Zuguang Gu authored on 02/08/2018 12:43:21
| ... | ... |
@@ -52,3 +52,7 @@ setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
|
| 52 | 52 |
setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
|
| 53 | 53 |
|
| 54 | 54 |
setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
|
| 55 |
+ |
|
| 56 |
+setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
|
|
| 57 |
+setGeneric('resize', function(object, ...) standardGeneric('resize'))
|
|
| 58 |
+ |
| 55 | 59 |
similarity index 57% |
| 56 | 60 |
rename from R/annotation_fun.R |
| 57 | 61 |
rename to R/AnnotationFunction-class.R |
| ... | ... |
@@ -8,25 +8,137 @@ AnnotationFunction = setClass("AnnotationFunction",
|
| 8 | 8 |
var_env = "environment", |
| 9 | 9 |
fun = "function", |
| 10 | 10 |
subset_rule = "list", |
| 11 |
- data_scale = "list" |
|
| 11 |
+ subsetable = "logical", |
|
| 12 |
+ data_scale = "numeric", |
|
| 13 |
+ extended = "ANY" |
|
| 12 | 14 |
), |
| 13 | 15 |
prototype = list( |
| 16 |
+ fun_name = "", |
|
| 14 | 17 |
width = unit(1, "npc"), |
| 15 | 18 |
height = unit(1, "npc"), |
| 16 | 19 |
subset_rule = list(), |
| 17 |
- data_scale = list(x = NULL, y = NULL), |
|
| 18 |
- n = 0 |
|
| 20 |
+ subsetable = FALSE, |
|
| 21 |
+ data_scale = c(0, 1), |
|
| 22 |
+ n = 0, |
|
| 23 |
+ extended = unit(c(0, 0, 0, 0), "mm") |
|
| 19 | 24 |
) |
| 20 | 25 |
) |
| 21 | 26 |
|
| 27 |
+anno_width_and_height = function(which, width = NULL, height = NULL, |
|
| 28 |
+ default = unit(1, "cm")) {
|
|
| 29 |
+ |
|
| 30 |
+ if(which == "column") {
|
|
| 31 |
+ if(is.null(height)) {
|
|
| 32 |
+ height = default |
|
| 33 |
+ } else {
|
|
| 34 |
+ if(!is_abs_unit(height)) {
|
|
| 35 |
+ stop("height can only be an absolute unit.")
|
|
| 36 |
+ } |
|
| 37 |
+ } |
|
| 38 |
+ if(is.null(width)) {
|
|
| 39 |
+ width = unit(1, "npc") |
|
| 40 |
+ } |
|
| 41 |
+ } |
|
| 42 |
+ if(which == "row") {
|
|
| 43 |
+ if(is.null(width)) {
|
|
| 44 |
+ width = default |
|
| 45 |
+ } else {
|
|
| 46 |
+ if(!is_abs_unit(width)) {
|
|
| 47 |
+ stop("width can only be an absolute unit.")
|
|
| 48 |
+ } |
|
| 49 |
+ } |
|
| 50 |
+ if(is.null(height)) {
|
|
| 51 |
+ height = unit(1, "npc") |
|
| 52 |
+ } |
|
| 53 |
+ } |
|
| 54 |
+ return(list(height = height, width = width)) |
|
| 55 |
+} |
|
| 56 |
+ |
|
| 57 |
+ |
|
| 58 |
+AnnotationFunction = function(fun, fun_name = "", which = c("column", "row"),
|
|
| 59 |
+ var_imported = list(), n = 0, data_scale = c(0, 1), subset_rule = list(), |
|
| 60 |
+ subsetable = FALSE, width = NULL, height = NULL) {
|
|
| 61 |
+ |
|
| 62 |
+ which = match.arg(which)[1] |
|
| 63 |
+ |
|
| 64 |
+ anno = new("AnnotationFunction")
|
|
| 65 |
+ |
|
| 66 |
+ anno@which = which |
|
| 67 |
+ anno@fun_name = fun_name |
|
| 68 |
+ |
|
| 69 |
+ anno_size = anno_width_and_height(which, width, height, unit(1, "cm")) |
|
| 70 |
+ anno@width = anno_size$width |
|
| 71 |
+ anno@height = anno_size$height |
|
| 72 |
+ |
|
| 73 |
+ anno@n = n |
|
| 74 |
+ anno@data_scale = data_scale |
|
| 75 |
+ |
|
| 76 |
+ anno@var_env = new.env() |
|
| 77 |
+ if(is.character(var_imported)) {
|
|
| 78 |
+ for(nm in var_imported) {
|
|
| 79 |
+ anno@var_env[[nm]] = get(nm, envir = parent.frame()) |
|
| 80 |
+ } |
|
| 81 |
+ } else if(inherits(var_imported, "list")) {
|
|
| 82 |
+ if(is.null(names(var_imported))) {
|
|
| 83 |
+ var_imported_nm = sapply(as.list(substitute(var_imported))[-1], as.character) |
|
| 84 |
+ names(var_imported) = var_imported_nm |
|
| 85 |
+ } |
|
| 86 |
+ |
|
| 87 |
+ for(nm in names(var_imported)) {
|
|
| 88 |
+ anno@var_env[[nm]] = var_imported[[nm]] |
|
| 89 |
+ } |
|
| 90 |
+ } else {
|
|
| 91 |
+ stop_wrap("`var_import` needs to be a character vector which contains variable names or a list of variables")
|
|
| 92 |
+ } |
|
| 93 |
+ |
|
| 94 |
+ environment(fun) = anno@var_env |
|
| 95 |
+ anno@fun = fun |
|
| 96 |
+ |
|
| 97 |
+ if(is.null(subset_rule)) {
|
|
| 98 |
+ for(nm in names(anno@var_env)) {
|
|
| 99 |
+ if(is.matrix(anno@var_env[[nm]])) {
|
|
| 100 |
+ anno@subset_rule[[nm]] = subset_matrix_by_row |
|
| 101 |
+ } else if(inherits(anno@var_env[[nm]], "gpar")) {
|
|
| 102 |
+ anno@subset_rule[[nm]] = subset_gp |
|
| 103 |
+ } else if(is.vector(anno@var_env[[nm]])) {
|
|
| 104 |
+ if(length(anno@var_env[[nm]]) > 1) {
|
|
| 105 |
+ anno@subset_rule[[nm]] = subset_vector |
|
| 106 |
+ } |
|
| 107 |
+ } |
|
| 108 |
+ } |
|
| 109 |
+ } else {
|
|
| 110 |
+ for(nm in names(subset_rule)) {
|
|
| 111 |
+ anno@subset_rule[[nm]] = subset_rule[[nm]] |
|
| 112 |
+ } |
|
| 113 |
+ } |
|
| 114 |
+ |
|
| 115 |
+ if(missing(subsetable)) {
|
|
| 116 |
+ # is user defined subset rule |
|
| 117 |
+ if(length(anno@subset_rule)) {
|
|
| 118 |
+ anno@subsetable = TRUE |
|
| 119 |
+ } |
|
| 120 |
+ } else {
|
|
| 121 |
+ anno@subsetable = subsetable |
|
| 122 |
+ } |
|
| 123 |
+ |
|
| 124 |
+ return(anno) |
|
| 125 |
+} |
|
| 126 |
+ |
|
| 22 | 127 |
|
| 23 | 128 |
"[.AnnotationFunction" = function(x, i) {
|
| 24 | 129 |
if(nargs() == 1) {
|
| 25 | 130 |
return(x) |
| 26 | 131 |
} else {
|
| 132 |
+ if(!x@subsetable) {
|
|
| 133 |
+ stop("This object is not subsetable.")
|
|
| 134 |
+ } |
|
| 27 | 135 |
x = copy_all(x) |
| 28 | 136 |
for(var in names(x@subset_rule)) {
|
| 29 |
- x@var_env[[var]] = x@subset_rule[[var]](x@var_env[[var]], i) |
|
| 137 |
+ oe = try(x@var_env[[var]] <- x@subset_rule[[var]](x@var_env[[var]], i), silent = TRUE) |
|
| 138 |
+ if(inherits(oe, "try-error")) {
|
|
| 139 |
+ message(paste0("An error when subsetting ", var))
|
|
| 140 |
+ stop(oe) |
|
| 141 |
+ } |
|
| 30 | 142 |
} |
| 31 | 143 |
if(is.logical(i)) {
|
| 32 | 144 |
x@n = sum(i) |
| ... | ... |
@@ -48,7 +160,7 @@ setMethod(f = "draw", |
| 48 | 160 |
} |
| 49 | 161 |
if(test2) {
|
| 50 | 162 |
grid.newpage() |
| 51 |
- pushViewport(viewport(width = 0.9, height = 0.9)) |
|
| 163 |
+ pushViewport(viewport(width = 0.8, height = 0.8)) |
|
| 52 | 164 |
} |
| 53 | 165 |
|
| 54 | 166 |
if(missing(index)) index = seq_len(object@n) |
| ... | ... |
@@ -61,7 +173,21 @@ setMethod(f = "draw", |
| 61 | 173 |
object@fun(index) |
| 62 | 174 |
if(test2) {
|
| 63 | 175 |
grid.text(test, y = unit(1, "npc") + unit(2, "mm"), just = "bottom") |
| 64 |
- grid.rect(gp = gpar(fill = "transparent", col = "red")) |
|
| 176 |
+ |
|
| 177 |
+ if(!identical(unit(0, "mm"), object@extended[1])) {
|
|
| 178 |
+ grid.rect(y = 1, height = unit(1, "npc") + object@extended[1], just = "top", |
|
| 179 |
+ gp = gpar(fill = "transparent", col = "red", lty = 2)) |
|
| 180 |
+ } else if(!identical(unit(0, "mm"), object@extended[[2]])) {
|
|
| 181 |
+ grid.rect(x = 1, width = unit(1, "npc") + object@extended[2], just = "right", |
|
| 182 |
+ gp = gpar(fill = "transparent", col = "red", lty = 2)) |
|
| 183 |
+ } else if(!identical(unit(0, "mm"), object@extended[[3]])) {
|
|
| 184 |
+ grid.rect(y = 0, height = unit(1, "npc") + object@extended[3], just = "bottom", |
|
| 185 |
+ gp = gpar(fill = "transparent", col = "red", lty = 2)) |
|
| 186 |
+ } else if(!identical(unit(0, "mm"), object@extended[[4]])) {
|
|
| 187 |
+ grid.rect(x = 0, width = unit(1, "npc") + object@extended[4], just = "left", |
|
| 188 |
+ gp = gpar(fill = "transparent", col = "red", lty = 2)) |
|
| 189 |
+ } |
|
| 190 |
+ |
|
| 65 | 191 |
} |
| 66 | 192 |
popViewport() |
| 67 | 193 |
|
| ... | ... |
@@ -71,7 +197,6 @@ setMethod(f = "draw", |
| 71 | 197 |
|
| 72 | 198 |
}) |
| 73 | 199 |
|
| 74 |
-setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
|
|
| 75 | 200 |
setMethod(f = "copy_all", |
| 76 | 201 |
signature = "AnnotationFunction", |
| 77 | 202 |
definition = function(object, i) {
|
| ... | ... |
@@ -88,54 +213,58 @@ setMethod(f = "show", |
| 88 | 213 |
signature = "AnnotationFunction", |
| 89 | 214 |
definition = function(object) {
|
| 90 | 215 |
|
| 91 |
- cat("An AnnotationFunction object generated by ", object@fun_name, "()\n", sep = "")
|
|
| 216 |
+ cat("An AnnotationFunction object\n")
|
|
| 217 |
+ if(object@fun_name == "") {
|
|
| 218 |
+ cat(" function: user-defined\n")
|
|
| 219 |
+ } else {
|
|
| 220 |
+ cat(" function: ", object@fun_name, "()\n", sep = "")
|
|
| 221 |
+ } |
|
| 92 | 222 |
cat(" position:", object@which, "\n")
|
| 93 | 223 |
cat(" items:", ifelse(object@n == 0, "unknown", object@n), "\n")
|
| 224 |
+ cat(" width:", as.character(object@width), "\n")
|
|
| 225 |
+ cat(" height:", as.character(object@height), "\n")
|
|
| 226 |
+ var_imported = names(anno@var_env) |
|
| 227 |
+ if(length(var_imported)) {
|
|
| 228 |
+ cat(" imported variable:", paste(var_imported, collapse = ", "), "\n")
|
|
| 229 |
+ var_subsetable = names(anno@subset_rule) |
|
| 230 |
+ if(length(var_subsetable)) {
|
|
| 231 |
+ cat(" subsetable variable:", paste(var_subsetable, collapse = ", "), "\n")
|
|
| 232 |
+ } |
|
| 233 |
+ } |
|
| 234 |
+ cat(" this object is", ifelse(object@subsetable, "\b", "not"), "subsetable\n")
|
|
| 235 |
+ dirt = c("bottom", "left", "top", "right")
|
|
| 236 |
+ for(i in 1:4) {
|
|
| 237 |
+ if(!identical(unit(0, "mm"), object@extended[i])) {
|
|
| 238 |
+ cat(" ", as.character(object@extended[i]), "extension on the", dirt[i], "\n")
|
|
| 239 |
+ } |
|
| 240 |
+ } |
|
| 241 |
+ |
|
| 94 | 242 |
}) |
| 95 | 243 |
|
| 96 | 244 |
anno_empty = function(which = c("column", "row"), border = TRUE, width = NULL, height = NULL) {
|
| 97 | 245 |
|
| 98 |
- if(exists(".__under_SingleAnnotation__", envir = parent.frame())) {
|
|
| 99 |
- which = get("which", envir = parent.frame())
|
|
| 100 |
- } else {
|
|
| 246 |
+ if(is.null(.ENV$current_annotation_which)) {
|
|
| 101 | 247 |
which = match.arg(which)[1] |
| 248 |
+ } else {
|
|
| 249 |
+ which = .ENV$current_annotation_which |
|
| 102 | 250 |
} |
| 103 | 251 |
|
| 104 |
- if(which == "column") {
|
|
| 105 |
- if(missing(height)) {
|
|
| 106 |
- height = unit(1, "cm") |
|
| 107 |
- } |
|
| 108 |
- if(missing(width)) {
|
|
| 109 |
- width = unit(1, "npc") |
|
| 110 |
- } |
|
| 111 |
- } |
|
| 112 |
- if(which == "row") {
|
|
| 113 |
- if(missing(width)) {
|
|
| 114 |
- width = unit(1, "cm") |
|
| 115 |
- } |
|
| 116 |
- if(missing(height)) {
|
|
| 117 |
- height = unit(1, "npc") |
|
| 118 |
- } |
|
| 119 |
- } |
|
| 120 |
- |
|
| 121 |
- anno = AnnotationFunction() |
|
| 122 |
- anno@which = which |
|
| 123 |
- anno@fun_name = "anno_empty" |
|
| 124 |
- anno@width = width |
|
| 125 |
- anno@height = height |
|
| 126 |
- |
|
| 127 |
- anno@var_env = new.env() |
|
| 128 |
- anno@var_env$border = border |
|
| 129 |
- |
|
| 252 |
+ anno_size = anno_width_and_height(which, width, height, unit(1, "cm")) |
|
| 253 |
+ |
|
| 130 | 254 |
fun = function(index) {
|
| 131 | 255 |
if(border) grid.rect() |
| 132 | 256 |
} |
| 133 | 257 |
|
| 134 |
- environment(fun) = anno@var_env |
|
| 135 |
- anno@fun = fun |
|
| 136 |
- |
|
| 137 |
- anno@subset_rule = list() |
|
| 138 |
- |
|
| 258 |
+ anno = AnnotationFunction( |
|
| 259 |
+ fun = fun, |
|
| 260 |
+ fun_name = "anno_empty", |
|
| 261 |
+ which = which, |
|
| 262 |
+ var_import = list(border), |
|
| 263 |
+ subset_rule = list(), |
|
| 264 |
+ subsetable = TRUE, |
|
| 265 |
+ height = anno_size$height, |
|
| 266 |
+ width = anno_size$width |
|
| 267 |
+ ) |
|
| 139 | 268 |
return(anno) |
| 140 | 269 |
} |
| 141 | 270 |
|
| ... | ... |
@@ -147,10 +276,10 @@ anno_simple = function(x, col, na_col = "grey", |
| 147 | 276 |
pch = NULL, pt_size = unit(1, "snpc")*0.8, pt_gp = gpar(), |
| 148 | 277 |
width = NULL, height = NULL) {
|
| 149 | 278 |
|
| 150 |
- if(exists(".__under_SingleAnnotation__", envir = parent.frame())) {
|
|
| 151 |
- which = get("which", envir = parent.frame())
|
|
| 152 |
- } else {
|
|
| 279 |
+ if(is.null(.ENV$current_annotation_which)) {
|
|
| 153 | 280 |
which = match.arg(which)[1] |
| 281 |
+ } else {
|
|
| 282 |
+ which = .ENV$current_annotation_which |
|
| 154 | 283 |
} |
| 155 | 284 |
|
| 156 | 285 |
if(is.data.frame(x)) x = as.matrix(x) |
| ... | ... |
@@ -161,23 +290,9 @@ anno_simple = function(x, col, na_col = "grey", |
| 161 | 290 |
} |
| 162 | 291 |
input_is_matrix = is.matrix(x) |
| 163 | 292 |
|
| 164 |
- if(which == "column") {
|
|
| 165 |
- if(missing(height)) {
|
|
| 166 |
- height = unit(5, "mm")*ifelse(input_is_matrix, ncol(x), 1) |
|
| 167 |
- } |
|
| 168 |
- if(missing(width)) {
|
|
| 169 |
- width = unit(1, "npc") |
|
| 170 |
- } |
|
| 171 |
- } |
|
| 172 |
- if(which == "row") {
|
|
| 173 |
- if(missing(width)) {
|
|
| 174 |
- width = unit(5, "mm")*ifelse(input_is_matrix, ncol(x), 1) |
|
| 175 |
- } |
|
| 176 |
- if(missing(height)) {
|
|
| 177 |
- height = unit(1, "npc") |
|
| 178 |
- } |
|
| 179 |
- } |
|
| 180 |
- |
|
| 293 |
+ anno_size = anno_width_and_height(which, width, height, |
|
| 294 |
+ unit(5, "mm")*ifelse(input_is_matrix, ncol(x), 1)) |
|
| 295 |
+ |
|
| 181 | 296 |
if(missing(col)) {
|
| 182 | 297 |
col = default_col(x) |
| 183 | 298 |
} |
| ... | ... |
@@ -188,7 +303,7 @@ anno_simple = function(x, col, na_col = "grey", |
| 188 | 303 |
} else if(inherits(col, "ColorMapping")) {
|
| 189 | 304 |
color_mapping = col |
| 190 | 305 |
} else {
|
| 191 |
- stop("`col` should be a named vector/a color mapping function/a ColorMapping object.")
|
|
| 306 |
+ stop_wrap("`col` should be a named vector/a color mapping function/a ColorMapping object.")
|
|
| 192 | 307 |
} |
| 193 | 308 |
|
| 194 | 309 |
value = x |
| ... | ... |
@@ -224,10 +339,12 @@ anno_simple = function(x, col, na_col = "grey", |
| 224 | 339 |
nc = ncol(value) |
| 225 | 340 |
for(i in seq_len(nc)) {
|
| 226 | 341 |
fill = map_to_colors(color_mapping, value[index, i]) |
| 227 |
- grid.rect(x = (i-0.5)/nc, y, height = 1/n, width = 1/nc, gp = do.call("gpar", c(list(fill = fill), gp)))
|
|
| 342 |
+ grid.rect(x = (i-0.5)/nc, y, height = 1/n, width = 1/nc, |
|
| 343 |
+ gp = do.call("gpar", c(list(fill = fill), gp)))
|
|
| 228 | 344 |
if(!is.null(pch)) {
|
| 229 | 345 |
l = !is.na(pch[, i]) |
| 230 |
- grid.points(x = rep((i-0.5)/nc, sum(l)), y = y[l], pch = pch[l, i], size = pt_size, gp = pt_gp) |
|
| 346 |
+ grid.points(x = rep((i-0.5)/nc, sum(l)), y = y[l], pch = pch[l, i], |
|
| 347 |
+ size = pt_size, gp = pt_gp) |
|
| 231 | 348 |
} |
| 232 | 349 |
} |
| 233 | 350 |
} else {
|
| ... | ... |
@@ -235,11 +352,13 @@ anno_simple = function(x, col, na_col = "grey", |
| 235 | 352 |
grid.rect(x = 0.5, y, height = 1/n, width = 1, gp = do.call("gpar", c(list(fill = fill), gp)))
|
| 236 | 353 |
if(!is.null(pch)) {
|
| 237 | 354 |
l = !is.na(pch) |
| 238 |
- grid.points(x = rep(0.5, sum(l)), y = y[l], pch = pch[l], size = pt_size[l], gp = subset_gp(pt_gp, which(l))) |
|
| 355 |
+ grid.points(x = rep(0.5, sum(l)), y = y[l], pch = pch[l], size = pt_size[l], |
|
| 356 |
+ gp = subset_gp(pt_gp, which(l))) |
|
| 239 | 357 |
} |
| 240 | 358 |
} |
| 241 | 359 |
if(border) grid.rect(gp = gpar(fill = "transparent")) |
| 242 | 360 |
} |
| 361 |
+ |
|
| 243 | 362 |
column_fun = function(index) {
|
| 244 | 363 |
n = length(index) |
| 245 | 364 |
x = (seq_len(n) - 0.5) / n |
| ... | ... |
@@ -270,43 +389,39 @@ anno_simple = function(x, col, na_col = "grey", |
| 270 | 389 |
fun = column_fun |
| 271 | 390 |
} |
| 272 | 391 |
|
| 273 |
- anno = AnnotationFunction() |
|
| 274 |
- anno@which = which |
|
| 275 |
- anno@fun_name = "anno_simple" |
|
| 276 |
- anno@width = width |
|
| 277 |
- anno@height = height |
|
| 278 |
- anno@n = n |
|
| 279 |
- if(which == "column") {
|
|
| 280 |
- anno@data_scale = list(x = c(0.5, n + 0.5), y = c(0.5, nc + 0.5)) |
|
| 281 |
- } else {
|
|
| 282 |
- anno@data_scale = list(x = c(0.5, nc + 0.5), y = c(0.5, n + 0.5)) |
|
| 283 |
- } |
|
| 284 |
- |
|
| 285 |
- anno@var_env = new.env() |
|
| 286 |
- anno@var_env$value = value |
|
| 287 |
- anno@var_env$gp = gp |
|
| 288 |
- anno@var_env$border = border |
|
| 289 |
- anno@var_env$color_mapping = color_mapping |
|
| 290 |
- anno@var_env$pt_size = pt_size |
|
| 291 |
- anno@var_env$pch = pch |
|
| 392 |
+ anno = AnnotationFunction( |
|
| 393 |
+ fun = fun, |
|
| 394 |
+ fun_name = "anno_simple", |
|
| 395 |
+ which = which, |
|
| 396 |
+ width = anno_size$width, |
|
| 397 |
+ height = anno_size$height, |
|
| 398 |
+ n = n, |
|
| 399 |
+ data_scale = c(0.5, nc + 0.5), |
|
| 400 |
+ var_import = list(value, gp, border, color_mapping, pt_gp, pt_size, pch) |
|
| 401 |
+ ) |
|
| 292 | 402 |
|
| 293 |
- environment(fun) = anno@var_env |
|
| 294 |
- anno@fun = fun |
|
| 295 |
- |
|
| 296 | 403 |
anno@subset_rule = list() |
| 297 | 404 |
if(input_is_matrix) {
|
| 298 | 405 |
anno@subset_rule$value = subset_matrix_by_row |
| 299 |
- anno@subset_rule$pch = subset_matrix_by_row |
|
| 406 |
+ if(!is.null(pch)) {
|
|
| 407 |
+ anno@subset_rule$pch = subset_matrix_by_row |
|
| 408 |
+ } |
|
| 300 | 409 |
} else {
|
| 301 | 410 |
anno@subset_rule$value = subset_vector |
| 302 |
- anno@subset_rule$pch = subset_vector |
|
| 411 |
+ if(!is.null(pch)) {
|
|
| 412 |
+ anno@subset_rule$pch = subset_vector |
|
| 413 |
+ anno@subset_rule$pt_size = subset_vector |
|
| 414 |
+ anno@subset_rule$pt_gp = subset_gp |
|
| 415 |
+ } |
|
| 303 | 416 |
} |
| 304 | 417 |
|
| 418 |
+ anno@subsetable = TRUE |
|
| 419 |
+ |
|
| 305 | 420 |
return(anno) |
| 306 | 421 |
} |
| 307 | 422 |
|
| 308 |
-anno_image = function(image, which = c("column", "row"), border = TRUE, gp = gpar(fill = NA, col = NA),
|
|
| 309 |
- space = unit(1, "mm"), width = NULL, height = NULL) {
|
|
| 423 |
+anno_image = function(image, which = c("column", "row"), border = TRUE,
|
|
| 424 |
+ gp = gpar(fill = NA, col = NA), space = unit(1, "mm"), width = NULL, height = NULL) {
|
|
| 310 | 425 |
|
| 311 | 426 |
allowed_image_type = c("png", "svg", "pdf", "eps", "jpeg", "jpg", "tiff")
|
| 312 | 427 |
|
| ... | ... |
@@ -372,30 +487,15 @@ anno_image = function(image, which = c("column", "row"), border = TRUE, gp = gpa
|
| 372 | 487 |
} |
| 373 | 488 |
}) |
| 374 | 489 |
|
| 375 |
- if(exists(".__under_SingleAnnotation__", envir = parent.frame())) {
|
|
| 376 |
- which = get("which", envir = parent.frame())
|
|
| 377 |
- } else {
|
|
| 490 |
+ if(is.null(.ENV$current_annotation_which)) {
|
|
| 378 | 491 |
which = match.arg(which)[1] |
| 492 |
+ } else {
|
|
| 493 |
+ which = .ENV$current_annotation_which |
|
| 379 | 494 |
} |
| 380 | 495 |
|
| 381 | 496 |
space = space[1] |
| 382 | 497 |
|
| 383 |
- if(which == "column") {
|
|
| 384 |
- if(missing(height)) {
|
|
| 385 |
- height = unit(1, "cm") |
|
| 386 |
- } |
|
| 387 |
- if(missing(width)) {
|
|
| 388 |
- width = unit(1, "npc") |
|
| 389 |
- } |
|
| 390 |
- } |
|
| 391 |
- if(which == "row") {
|
|
| 392 |
- if(missing(width)) {
|
|
| 393 |
- width = unit(1, "cm") |
|
| 394 |
- } |
|
| 395 |
- if(missing(height)) {
|
|
| 396 |
- height = unit(1, "npc") |
|
| 397 |
- } |
|
| 398 |
- } |
|
| 498 |
+ anno_size = anno_width_and_height(which, width, height, unit(1, "cm")) |
|
| 399 | 499 |
|
| 400 | 500 |
gp = recycle_gp(gp, n_image) |
| 401 | 501 |
|
| ... | ... |
@@ -416,14 +516,17 @@ anno_image = function(image, which = c("column", "row"), border = TRUE, gp = gpa
|
| 416 | 516 |
if(image_class[ index[i] ] == "raster") {
|
| 417 | 517 |
grid.raster(image_list[[i]], x = (i-0.5)/n, width = width, height = height) |
| 418 | 518 |
} else if(image_class[ index[i] ] == "grImport::Picture") {
|
| 419 |
- getFromNamespace("grid.picture", ns = "grImport")(image_list[[i]], x = (i-0.5)/n, width = width, height = height)
|
|
| 519 |
+ grid.picture = getFromNamespace("grid.picture", ns = "grImport")
|
|
| 520 |
+ grid.picture(image_list[[i]], x = (i-0.5)/n, width = width, height = height) |
|
| 420 | 521 |
} else if(image_class[ index[i] ] == "grImport2::Picture") {
|
| 421 |
- getFromNamespace("grid.picture", ns = "grImport2")(image_list[[i]], x = (i-0.5)/n, width = width, height = height)
|
|
| 522 |
+ grid.picture = getFromNamespace("grid.picture", ns = "grImport2")
|
|
| 523 |
+ grid.picture(image_list[[i]], x = (i-0.5)/n, width = width, height = height) |
|
| 422 | 524 |
} |
| 423 | 525 |
} |
| 424 | 526 |
if(border) grid.rect(gp = gpar(fill = "transparent")) |
| 425 |
- upViewport() |
|
| 527 |
+ popViewport() |
|
| 426 | 528 |
} |
| 529 |
+ |
|
| 427 | 530 |
row_fun = function(index) {
|
| 428 | 531 |
n = length(index) |
| 429 | 532 |
|
| ... | ... |
@@ -441,13 +544,15 @@ anno_image = function(image, which = c("column", "row"), border = TRUE, gp = gpa
|
| 441 | 544 |
if(image_class[ index[i] ] == "raster") {
|
| 442 | 545 |
grid.raster(image_list[[i]], y = (n - i + 0.5)/n, width = width, height = height) |
| 443 | 546 |
} else if(image_class[ index[i] ] == "grImport::Picture") {
|
| 444 |
- getFromNamespace("grid.picture", ns = "grImport")(image_list[[i]], y = (n - i + 0.5)/n, width = width, height = height)
|
|
| 547 |
+ grid.picture = getFromNamespace("grid.picture", ns = "grImport")
|
|
| 548 |
+ grid.picture(image_list[[i]], y = (n - i + 0.5)/n, width = width, height = height) |
|
| 445 | 549 |
} else if(image_class[ index[i] ] == "grImport2::Picture") {
|
| 446 |
- getFromNamespace("grid.picture", ns = "grImport2")(image_list[[i]], y = (n - i + 0.5)/n, width = width, height = height)
|
|
| 550 |
+ grid.picture = getFromNamespace("grid.picture", ns = "grImport2")
|
|
| 551 |
+ grid.picture(image_list[[i]], y = (n - i + 0.5)/n, width = width, height = height) |
|
| 447 | 552 |
} |
| 448 | 553 |
} |
| 449 | 554 |
if(border) grid.rect(gp = gpar(fill = "transparent")) |
| 450 |
- upViewport() |
|
| 555 |
+ popViewport() |
|
| 451 | 556 |
} |
| 452 | 557 |
|
| 453 | 558 |
if(which == "row") {
|
| ... | ... |
@@ -456,38 +561,64 @@ anno_image = function(image, which = c("column", "row"), border = TRUE, gp = gpa
|
| 456 | 561 |
fun = column_fun |
| 457 | 562 |
} |
| 458 | 563 |
|
| 459 |
- n = n_image |
|
| 460 |
- anno = AnnotationFunction() |
|
| 461 |
- anno@which = which |
|
| 462 |
- anno@fun_name = "anno_image" |
|
| 463 |
- anno@width = width |
|
| 464 |
- anno@height = height |
|
| 465 |
- anno@n = n |
|
| 466 |
- if(which == "column") {
|
|
| 467 |
- anno@data_scale = list(x = c(0.5, n + 0.5), y = c(0.5, 1.5)) |
|
| 468 |
- } else {
|
|
| 469 |
- anno@data_scale = list(x = c(0.5, 1.5), y = c(0.5, n + 0.5)) |
|
| 470 |
- } |
|
| 471 |
- |
|
| 472 |
- anno@var_env = new.env() |
|
| 473 |
- anno@var_env$gp = gp |
|
| 474 |
- anno@var_env$border = border |
|
| 475 |
- anno@var_env$space = space |
|
| 476 |
- anno@var_env$yx_asp = yx_asp |
|
| 477 |
- anno@var_env$image_list = image_list |
|
| 478 |
- anno@var_env$image_class = image_class |
|
| 564 |
+ anno = AnnotationFunction( |
|
| 565 |
+ fun = fun, |
|
| 566 |
+ fun_name = "anno_image", |
|
| 567 |
+ which = which, |
|
| 568 |
+ width = anno_size$width, |
|
| 569 |
+ height = anno_size$height, |
|
| 570 |
+ n = n_image, |
|
| 571 |
+ data_scale = c(0.5, 1.5), |
|
| 572 |
+ var_import = list(gp, border, space, yx_asp, image_list, image_class) |
|
| 573 |
+ ) |
|
| 479 | 574 |
|
| 480 |
- environment(fun) = anno@var_env |
|
| 481 |
- anno@fun = fun |
|
| 482 |
- |
|
| 483 |
- anno@subset_rule = list() |
|
| 484 | 575 |
anno@subset_rule$gp = subset_vector |
| 485 | 576 |
anno@subset_rule$image_list = subset_vector |
| 486 | 577 |
anno@subset_rule$image_class = subset_vector |
| 487 | 578 |
|
| 579 |
+ anno@subsetable = TRUE |
|
| 580 |
+ |
|
| 488 | 581 |
return(anno) |
| 489 | 582 |
} |
| 490 | 583 |
|
| 584 |
+default_axis_param = function(which) {
|
|
| 585 |
+ list( |
|
| 586 |
+ at = NULL, |
|
| 587 |
+ labels = NULL, |
|
| 588 |
+ labels_rot = ifelse(which == "column", 0, 90), |
|
| 589 |
+ gp = gpar(fontsize = 8), |
|
| 590 |
+ side = ifelse(which == "column", "left", "bottom"), |
|
| 591 |
+ facing = "outside" |
|
| 592 |
+ ) |
|
| 593 |
+} |
|
| 594 |
+ |
|
| 595 |
+validate_axis_param = function(axis_param, which) {
|
|
| 596 |
+ dft = default_axis_param(which) |
|
| 597 |
+ for(nm in names(axis_param)) {
|
|
| 598 |
+ dft[[nm]] = axis_param[[nm]] |
|
| 599 |
+ } |
|
| 600 |
+ return(dft) |
|
| 601 |
+} |
|
| 602 |
+ |
|
| 603 |
+construct_axis_grob = function(axis_param, which, data_scale) {
|
|
| 604 |
+ axis_param_default = default_axis_param(which) |
|
| 605 |
+ |
|
| 606 |
+ for(nm in setdiff(names(axis_param_default), names(axis_param))) {
|
|
| 607 |
+ axis_param[[nm]] = axis_param_default[[nm]] |
|
| 608 |
+ } |
|
| 609 |
+ |
|
| 610 |
+ if(is.null(axis_param$at)) {
|
|
| 611 |
+ at = pretty_breaks(data_scale) |
|
| 612 |
+ axis_param$at = at |
|
| 613 |
+ axis_param$labels = at |
|
| 614 |
+ } |
|
| 615 |
+ if(is.null(axis_param$labels)) {
|
|
| 616 |
+ axis_param$labels = axis_param$at |
|
| 617 |
+ } |
|
| 618 |
+ axis_grob = do.call(annotation_axis_grob, axis_param) |
|
| 619 |
+ |
|
| 620 |
+ return(axis_grob) |
|
| 621 |
+} |
|
| 491 | 622 |
|
| 492 | 623 |
# == title |
| 493 | 624 |
# Using points as annotation |
| ... | ... |
@@ -514,16 +645,14 @@ anno_image = function(image, which = c("column", "row"), border = TRUE, gp = gpa
|
| 514 | 645 |
# Zuguang Gu <z.gu@dkfz.de> |
| 515 | 646 |
# |
| 516 | 647 |
anno_points = function(x, which = c("column", "row"), border = TRUE, gp = gpar(), pch = 16,
|
| 517 |
- size = unit(2, "mm"), ylim = NULL, extend = 0.05, axis = TRUE, axis_side = NULL, |
|
| 518 |
- axis_gp = gpar(fontsize = 8), axis_direction = c("normal", "reverse"),
|
|
| 648 |
+ size = unit(2, "mm"), ylim = NULL, extend = 0.05, axis = TRUE, |
|
| 649 |
+ axis_param = default_axis_param(which), |
|
| 519 | 650 |
width = NULL, height = NULL) {
|
| 520 | 651 |
|
| 521 |
- axis_direction = match.arg(axis_direction)[1] |
|
| 522 |
- |
|
| 523 |
- if(exists(".__under_SingleAnnotation__", envir = parent.frame())) {
|
|
| 524 |
- which = get("which", envir = parent.frame())
|
|
| 525 |
- } else {
|
|
| 652 |
+ if(is.null(.ENV$current_annotation_which)) {
|
|
| 526 | 653 |
which = match.arg(which)[1] |
| 654 |
+ } else {
|
|
| 655 |
+ which = .ENV$current_annotation_which |
|
| 527 | 656 |
} |
| 528 | 657 |
|
| 529 | 658 |
if(is.data.frame(x)) x = as.matrix(x) |
| ... | ... |
@@ -534,22 +663,7 @@ anno_points = function(x, which = c("column", "row"), border = TRUE, gp = gpar()
|
| 534 | 663 |
} |
| 535 | 664 |
input_is_matrix = is.matrix(x) |
| 536 | 665 |
|
| 537 |
- if(which == "column") {
|
|
| 538 |
- if(missing(height)) {
|
|
| 539 |
- height = unit(1, "cm") |
|
| 540 |
- } |
|
| 541 |
- if(missing(width)) {
|
|
| 542 |
- width = unit(1, "npc") |
|
| 543 |
- } |
|
| 544 |
- } |
|
| 545 |
- if(which == "row") {
|
|
| 546 |
- if(missing(width)) {
|
|
| 547 |
- width = unit(1, "cm") |
|
| 548 |
- } |
|
| 549 |
- if(missing(height)) {
|
|
| 550 |
- height = unit(1, "npc") |
|
| 551 |
- } |
|
| 552 |
- } |
|
| 666 |
+ anno_size = anno_width_and_height(which, width, height, unit(1, "cm")) |
|
| 553 | 667 |
|
| 554 | 668 |
if(is.matrix(x)) {
|
| 555 | 669 |
n = nrow(x) |
| ... | ... |
@@ -572,54 +686,39 @@ anno_points = function(x, which = c("column", "row"), border = TRUE, gp = gpar()
|
| 572 | 686 |
} |
| 573 | 687 |
|
| 574 | 688 |
if(is.null(ylim)) {
|
| 575 |
- data_scale = pretty_scale(range(x, na.rm = TRUE)) |
|
| 689 |
+ data_scale = range(x, na.rm = TRUE) |
|
| 576 | 690 |
} else {
|
| 577 | 691 |
data_scale = ylim |
| 578 | 692 |
} |
| 579 | 693 |
data_scale = data_scale + c(-extend, extend)*(data_scale[2] - data_scale[1]) |
| 580 | 694 |
|
| 581 |
- if(which == "column") {
|
|
| 582 |
- if(is.null(axis_side)) axis_side = "left" |
|
| 583 |
- if(axis_side == "top" || axis_side == "bottom") {
|
|
| 584 |
- stop("`axis_side` can only be 'left' and 'right' for column annotations")
|
|
| 585 |
- } |
|
| 586 |
- } |
|
| 587 |
- if(which == "row") {
|
|
| 588 |
- if(is.null(axis_side)) axis_side = "bottom" |
|
| 589 |
- if(axis_side == "left" || axis_side == "right") {
|
|
| 590 |
- stop("`axis_side` can only be 'top' and 'bottom' for row annotations")
|
|
| 591 |
- } |
|
| 592 |
- } |
|
| 593 |
- |
|
| 594 | 695 |
value = x |
| 595 | 696 |
|
| 697 |
+ axis_param = validate_axis_param(axis_param, which) |
|
| 698 |
+ axis_grob = if(axis) construct_axis_grob(axis_param, which, data_scale) else NULL |
|
| 699 |
+ |
|
| 596 | 700 |
row_fun = function(index) {
|
| 597 | 701 |
n = length(index) |
| 598 | 702 |
|
| 599 | 703 |
pushViewport(viewport(xscale = data_scale, yscale = c(0.5, n+0.5))) |
| 600 |
- if(axis_direction == "reverse") x = data_scale[2] - x + data_scale[1] |
|
| 601 | 704 |
if(is.matrix(value)) {
|
| 602 | 705 |
for(i in seq_len(ncol(value))) {
|
| 603 |
- grid.points(value[index, i], n - seq_along(index) + 1, gp = subset_gp(gp, i), default.units = "native", pch = pch[i], size = size[i]) |
|
| 706 |
+ grid.points(value[index, i], n - seq_along(index) + 1, gp = subset_gp(gp, i), |
|
| 707 |
+ default.units = "native", pch = pch[i], size = size[i]) |
|
| 604 | 708 |
} |
| 605 | 709 |
} else {
|
| 606 |
- grid.points(value[index], n - seq_along(index) + 1, gp = gp, default.units = "native", pch = pch[index], size = size[index]) |
|
| 607 |
- } |
|
| 608 |
- if(axis) {
|
|
| 609 |
- if(axis_side == "top") {
|
|
| 610 |
- grid.xaxis(main = FALSE, gp = axis_gp, axis_direction = axis_direction) |
|
| 611 |
- } else if(axis_side == "bottom") {
|
|
| 612 |
- grid.xaxis(gp = axis_gp, axis_direction = axis_direction) |
|
| 613 |
- } |
|
| 710 |
+ grid.points(value[index], n - seq_along(index) + 1, gp = gp, default.units = "native", |
|
| 711 |
+ pch = pch[index], size = size[index]) |
|
| 614 | 712 |
} |
| 713 |
+ if(axis) grid.draw(axis_grob) |
|
| 615 | 714 |
if(border) grid.rect(gp = gpar(fill = "transparent")) |
| 616 |
- upViewport() |
|
| 715 |
+ popViewport() |
|
| 617 | 716 |
} |
| 717 |
+ |
|
| 618 | 718 |
column_fun = function(index) {
|
| 619 | 719 |
n = length(index) |
| 620 | 720 |
|
| 621 | 721 |
pushViewport(viewport(yscale = data_scale, xscale = c(0.5, n+0.5))) |
| 622 |
- if(axis_direction == "reverse") x = data_scale[2] - x + data_scale[1] |
|
| 623 | 722 |
if(is.matrix(value)) {
|
| 624 | 723 |
for(i in seq_len(ncol(value))) {
|
| 625 | 724 |
grid.points(seq_along(index), value[index, i], gp = subset_gp(gp, i), default.units = "native", pch = pch[i], size = size[i]) |
| ... | ... |
@@ -627,15 +726,9 @@ anno_points = function(x, which = c("column", "row"), border = TRUE, gp = gpar()
|
| 627 | 726 |
} else {
|
| 628 | 727 |
grid.points(seq_along(index), value[index], gp = gp, default.units = "native", pch = pch[index], size = size[index]) |
| 629 | 728 |
} |
| 630 |
- if(axis) {
|
|
| 631 |
- if(axis_side == "right") {
|
|
| 632 |
- grid.yaxis(main = FALSE, gp = axis_gp) |
|
| 633 |
- } else if(axis_side == "left") {
|
|
| 634 |
- grid.yaxis(gp = axis_gp) |
|
| 635 |
- } |
|
| 636 |
- } |
|
| 729 |
+ if(axis) grid.draw(axis_grob) |
|
| 637 | 730 |
if(border) grid.rect(gp = gpar(fill = "transparent")) |
| 638 |
- upViewport() |
|
| 731 |
+ popViewport() |
|
| 639 | 732 |
} |
| 640 | 733 |
|
| 641 | 734 |
if(which == "row") {
|
| ... | ... |
@@ -644,34 +737,17 @@ anno_points = function(x, which = c("column", "row"), border = TRUE, gp = gpar()
|
| 644 | 737 |
fun = column_fun |
| 645 | 738 |
} |
| 646 | 739 |
|
| 647 |
- anno = AnnotationFunction() |
|
| 648 |
- anno@which = which |
|
| 649 |
- anno@fun_name = "anno_points" |
|
| 650 |
- anno@width = width |
|
| 651 |
- anno@height = height |
|
| 652 |
- anno@n = n |
|
| 653 |
- if(which == "column") {
|
|
| 654 |
- anno@data_scale = list(x = c(0.5, n + 0.5), y = data_scale) |
|
| 655 |
- } else {
|
|
| 656 |
- anno@data_scale = list(x = data_scale, y = c(0.5, n + 0.5)) |
|
| 657 |
- } |
|
| 658 |
- |
|
| 659 |
- anno@var_env = new.env() |
|
| 660 |
- anno@var_env$value = value |
|
| 661 |
- anno@var_env$gp = gp |
|
| 662 |
- anno@var_env$border = border |
|
| 663 |
- anno@var_env$pch = pch |
|
| 664 |
- anno@var_env$size = size |
|
| 665 |
- anno@var_env$axis = axis |
|
| 666 |
- anno@var_env$axis_side = axis_side |
|
| 667 |
- anno@var_env$axis_gp = axis_gp |
|
| 668 |
- anno@var_env$axis_direction = axis_direction |
|
| 669 |
- anno@var_env$data_scale = data_scale |
|
| 740 |
+ anno = AnnotationFunction( |
|
| 741 |
+ fun = fun, |
|
| 742 |
+ fun_name = "anno_points", |
|
| 743 |
+ which = which, |
|
| 744 |
+ width = anno_size$width, |
|
| 745 |
+ height = anno_size$height, |
|
| 746 |
+ n = n, |
|
| 747 |
+ data_scale = data_scale, |
|
| 748 |
+ var_import = list(value, gp, border, pch, size, axis, axis_param, axis_grob, data_scale) |
|
| 749 |
+ ) |
|
| 670 | 750 |
|
| 671 |
- environment(fun) = anno@var_env |
|
| 672 |
- anno@fun = fun |
|
| 673 |
- |
|
| 674 |
- anno@subset_rule = list() |
|
| 675 | 751 |
anno@subset_rule$gp = subset_vector |
| 676 | 752 |
if(input_is_matrix) {
|
| 677 | 753 |
anno@subset_rule$value = subset_matrix_by_row |
| ... | ... |
@@ -681,10 +757,30 @@ anno_points = function(x, which = c("column", "row"), border = TRUE, gp = gpar()
|
| 681 | 757 |
anno@subset_rule$size = subset_vector |
| 682 | 758 |
anno@subset_rule$pch = subset_vector |
| 683 | 759 |
} |
| 684 |
- |
|
| 760 |
+ |
|
| 761 |
+ anno@subsetable = TRUE |
|
| 762 |
+ |
|
| 763 |
+ anno@extended = update_anno_extend(anno, axis_grob, axis_param) |
|
| 764 |
+ |
|
| 685 | 765 |
return(anno) |
| 686 | 766 |
} |
| 687 | 767 |
|
| 768 |
+update_anno_extend = function(anno, axis_grob, axis_param) {
|
|
| 769 |
+ extended = anno@extended |
|
| 770 |
+ if(axis_param$facing == "outside") {
|
|
| 771 |
+ if(axis_param$side == "left") {
|
|
| 772 |
+ extended[[2]] = convertWidth(grobWidth(axis_grob), "mm", valueOnly = TRUE) |
|
| 773 |
+ } else if(axis_param$side == "right") {
|
|
| 774 |
+ extended[[4]] = convertWidth(grobWidth(axis_grob), "mm", valueOnly = TRUE) |
|
| 775 |
+ } else if(axis_param$side == "top") {
|
|
| 776 |
+ extended[[3]] = convertHeight(grobHeight(axis_grob), "mm", valueOnly = TRUE) |
|
| 777 |
+ } else if(axis_param$side == "bottom") {
|
|
| 778 |
+ extended[[1]] = convertHeight(grobHeight(axis_grob), "mm", valueOnly = TRUE) |
|
| 779 |
+ } |
|
| 780 |
+ } |
|
| 781 |
+ return(extended) |
|
| 782 |
+} |
|
| 783 |
+ |
|
| 688 | 784 |
# == title |
| 689 | 785 |
# Using barplot as annotation |
| 690 | 786 |
# |
| ... | ... |
@@ -713,8 +809,8 @@ anno_points = function(x, which = c("column", "row"), border = TRUE, gp = gpar()
|
| 713 | 809 |
# Zuguang Gu <z.gu@dkfz.de> |
| 714 | 810 |
# |
| 715 | 811 |
anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TRUE, bar_width = 0.6,
|
| 716 |
- gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, axis = TRUE, axis_side = NULL, |
|
| 717 |
- axis_gp = gpar(fontsize = 8), axis_direction = c("normal", "reverse"),
|
|
| 812 |
+ gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, axis = TRUE, |
|
| 813 |
+ axis_param = default_axis_param(which), |
|
| 718 | 814 |
width = NULL, height = NULL) {
|
| 719 | 815 |
|
| 720 | 816 |
if(inherits(x, "list")) x = do.call("cbind", x)
|
| ... | ... |
@@ -722,7 +818,7 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR
|
| 722 | 818 |
if(inherits(x, "matrix")) {
|
| 723 | 819 |
sg = apply(x, 1, function(xx) all(sign(xx) %in% c(1, 0)) || all(sign(xx) %in% c(-1, 0))) |
| 724 | 820 |
if(!all(sg)) {
|
| 725 |
- stop("Since `x` is a matrix, the sign of each row should be either all positive or all negative.")
|
|
| 821 |
+ stop_wrap("Since `x` is a matrix, the sign of each row should be either all positive or all negative.")
|
|
| 726 | 822 |
} |
| 727 | 823 |
} |
| 728 | 824 |
# convert everything to matrix |
| ... | ... |
@@ -752,43 +848,13 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR
|
| 752 | 848 |
} |
| 753 | 849 |
} |
| 754 | 850 |
|
| 755 |
- axis_direction = match.arg(axis_direction)[1] |
|
| 756 |
- |
|
| 757 |
- if(exists(".__under_SingleAnnotation__", envir = parent.frame())) {
|
|
| 758 |
- which = get("which", envir = parent.frame())
|
|
| 759 |
- } else {
|
|
| 851 |
+ if(is.null(.ENV$current_annotation_which)) {
|
|
| 760 | 852 |
which = match.arg(which)[1] |
| 853 |
+ } else {
|
|
| 854 |
+ which = .ENV$current_annotation_which |
|
| 761 | 855 |
} |
| 762 | 856 |
|
| 763 |
- if(which == "column") {
|
|
| 764 |
- if(missing(height)) {
|
|
| 765 |
- height = unit(1, "cm") |
|
| 766 |
- } |
|
| 767 |
- if(missing(width)) {
|
|
| 768 |
- width = unit(1, "npc") |
|
| 769 |
- } |
|
| 770 |
- } |
|
| 771 |
- if(which == "row") {
|
|
| 772 |
- if(missing(width)) {
|
|
| 773 |
- width = unit(1, "cm") |
|
| 774 |
- } |
|
| 775 |
- if(missing(height)) {
|
|
| 776 |
- height = unit(1, "npc") |
|
| 777 |
- } |
|
| 778 |
- } |
|
| 779 |
- |
|
| 780 |
- if(which == "column") {
|
|
| 781 |
- if(is.null(axis_side)) axis_side = "left" |
|
| 782 |
- if(axis_side == "top" || axis_side == "bottom") {
|
|
| 783 |
- stop("`axis_side` can only be 'left' and 'right' for column annotations")
|
|
| 784 |
- } |
|
| 785 |
- } |
|
| 786 |
- if(which == "row") {
|
|
| 787 |
- if(is.null(axis_side)) axis_side = "bottom" |
|
| 788 |
- if(axis_side == "left" || axis_side == "right") {
|
|
| 789 |
- stop("`axis_side` can only be 'top' and 'bottom' for row annotations")
|
|
| 790 |
- } |
|
| 791 |
- } |
|
| 857 |
+ anno_size = anno_width_and_height(which, width, height, unit(1, "cm")) |
|
| 792 | 858 |
|
| 793 | 859 |
if(nc == 1) {
|
| 794 | 860 |
gp = recycle_gp(gp, nrow(x)) |
| ... | ... |
@@ -797,14 +863,12 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR
|
| 797 | 863 |
} |
| 798 | 864 |
|
| 799 | 865 |
value = x |
| 800 |
- |
|
| 866 |
+ axis_param = validate_axis_param(axis_param, which) |
|
| 867 |
+ axis_grob = if(axis) construct_axis_grob(axis_param, which, data_scale) else NULL |
|
| 868 |
+ |
|
| 801 | 869 |
row_fun = function(index) {
|
| 802 | 870 |
n = length(index) |
| 803 | 871 |
|
| 804 |
- if(axis_direction == "reverse") {
|
|
| 805 |
- value = data_scale[2] - value + data_scale[1] |
|
| 806 |
- baseline = data_scale[2] - baseline + data_scale[1] |
|
| 807 |
- } |
|
| 808 | 872 |
pushViewport(viewport(xscale = data_scale, yscale = c(0.5, n+0.5))) |
| 809 | 873 |
if(ncol(value) == 1) {
|
| 810 | 874 |
width = value[index] - baseline |
| ... | ... |
@@ -817,15 +881,9 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR
|
| 817 | 881 |
grid.rect(x = x_coor, y = n - seq_along(index) + 1, width = abs(width), height = 1*bar_width, default.units = "native", gp = subset_gp(gp, i)) |
| 818 | 882 |
} |
| 819 | 883 |
} |
| 820 |
- if(axis) {
|
|
| 821 |
- if(axis_side == "top") {
|
|
| 822 |
- grid.xaxis(main = FALSE, gp = axis_gp, axis_direction = axis_direction) |
|
| 823 |
- } else if(axis_side == "bottom") {
|
|
| 824 |
- grid.xaxis(gp = axis_gp, axis_direction = axis_direction) |
|
| 825 |
- } |
|
| 826 |
- } |
|
| 884 |
+ if(axis) grid.draw(axis_grob) |
|
| 827 | 885 |
if(border) grid.rect(gp = gpar(fill = "transparent")) |
| 828 |
- upViewport() |
|
| 886 |
+ popViewport() |
|
| 829 | 887 |
} |
| 830 | 888 |
column_fun = function(index) {
|
| 831 | 889 |
n = length(index) |
| ... | ... |
@@ -842,15 +900,9 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR
|
| 842 | 900 |
grid.rect(y = y_coor, x = seq_along(index), height = abs(height), width = 1*bar_width, default.units = "native", gp = subset_gp(gp, i)) |
| 843 | 901 |
} |
| 844 | 902 |
} |
| 845 |
- if(axis) {
|
|
| 846 |
- if(axis_side == "right") {
|
|
| 847 |
- grid.yaxis(main = FALSE, gp = axis_gp) |
|
| 848 |
- } else if(axis_side == "left") {
|
|
| 849 |
- grid.yaxis(gp = axis_gp) |
|
| 850 |
- } |
|
| 851 |
- } |
|
| 903 |
+ if(axis) grid.draw(axis_grob) |
|
| 852 | 904 |
if(border) grid.rect(gp = gpar(fill = "transparent")) |
| 853 |
- upViewport() |
|
| 905 |
+ popViewport() |
|
| 854 | 906 |
} |
| 855 | 907 |
|
| 856 | 908 |
if(which == "row") {
|
| ... | ... |
@@ -860,40 +912,26 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR
|
| 860 | 912 |
} |
| 861 | 913 |
n = nrow(value) |
| 862 | 914 |
|
| 863 |
- anno = AnnotationFunction() |
|
| 864 |
- anno@which = which |
|
| 865 |
- anno@fun_name = "anno_barplot" |
|
| 866 |
- anno@width = width |
|
| 867 |
- anno@height = height |
|
| 868 |
- anno@n = n |
|
| 869 |
- if(which == "column") {
|
|
| 870 |
- anno@data_scale = list(x = c(0.5, n + 0.5), y = data_scale) |
|
| 871 |
- } else {
|
|
| 872 |
- anno@data_scale = list(x = data_scale, y = c(0.5, n + 0.5)) |
|
| 873 |
- } |
|
| 874 |
- |
|
| 875 |
- anno@var_env = new.env() |
|
| 876 |
- anno@var_env$value = value |
|
| 877 |
- anno@var_env$gp = gp |
|
| 878 |
- anno@var_env$border = border |
|
| 879 |
- anno@var_env$bar_width = bar_width |
|
| 880 |
- anno@var_env$baseline = baseline |
|
| 881 |
- anno@var_env$axis = axis |
|
| 882 |
- anno@var_env$axis_side = axis_side |
|
| 883 |
- anno@var_env$axis_gp = axis_gp |
|
| 884 |
- anno@var_env$axis_direction = axis_direction |
|
| 885 |
- anno@var_env$data_scale = data_scale |
|
| 915 |
+ anno = AnnotationFunction( |
|
| 916 |
+ fun = fun, |
|
| 917 |
+ fun_name = "anno_barplot", |
|
| 918 |
+ which = which, |
|
| 919 |
+ width = anno_size$width, |
|
| 920 |
+ height = anno_size$height, |
|
| 921 |
+ n = n, |
|
| 922 |
+ data_scale = data_scale, |
|
| 923 |
+ var_import = list(value, gp, border, bar_width, baseline, axis, axis_param, axis_grob, data_scale) |
|
| 924 |
+ ) |
|
| 886 | 925 |
|
| 887 |
- environment(fun) = anno@var_env |
|
| 888 |
- anno@fun = fun |
|
| 889 |
- |
|
| 890 |
- anno@subset_rule = list() |
|
| 891 | 926 |
anno@subset_rule$value = subset_matrix_by_row |
| 892 |
- |
|
| 893 | 927 |
if(ncol(value) == 1) {
|
| 894 | 928 |
anno@subset_rule$gp = subset_gp |
| 895 | 929 |
} |
| 896 |
- |
|
| 930 |
+ |
|
| 931 |
+ anno@subsetable = TRUE |
|
| 932 |
+ |
|
| 933 |
+ anno@extended = update_anno_extend(anno, axis_grob, axis_param) |
|
| 934 |
+ |
|
| 897 | 935 |
return(anno) |
| 898 | 936 |
} |
| 899 | 937 |
|
| ... | ... |
@@ -924,47 +962,16 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR
|
| 924 | 962 |
# |
| 925 | 963 |
anno_boxplot = function(x, which = c("column", "row"), border = TRUE,
|
| 926 | 964 |
gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, outline = TRUE, box_width = 0.6, |
| 927 |
- pch = 1, size = unit(2, "mm"), axis = TRUE, axis_side = NULL, |
|
| 928 |
- axis_gp = gpar(fontsize = 8), axis_direction = c("normal", "reverse"),
|
|
| 965 |
+ pch = 1, size = unit(2, "mm"), axis = TRUE, axis_param = default_axis_param(which), |
|
| 929 | 966 |
width = NULL, height = NULL) {
|
| 930 | 967 |
|
| 931 |
- axis_direction = match.arg(axis_direction)[1] |
|
| 932 |
- |
|
| 933 |
- if(exists(".__under_SingleAnnotation__", envir = parent.frame())) {
|
|
| 934 |
- which = get("which", envir = parent.frame())
|
|
| 935 |
- } else {
|
|
| 968 |
+ if(is.null(.ENV$current_annotation_which)) {
|
|
| 936 | 969 |
which = match.arg(which)[1] |
| 970 |
+ } else {
|
|
| 971 |
+ which = .ENV$current_annotation_which |
|
| 937 | 972 |
} |
| 938 | 973 |
|
| 939 |
- if(which == "column") {
|
|
| 940 |
- if(missing(height)) {
|
|
| 941 |
- height = unit(1, "cm") |
|
| 942 |
- } |
|
| 943 |
- if(missing(width)) {
|
|
| 944 |
- width = unit(1, "npc") |
|
| 945 |
- } |
|
| 946 |
- } |
|
| 947 |
- if(which == "row") {
|
|
| 948 |
- if(missing(width)) {
|
|
| 949 |
- width = unit(1, "cm") |
|
| 950 |
- } |
|
| 951 |
- if(missing(height)) {
|
|
| 952 |
- height = unit(1, "npc") |
|
| 953 |
- } |
|
| 954 |
- } |
|
| 955 |
- |
|
| 956 |
- if(which == "column") {
|
|
| 957 |
- if(is.null(axis_side)) axis_side = "left" |
|
| 958 |
- if(axis_side == "top" || axis_side == "bottom") {
|
|
| 959 |
- stop("`axis_side` can only be 'left' and 'right' for column annotations")
|
|
| 960 |
- } |
|
| 961 |
- } |
|
| 962 |
- if(which == "row") {
|
|
| 963 |
- if(is.null(axis_side)) axis_side = "bottom" |
|
| 964 |
- if(axis_side == "left" || axis_side == "right") {
|
|
| 965 |
- stop("`axis_side` can only be 'top' and 'bottom' for row annotations")
|
|
| 966 |
- } |
|
| 967 |
- } |
|
| 974 |
+ anno_size = anno_width_and_height(which, width, height, unit(2, "cm")) |
|
| 968 | 975 |
|
| 969 | 976 |
## convert matrix all to list (or data frame) |
| 970 | 977 |
if(is.matrix(x)) {
|
| ... | ... |
@@ -994,10 +1001,12 @@ anno_boxplot = function(x, which = c("column", "row"), border = TRUE,
|
| 994 | 1001 |
if(length(pch) == 1) pch = rep(pch, n) |
| 995 | 1002 |
if(length(size) == 1) size = rep(size, n) |
| 996 | 1003 |
|
| 1004 |
+ axis_param = validate_axis_param(axis_param, which) |
|
| 1005 |
+ axis_grob = if(axis) construct_axis_grob(axis_param, which, data_scale) else NULL |
|
| 1006 |
+ |
|
| 997 | 1007 |
row_fun = function(index) {
|
| 998 | 1008 |
|
| 999 | 1009 |
n_all = length(value) |
| 1000 |
- if(axis_direction == "reverse") value = lapply(value, function(y) data_scale[2] - y + data_scale[1]) |
|
| 1001 | 1010 |
value = value[index] |
| 1002 | 1011 |
boxplot_stats = boxplot(value, plot = FALSE)$stats |
| 1003 | 1012 |
|
| ... | ... |
@@ -1011,36 +1020,32 @@ anno_boxplot = function(x, which = c("column", "row"), border = TRUE,
|
| 1011 | 1020 |
|
| 1012 | 1021 |
grid.segments(boxplot_stats[5, ], n - seq_along(index) + 1 - 0.5*box_width, |
| 1013 | 1022 |
boxplot_stats[5, ], n - seq_along(index) + 1 + 0.5*box_width, |
| 1014 |
- default.units = "native", gp = gp) |
|
| 1023 |
+ default.units = "native", gp = gp) |
|
| 1015 | 1024 |
grid.segments(boxplot_stats[5, ], n - seq_along(index) + 1, |
| 1016 | 1025 |
boxplot_stats[4, ], n - seq_along(index) + 1, |
| 1017 |
- default.units = "native", gp = gp) |
|
| 1026 |
+ default.units = "native", gp = gp) |
|
| 1018 | 1027 |
grid.segments(boxplot_stats[1, ], n - seq_along(index) + 1, |
| 1019 | 1028 |
boxplot_stats[2, ], n - seq_along(index) + 1, |
| 1020 |
- default.units = "native", gp = gp) |
|
| 1029 |
+ default.units = "native", gp = gp) |
|
| 1021 | 1030 |
grid.segments(boxplot_stats[1, ], n - seq_along(index) + 1 - 0.5*box_width, |
| 1022 | 1031 |
boxplot_stats[1, ], n - seq_along(index) + 1 + 0.5*box_width, |
| 1023 |
- default.units = "native", gp = gp) |
|
| 1032 |
+ default.units = "native", gp = gp) |
|
| 1024 | 1033 |
grid.segments(boxplot_stats[3, ], n - seq_along(index) + 1 - 0.5*box_width, |
| 1025 | 1034 |
boxplot_stats[3, ], n - seq_along(index) + 1 + 0.5*box_width, |
| 1026 |
- default.units = "native", gp = gp) |
|
| 1035 |
+ default.units = "native", gp = gp) |
|
| 1027 | 1036 |
if(outline) {
|
| 1028 | 1037 |
for(i in seq_along(value)) {
|
| 1029 | 1038 |
l1 = value[[i]] > boxplot_stats[5,i] |
| 1030 |
- if(sum(l1)) grid.points(y = rep(n - i + 1, sum(l1)), x = value[[i]][l1], default.units = "native", gp = subset_gp(gp, i), pch = pch[i], size = size[i]) |
|
| 1039 |
+ if(sum(l1)) grid.points(y = rep(n - i + 1, sum(l1)), x = value[[i]][l1], |
|
| 1040 |
+ default.units = "native", gp = subset_gp(gp, i), pch = pch[i], size = size[i]) |
|
| 1031 | 1041 |
l2 = value[[i]] < boxplot_stats[1,i] |
| 1032 |
- if(sum(l2)) grid.points(y = rep(n - i + 1, sum(l2)), x = value[[i]][l2], default.units = "native", gp = subset_gp(gp, i), pch = pch[i], size = size[i]) |
|
| 1033 |
- } |
|
| 1034 |
- } |
|
| 1035 |
- if(axis) {
|
|
| 1036 |
- if(axis_side == "top") {
|
|
| 1037 |
- grid.xaxis(main = FALSE, gp = axis_gp, axis_direction = axis_direction) |
|
| 1038 |
- } else if(axis_side == "bottom") {
|
|
| 1039 |
- grid.xaxis(gp = axis_gp, axis_direction = axis_direction) |
|
| 1042 |
+ if(sum(l2)) grid.points(y = rep(n - i + 1, sum(l2)), x = value[[i]][l2], |
|
| 1043 |
+ default.units = "native", gp = subset_gp(gp, i), pch = pch[i], size = size[i]) |
|
| 1040 | 1044 |
} |
| 1041 | 1045 |
} |
| 1046 |
+ if(axis) grid.draw(axis_grob) |
|
| 1042 | 1047 |
if(border) grid.rect(gp = gpar(fill = "transparent")) |
| 1043 |
- upViewport() |
|
| 1048 |
+ popViewport() |
|
| 1044 | 1049 |
} |
| 1045 | 1050 |
column_fun = function(index) {
|
| 1046 | 1051 |
value = value[index] |
| ... | ... |
@@ -1052,34 +1057,35 @@ anno_boxplot = function(x, which = c("column", "row"), border = TRUE,
|
| 1052 | 1057 |
grid.rect(x = seq_along(index), y = boxplot_stats[2, ], |
| 1053 | 1058 |
height = boxplot_stats[4, ] - boxplot_stats[2, ], width = 1*box_width, just = "bottom", |
| 1054 | 1059 |
default.units = "native", gp = gp) |
| 1060 |
+ |
|
| 1055 | 1061 |
grid.segments(seq_along(index) - 0.5*box_width, boxplot_stats[5, ], |
| 1056 |
- seq_along(index) + 0.5*box_width, boxplot_stats[5, ], default.units = "native", gp = gp) |
|
| 1062 |
+ seq_along(index) + 0.5*box_width, boxplot_stats[5, ], |
|
| 1063 |
+ default.units = "native", gp = gp) |
|
| 1057 | 1064 |
grid.segments(seq_along(index), boxplot_stats[5, ], |
| 1058 |
- seq_along(index), boxplot_stats[4, ], default.units = "native", gp = gp) |
|
| 1065 |
+ seq_along(index), boxplot_stats[4, ], |
|
| 1066 |
+ default.units = "native", gp = gp) |
|
| 1059 | 1067 |
grid.segments(seq_along(index), boxplot_stats[1, ], |
| 1060 |
- seq_along(index), boxplot_stats[2, ], default.units = "native", gp = gp) |
|
| 1068 |
+ seq_along(index), boxplot_stats[2, ], |
|
| 1069 |
+ default.units = "native", gp = gp) |
|
| 1061 | 1070 |
grid.segments(seq_along(index) - 0.5*box_width, boxplot_stats[1, ], |
| 1062 |
- seq_along(index) + 0.5*box_width, boxplot_stats[1, ], default.units = "native", gp = gp) |
|
| 1071 |
+ seq_along(index) + 0.5*box_width, boxplot_stats[1, ], |
|
| 1072 |
+ default.units = "native", gp = gp) |
|
| 1063 | 1073 |
grid.segments(seq_along(index) - 0.5*box_width, boxplot_stats[3, ], |
| 1064 | 1074 |
seq_along(index) + 0.5*box_width, boxplot_stats[3, ], |
| 1065 |
- default.units = "native", gp = gp) |
|
| 1075 |
+ default.units = "native", gp = gp) |
|
| 1066 | 1076 |
if(outline) {
|
| 1067 | 1077 |
for(i in seq_along(value)) {
|
| 1068 | 1078 |
l1 = value[[i]] > boxplot_stats[5,i] |
| 1069 |
- if(sum(l1)) grid.points(x = rep(i, sum(l1)), y = value[[i]][l1], default.units = "native", gp = subset_gp(gp, i), pch = pch[i], size = size[i]) |
|
| 1079 |
+ if(sum(l1)) grid.points(x = rep(i, sum(l1)), y = value[[i]][l1], |
|
| 1080 |
+ default.units = "native", gp = subset_gp(gp, i), pch = pch[i], size = size[i]) |
|
| 1070 | 1081 |
l2 = value[[i]] < boxplot_stats[1,i] |
| 1071 |
- if(sum(l2)) grid.points(x = rep(i, sum(l2)), y = value[[i]][l2], default.units = "native", gp = subset_gp(gp, i), pch = pch[i], size = size[i]) |
|
| 1072 |
- } |
|
| 1073 |
- } |
|
| 1074 |
- if(axis) {
|
|
| 1075 |
- if(axis_side == "right") {
|
|
| 1076 |
- grid.yaxis(main = FALSE, gp = axis_gp) |
|
| 1077 |
- } else if(axis_side == "left") {
|
|
| 1078 |
- grid.yaxis(gp = axis_gp) |
|
| 1082 |
+ if(sum(l2)) grid.points(x = rep(i, sum(l2)), y = value[[i]][l2], |
|
| 1083 |
+ default.units = "native", gp = subset_gp(gp, i), pch = pch[i], size = size[i]) |
|
| 1079 | 1084 |
} |
| 1080 | 1085 |
} |
| 1086 |
+ if(axis) grid.draw(axis_grob) |
|
| 1081 | 1087 |
if(border) grid.rect(gp = gpar(fill = "transparent")) |
| 1082 |
- upViewport() |
|
| 1088 |
+ popViewport() |
|
| 1083 | 1089 |
} |
| 1084 | 1090 |
|
| 1085 | 1091 |
if(which == "row") {
|
| ... | ... |
@@ -1088,41 +1094,26 @@ anno_boxplot = function(x, which = c("column", "row"), border = TRUE,
|
| 1088 | 1094 |
fun = column_fun |
| 1089 | 1095 |
} |
| 1090 | 1096 |
|
| 1091 |
- anno = AnnotationFunction() |
|
| 1092 |
- anno@which = which |
|
| 1093 |
- anno@fun_name = "anno_boxplot" |
|
| 1094 |
- anno@width = width |
|
| 1095 |
- anno@height = height |
|
| 1096 |
- anno@n = n |
|
| 1097 |
- if(which == "column") {
|
|
| 1098 |
- anno@data_scale = list(x = c(0.5, n + 0.5), y = data_scale) |
|
| 1099 |
- } else {
|
|
| 1100 |
- anno@data_scale = list(x = data_scale, y = c(0.5, n + 0.5)) |
|
| 1101 |
- } |
|
| 1102 |
- |
|
| 1103 |
- anno@var_env = new.env() |
|
| 1104 |
- anno@var_env$value = value |
|
| 1105 |
- anno@var_env$gp = gp |
|
| 1106 |
- anno@var_env$border = border |
|
| 1107 |
- anno@var_env$box_width = box_width |
|
| 1108 |
- anno@var_env$axis = axis |
|
| 1109 |
- anno@var_env$axis_side = axis_side |
|
| 1110 |
- anno@var_env$axis_gp = axis_gp |
|
| 1111 |
- anno@var_env$axis_direction = axis_direction |
|
| 1112 |
- anno@var_env$data_scale = data_scale |
|
| 1113 |
- anno@var_env$pch = pch |
|
| 1114 |
- anno@var_env$size = size |
|
| 1115 |
- anno@var_env$outline = outline |
|
| 1097 |
+ anno = AnnotationFunction( |
|
| 1098 |
+ fun = fun, |
|
| 1099 |
+ fun_name = "anno_boxplot", |
|
| 1100 |
+ which = which, |
|
| 1101 |
+ n = n, |
|
| 1102 |
+ width = anno_size$width, |
|
| 1103 |
+ height = anno_size$height, |
|
| 1104 |
+ data_scale = data_scale, |
|
| 1105 |
+ var_import = list(value, gp, border, box_width, axis, axis_param, axis_grob, data_scale, pch, size, outline) |
|
| 1106 |
+ ) |
|
| 1116 | 1107 |
|
| 1117 |
- environment(fun) = anno@var_env |
|
| 1118 |
- anno@fun = fun |
|
| 1119 |
- |
|
| 1120 |
- anno@subset_rule = list() |
|
| 1121 | 1108 |
anno@subset_rule$value = subset_vector |
| 1122 | 1109 |
anno@subset_rule$gp = subset_gp |
| 1123 | 1110 |
anno@subset_rule$pch = subset_vector |
| 1124 | 1111 |
anno@subset_rule$size = subset_vector |
| 1125 | 1112 |
|
| 1113 |
+ anno@subsetable = TRUE |
|
| 1114 |
+ |
|
| 1115 |
+ anno@extended = update_anno_extend(anno, axis_grob, axis_param) |
|
| 1116 |
+ |
|
| 1126 | 1117 |
return(anno) |
| 1127 | 1118 |
} |
| 1128 | 1119 |
|
| ... | ... |
@@ -1144,44 +1135,16 @@ anno_boxplot = function(x, which = c("column", "row"), border = TRUE,
|
| 1144 | 1135 |
# |
| 1145 | 1136 |
anno_histogram = function(x, which = c("column", "row"), n_breaks = 11,
|
| 1146 | 1137 |
border = FALSE, gp = gpar(fill = "#CCCCCC"), |
| 1147 |
- axis = TRUE, axis_side = NULL, axis_gp = gpar(fontsize = 8), |
|
| 1138 |
+ axis = TRUE, axis_param = default_axis_param(which), |
|
| 1148 | 1139 |
width = NULL, height = NULL) {
|
| 1149 | 1140 |
|
| 1150 |
- if(exists(".__under_SingleAnnotation__", envir = parent.frame())) {
|
|
| 1151 |
- which = get("which", envir = parent.frame())
|
|
| 1152 |
- } else {
|
|
| 1141 |
+ if(is.null(.ENV$current_annotation_which)) {
|
|
| 1153 | 1142 |
which = match.arg(which)[1] |
| 1143 |
+ } else {
|
|
| 1144 |
+ which = .ENV$current_annotation_which |
|
| 1154 | 1145 |
} |
| 1155 | 1146 |
|
| 1156 |
- if(which == "column") {
|
|
| 1157 |
- if(missing(height)) {
|
|
| 1158 |
- height = unit(4, "cm") |
|
| 1159 |
- } |
|
| 1160 |
- if(missing(width)) {
|
|
| 1161 |
- width = unit(1, "npc") |
|
| 1162 |
- } |
|
| 1163 |
- } |
|
| 1164 |
- if(which == "row") {
|
|
| 1165 |
- if(missing(width)) {
|
|
| 1166 |
- width = unit(4, "cm") |
|
| 1167 |
- } |
|
| 1168 |
- if(missing(height)) {
|
|
| 1169 |
- height = unit(1, "npc") |
|
| 1170 |
- } |
|
| 1171 |
- } |
|
| 1172 |
- |
|
| 1173 |
- if(which == "column") {
|
|
| 1174 |
- if(is.null(axis_side)) axis_side = "left" |
|
| 1175 |
- if(axis_side == "top" || axis_side == "bottom") {
|
|
| 1176 |
- stop("`axis_side` can only be 'left' and 'right' for column annotations")
|
|
| 1177 |
- } |
|
| 1178 |
- } |
|
| 1179 |
- if(which == "row") {
|
|
| 1180 |
- if(is.null(axis_side)) axis_side = "bottom" |
|
| 1181 |
- if(axis_side == "left" || axis_side == "right") {
|
|
| 1182 |
- stop("`axis_side` can only be 'top' and 'bottom' for row annotations")
|
|
| 1183 |
- } |
|
| 1184 |
- } |
|
| 1147 |
+ anno_size = anno_width_and_height(which, width, height, unit(4, "cm")) |
|
| 1185 | 1148 |
|
| 1186 | 1149 |
## convert matrix all to list (or data frame) |
| 1187 | 1150 |
if(is.matrix(x)) {
|
| ... | ... |
@@ -1204,8 +1167,10 @@ anno_histogram = function(x, which = c("column", "row"), n_breaks = 11,
|
| 1204 | 1167 |
xscale = xscale + c(0, 0.05)*(xscale[2] - xscale[1]) |
| 1205 | 1168 |
yscale = c(0, max(unlist(histogram_counts))) |
| 1206 | 1169 |
yscale[2] = yscale[2]*1.05 |
| 1207 |
- |
|
| 1170 |
+ |
|
| 1208 | 1171 |
gp = recycle_gp(gp, n) |
| 1172 |
+ axis_param = validate_axis_param(axis_param, which) |
|
| 1173 |
+ axis_grob = if(axis) construct_axis_grob(axis_param, which, xscale) else NULL |
|
| 1209 | 1174 |
|
| 1210 | 1175 |
row_fun = function(index) {
|
| 1211 | 1176 |
|
| ... | ... |
@@ -1213,7 +1178,9 @@ anno_histogram = function(x, which = c("column", "row"), n_breaks = 11,
|
| 1213 | 1178 |
value = value[index] |
| 1214 | 1179 |
|
| 1215 | 1180 |
n = length(index) |
| 1216 |
- |
|
| 1181 |
+ histogram_breaks = histogram_breaks[index] |
|
| 1182 |
+ histogram_counts = histogram_counts[index] |
|
| 1183 |
+ |
|
| 1217 | 1184 |
gp = subset_gp(gp, index) |
| 1218 | 1185 |
for(i in seq_len(n)) {
|
| 1219 | 1186 |
n_breaks = length(histogram_breaks[[i]]) |
| ... | ... |
@@ -1222,13 +1189,7 @@ anno_histogram = function(x, which = c("column", "row"), n_breaks = 11,
|
| 1222 | 1189 |
popViewport() |
| 1223 | 1190 |
} |
| 1224 | 1191 |
pushViewport(viewport(xscale = xscale)) |
| 1225 |
- if(axis) {
|
|
| 1226 |
- if(axis_side == "top") {
|
|
| 1227 |
- grid.xaxis(main = FALSE, gp = axis_gp) |
|
| 1228 |
- } else if(axis_side == "bottom") {
|
|
| 1229 |
- grid.xaxis(gp = axis_gp) |
|
| 1230 |
- } |
|
| 1231 |
- } |
|
| 1192 |
+ if(axis) grid.draw(axis_grob) |
|
| 1232 | 1193 |
if(border) grid.rect(gp = gpar(fill = "transparent")) |
| 1233 | 1194 |
popViewport() |
| 1234 | 1195 |
} |
| ... | ... |
@@ -1240,6 +1201,8 @@ anno_histogram = function(x, which = c("column", "row"), n_breaks = 11,
|
| 1240 | 1201 |
foo = yscale |
| 1241 | 1202 |
yscale = xscale |
| 1242 | 1203 |
xscale = foo |
| 1204 |
+ histogram_breaks = histogram_breaks[index] |
|
| 1205 |
+ histogram_counts = histogram_counts[index] |
|
| 1243 | 1206 |
|
| 1244 | 1207 |
n = length(index) |
| 1245 | 1208 |
|
| ... | ... |
@@ -1253,13 +1216,7 @@ anno_histogram = function(x, which = c("column", "row"), n_breaks = 11,
|
| 1253 | 1216 |
popViewport() |
| 1254 | 1217 |
} |
| 1255 | 1218 |
pushViewport(viewport(yscale = yscale)) |
| 1256 |
- if(axis) {
|
|
| 1257 |
- if(axis_side == "right") {
|
|
| 1258 |
- grid.yaxis(main = FALSE, gp = axis_gp) |
|
| 1259 |
- } else if(axis_side == "left") {
|
|
| 1260 |
- grid.yaxis(gp = axis_gp) |
|
| 1261 |
- } |
|
| 1262 |
- } |
|
| 1219 |
+ if(axis) grid.draw(axis_grob) |
|
| 1263 | 1220 |
if(border) grid.rect(gp = gpar(fill = "transparent")) |
| 1264 | 1221 |
popViewport() |
| 1265 | 1222 |
} |
| ... | ... |
@@ -1270,39 +1227,27 @@ anno_histogram = function(x, which = c("column", "row"), n_breaks = 11,
|
| 1270 | 1227 |
fun = column_fun |
| 1271 | 1228 |
} |
| 1272 | 1229 |
|
| 1273 |
- anno = AnnotationFunction() |
|
| 1274 |
- anno@which = which |
|
| 1275 |
- anno@fun_name = "anno_histogram" |
|
| 1276 |
- anno@width = width |
|
| 1277 |
- anno@height = height |
|
| 1278 |
- anno@n = n |
|
| 1279 |
- if(which == "column") {
|
|
| 1280 |
- anno@data_scale = list(x = c(0.5, n + 0.5), y = xscale) |
|
| 1281 |
- } else {
|
|
| 1282 |
- anno@data_scale = list(x = xscale, y = c(0.5, n + 0.5)) |
|
| 1283 |
- } |
|
| 1284 |
- |
|
| 1285 |
- anno@var_env = new.env() |
|
| 1286 |
- anno@var_env$value = value |
|
| 1287 |
- anno@var_env$gp = gp |
|
| 1288 |
- anno@var_env$border = border |
|
| 1289 |
- anno@var_env$axis = axis |
|
| 1290 |
- anno@var_env$axis_side = axis_side |
|
| 1291 |
- anno@var_env$axis_gp = axis_gp |
|
| 1292 |
- anno@var_env$xscale = xscale |
|
| 1293 |
- anno@var_env$yscale = yscale |
|
| 1294 |
- anno@var_env$histogram_breaks = histogram_breaks |
|
| 1295 |
- anno@var_env$histogram_counts = histogram_counts |
|
| 1230 |
+ anno = AnnotationFunction( |
|
| 1231 |
+ fun = fun, |
|
| 1232 |
+ fun_name = "anno_histogram", |
|
| 1233 |
+ which = which, |
|
| 1234 |
+ width = anno_size$width, |
|
| 1235 |
+ height = anno_size$height, |
|
| 1236 |
+ n = n, |
|
| 1237 |
+ data_scale = xscale, |
|
| 1238 |
+ var_import = list(value, gp, border, axis, axis_param, axis_grob, xscale, yscale, |
|
| 1239 |
+ histogram_breaks, histogram_counts) |
|
| 1240 |
+ ) |
|
| 1296 | 1241 |
|
| 1297 |
- environment(fun) = anno@var_env |
|
| 1298 |
- anno@fun = fun |
|
| 1299 |
- |
|
| 1300 |
- anno@subset_rule = list() |
|
| 1301 | 1242 |
anno@subset_rule$value = subset_vector |
| 1302 | 1243 |
anno@subset_rule$gp = subset_gp |
| 1303 | 1244 |
anno@subset_rule$histogram_breaks = subset_vector |
| 1304 | 1245 |
anno@subset_rule$histogram_counts = subset_vector |
| 1305 | 1246 |
|
| 1247 |
+ anno@subsetable = TRUE |
|
| 1248 |
+ |
|
| 1249 |
+ anno@extended = update_anno_extend(anno, axis_grob, axis_param) |
|
| 1250 |
+ |
|
| 1306 | 1251 |
return(anno) |
| 1307 | 1252 |
} |
| 1308 | 1253 |
|
| ... | ... |
@@ -1325,59 +1270,19 @@ anno_histogram = function(x, which = c("column", "row"), n_breaks = 11,
|
| 1325 | 1270 |
# |
| 1326 | 1271 |
anno_density = function(x, which = c("column", "row"), gp = gpar(fill = "#CCCCCC"),
|
| 1327 | 1272 |
type = c("lines", "violin", "heatmap"),
|
| 1328 |
- heatmap_color_schema = rev(brewer.pal(name = "RdYlBu", n = 11)), |
|
| 1329 |
- joyplot_scale = 1, border = FALSE, |
|
| 1330 |
- axis = TRUE, axis_side = NULL, |
|
| 1331 |
- axis_gp = gpar(fontsize = 8), |
|
| 1273 |
+ heatmap_colors = rev(brewer.pal(name = "RdYlBu", n = 11)), |
|
| 1274 |
+ joyplot_scale = 1, border = TRUE, |
|
| 1275 |
+ axis = TRUE, axis_param = default_axis_param(which), |
|
| 1332 | 1276 |
width = NULL, height = NULL) {
|
| 1333 | 1277 |
|
| 1334 |
- if(exists(".__under_SingleAnnotation__", envir = parent.frame())) {
|
|
| 1335 |
- which = get("which", envir = parent.frame())
|
|
| 1336 |
- } else {
|
|
| 1278 |
+ if(is.null(.ENV$current_annotation_which)) {
|
|
| 1337 | 1279 |
which = match.arg(which)[1] |
| 1338 |
- } |
|
| 1339 |
- |
|
| 1340 |
- if(which == "column") {
|
|
| 1341 |
- if(missing(height)) {
|
|
| 1342 |
- height = unit(4, "cm") |
|
| 1343 |
- } |
|
| 1344 |
- if(missing(width)) {
|
|
| 1345 |
- width = unit(1, "npc") |
|
| 1346 |
- } |
|
| 1347 |
- } |
|
| 1348 |
- if(which == "row") {
|
|
| 1349 |
- if(missing(width)) {
|
|
| 1350 |
- width = unit(4, "cm") |
|
| 1351 |
- } |
|
| 1352 |
- if(missing(height)) {
|
|
| 1353 |
- height = unit(1, "npc") |
|
| 1354 |
- } |
|
| 1355 |
- } |
|
| 1356 |
- |
|
| 1357 |
- if(which == "column") {
|
|
| 1358 |
- if(is.null(axis_side)) axis_side = "left" |
|
| 1359 |
- if(axis_side == "top" || axis_side == "bottom") {
|
|
| 1360 |
- stop("`axis_side` can only be 'left' and 'right' for column annotations")
|
|
| 1361 |