|
| 1114 |
+ if(length(object@anno_list) > 1) {
|
|
| 1115 |
+ warning_wrap("`annotation_width` is set with length of one while with multiplt annotations, `annotation_width` is treated as `width`.")
|
|
| 1116 |
+ } |
|
| 1117 |
+ width = annotation_width[1] |
|
| 1118 |
+ if(!inherits(width, "unit")) {
|
|
| 1119 |
+ stop_wrap("`width` should be a `unit` object")
|
|
| 1120 |
+ } |
|
| 1121 |
+ if(!is_abs_unit(width)) {
|
|
| 1122 |
+ stop_wrap("`width` should be an absolute unit.")
|
|
| 1123 |
+ } |
|
| 1124 |
+ is_size_set = TRUE |
|
| 1125 |
+ is_annotation_size_set = FALSE |
|
| 1126 |
+ } else {
|
|
| 1127 |
+ is_annotation_size_set = TRUE |
|
| 1128 |
+ annotation_size_adjusted = annotation_width |
|
| 1129 |
+ } |
|
| 1100 | 1130 |
} |
| 1101 | 1131 |
size_adjusted = width |
| 1102 | 1132 |
size_name = "width" |
jokergoo authored on 02/11/2018 15:43:14
Zuguang Gu authored on 02/11/2018 07:57:06 | ... | ... |
@@ -243,7 +243,7 @@ HeatmapAnnotation = function(..., |
| 243 | 243 |
an = names(anno_value_list) |
| 244 | 244 |
show_annotation_name = recycle_param(show_annotation_name, an, TRUE) |
| 245 | 245 |
annotation_name_side = recycle_param(annotation_name_side, an, ifelse(which == "column", "right", "bottom")) |
| 246 |
- if(inherits(annotation_name_offset, "unit")) annotation_name_offset = unit_to_str(annotation_name_offset) |
|
| 246 |
+ if(inherits(annotation_name_offset, "unit")) annotation_name_offset = to_unit_str(annotation_name_offset) |
|
| 247 | 247 |
annotation_name_offset = recycle_param(annotation_name_offset, an, NULL, as.list = TRUE) |
| 248 | 248 |
annotation_name_rot = recycle_param(annotation_name_rot, an, NULL, as.list = TRUE) |
| 249 | 249 |
if(missing(border)) {
|
Zuguang Gu authored on 31/10/2018 15:23:59 | ... | ... |
@@ -101,9 +101,9 @@ HeatmapAnnotation = function(..., |
| 101 | 101 |
|
| 102 | 102 |
show_annotation_name = TRUE, |
| 103 | 103 |
annotation_name_gp = gpar(), |
| 104 |
- annotation_name_offset = unit(1, "mm"), |
|
| 104 |
+ annotation_name_offset = NULL, |
|
| 105 | 105 |
annotation_name_side = ifelse(which == "column", "right", "bottom"), |
| 106 |
- annotation_name_rot = ifelse(which == "column", 0, 90), |
|
| 106 |
+ annotation_name_rot = NULL, |
|
| 107 | 107 |
|
| 108 | 108 |
annotation_height = NULL, |
| 109 | 109 |
annotation_width = NULL, |
| ... | ... |
@@ -242,9 +242,10 @@ HeatmapAnnotation = function(..., |
| 242 | 242 |
|
| 243 | 243 |
an = names(anno_value_list) |
| 244 | 244 |
show_annotation_name = recycle_param(show_annotation_name, an, TRUE) |
| 245 |
- annotation_name_offset = recycle_param(annotation_name_offset, an, TRUE) |
|
| 246 |
- annotation_name_side = recycle_param(annotation_name_side, an, TRUE) |
|
| 247 |
- annotation_name_rot = recycle_param(annotation_name_rot, an, TRUE) |
|
| 245 |
+ annotation_name_side = recycle_param(annotation_name_side, an, ifelse(which == "column", "right", "bottom")) |
|
| 246 |
+ if(inherits(annotation_name_offset, "unit")) annotation_name_offset = unit_to_str(annotation_name_offset) |
|
| 247 |
+ annotation_name_offset = recycle_param(annotation_name_offset, an, NULL, as.list = TRUE) |
|
| 248 |
+ annotation_name_rot = recycle_param(annotation_name_rot, an, NULL, as.list = TRUE) |
|
| 248 | 249 |
if(missing(border)) {
|
| 249 | 250 |
if(!is.null(ht_opt$annotation_border)) border = ht_opt$annotation_border |
| 250 | 251 |
} |
| ... | ... |
@@ -296,16 +297,11 @@ HeatmapAnnotation = function(..., |
| 296 | 297 |
arg_list = list(name = ag, which = which, |
| 297 | 298 |
show_name = show_annotation_name[i_anno], |
| 298 | 299 |
name_gp = subset_gp(annotation_name_gp, i_anno), |
| 299 |
- name_offset = annotation_name_offset[i_anno], |
|
| 300 |
+ name_offset = annotation_name_offset[[i_anno]], |
|
| 300 | 301 |
name_side = annotation_name_side[i_anno], |
| 301 |
- name_rot = annotation_name_rot[i_anno], |
|
| 302 |
+ name_rot = annotation_name_rot[[i_anno]], |
|
| 302 | 303 |
border = border[i_anno]) |
| 303 |
- # if(!is_name_offset_called) {
|
|
| 304 |
- # arg_list$name_rot = NULL |
|
| 305 |
- # } |
|
| 306 |
- # if(!is_name_rot_called) {
|
|
| 307 |
- # arg_list$name_offset = NULL |
|
| 308 |
- # } |
|
| 304 |
+ |
|
| 309 | 305 |
if(inherits(anno_value_list[[ag]], c("function", "AnnotationFunction"))) {
|
| 310 | 306 |
arg_list$fun = anno_value_list[[ag]] |
| 311 | 307 |
if(inherits(anno_value_list[[ag]], "function")) {
|
jokergoo authored on 29/10/2018 15:16:09
Zuguang Gu authored on 28/10/2018 18:31:16 | ... | ... |
@@ -818,7 +818,17 @@ setMethod(f = "add_heatmap", |
| 818 | 818 |
# ha |
| 819 | 819 |
c.HeatmapAnnotation = function(..., gap = unit(0, "mm")) {
|
| 820 | 820 |
anno_list = list(...) |
| 821 |
+ if(length(anno_list) == 1) {
|
|
| 822 |
+ return(anno_list[[1]]) |
|
| 823 |
+ } |
|
| 824 |
+ # remove NULL |
|
| 825 |
+ anno_list = anno_list[ !sapply(anno_list, is.null) ] |
|
| 826 |
+ if(length(anno_list) == 1) {
|
|
| 827 |
+ return(anno_list[[1]]) |
|
| 828 |
+ } |
|
| 829 |
+ |
|
| 821 | 830 |
n = length(anno_list) |
| 831 |
+ |
|
| 822 | 832 |
if(length(unique(sapply(anno_list, function(x) x@which))) != 1) {
|
| 823 | 833 |
stop_wrap("All annotations should be all row annotation or all column annotation.")
|
| 824 | 834 |
} |
Zuguang Gu authored on 27/10/2018 20:25:57 | ... | ... |
@@ -300,12 +300,12 @@ HeatmapAnnotation = function(..., |
| 300 | 300 |
name_side = annotation_name_side[i_anno], |
| 301 | 301 |
name_rot = annotation_name_rot[i_anno], |
| 302 | 302 |
border = border[i_anno]) |
| 303 |
- if(!is_name_offset_called) {
|
|
| 304 |
- arg_list$name_rot = NULL |
|
| 305 |
- } |
|
| 306 |
- if(!is_name_rot_called) {
|
|
| 307 |
- arg_list$name_offset = NULL |
|
| 308 |
- } |
|
| 303 |
+ # if(!is_name_offset_called) {
|
|
| 304 |
+ # arg_list$name_rot = NULL |
|
| 305 |
+ # } |
|
| 306 |
+ # if(!is_name_rot_called) {
|
|
| 307 |
+ # arg_list$name_offset = NULL |
|
| 308 |
+ # } |
|
| 309 | 309 |
if(inherits(anno_value_list[[ag]], c("function", "AnnotationFunction"))) {
|
| 310 | 310 |
arg_list$fun = anno_value_list[[ag]] |
| 311 | 311 |
if(inherits(anno_value_list[[ag]], "function")) {
|
Zuguang Gu authored on 25/10/2018 19:37:48 | ... | ... |
@@ -348,8 +348,22 @@ HeatmapAnnotation = function(..., |
| 348 | 348 |
} |
| 349 | 349 |
} |
| 350 | 350 |
|
| 351 |
+ |
|
| 351 | 352 |
n_total_anno = length(anno_list) |
| 352 | 353 |
|
| 354 |
+ ## check whether anno_list contains zoomed anno_empty |
|
| 355 |
+ if(n_total_anno > 1) {
|
|
| 356 |
+ for(i in seq_len(n_total_anno)) {
|
|
| 357 |
+ anno = anno_list[[i]]@fun |
|
| 358 |
+ if(identical(anno@fun_name, "anno_empty")) {
|
|
| 359 |
+ if(anno@var_env$zoom) {
|
|
| 360 |
+ stop_wrap("You set `zoom = TRUE` in `anno_empty()` for the empty annotation. The HeatmapAnnotation object only allows to contain one single annotation if it is a zoomed empty annotation.")
|
|
| 361 |
+ } |
|
| 362 |
+ } |
|
| 363 |
+ } |
|
| 364 |
+ } |
|
| 365 |
+ |
|
| 366 |
+ |
|
| 353 | 367 |
if(is.null(gap)) gap = unit(0, "mm") |
| 354 | 368 |
|
| 355 | 369 |
# the nth gap does not really matter |
| ... | ... |
@@ -559,6 +573,7 @@ setMethod(f = "draw", |
| 559 | 573 |
n_anno = length(object@anno_list) |
| 560 | 574 |
anno_size = object@anno_size |
| 561 | 575 |
gap = object@gap |
| 576 |
+ vp_param = list(...) |
|
| 562 | 577 |
|
| 563 | 578 |
if(is.character(test)) {
|
| 564 | 579 |
test2 = TRUE |
| ... | ... |
@@ -572,7 +587,7 @@ setMethod(f = "draw", |
| 572 | 587 |
if(which == "column") pushViewport(viewport(width = unit(1, "npc") - unit(3, "cm"), height = object@height)) |
| 573 | 588 |
if(which == "row") pushViewport(viewport(height = unit(1, "npc") - unit(3, "cm"), width = object@width)) |
| 574 | 589 |
} else {
|
| 575 |
- pushViewport(viewport(...)) |
|
| 590 |
+ pushViewport(do.call(viewport, vp_param)) |
|
| 576 | 591 |
} |
| 577 | 592 |