| ... | ... |
@@ -10,6 +10,7 @@ CHANGES in VERSIONS 1.17.1 |
| 10 | 10 |
ordered by number of samples that have mutations |
| 11 | 11 |
* correctly reorder rows |
| 12 | 12 |
* add `row_gap` argument for list of heatmaps |
| 13 |
+* `oncoPrint()`: add `j` and `i` as optional argument for `alter_fun` |
|
| 13 | 14 |
|
| 14 | 15 |
======================= |
| 15 | 16 |
|
| ... | ... |
@@ -156,13 +156,13 @@ oncoPrint = function(mat, get_type = function(x) x, |
| 156 | 156 |
|
| 157 | 157 |
if(missing(alter_fun) && missing(col)) {
|
| 158 | 158 |
if(length(mat_list) == 1) {
|
| 159 |
- af = function(x, y, w, h, v) {
|
|
| 159 |
+ af = function(x, y, w, h, v, j, i) {
|
|
| 160 | 160 |
grid.rect(x, y, w, h, gp = gpar(fill = "#CCCCCC", col = NA)) |
| 161 | 161 |
if(v[1]) grid.rect(x, y, w*0.9, h*0.9, gp = gpar(fill = "red", col = NA)) |
| 162 | 162 |
} |
| 163 | 163 |
col = "red" |
| 164 | 164 |
} else if(length(mat_list) == 2) {
|
| 165 |
- af = function(x, y, w, h, v) {
|
|
| 165 |
+ af = function(x, y, w, h, v, j, i) {
|
|
| 166 | 166 |
grid.rect(x, y, w, h, gp = gpar(fill = "#CCCCCC", col = NA)) |
| 167 | 167 |
if(v[1]) grid.rect(x, y, w*0.9, h*0.9, gp = gpar(fill = "red", col = NA)) |
| 168 | 168 |
if(v[2]) grid.rect(x, y, w*0.9, h*0.4, gp = gpar(fill = "blue", col = NA)) |
| ... | ... |
@@ -183,19 +183,33 @@ oncoPrint = function(mat, get_type = function(x) x, |
| 183 | 183 |
|
| 184 | 184 |
alter_fun = alter_fun[unique(c("background", intersect(names(alter_fun), all_type)))]
|
| 185 | 185 |
|
| 186 |
- af = function(x, y, w, h, v) {
|
|
| 186 |
+ af = function(x, y, w, h, v, j, i) {
|
|
| 187 | 187 |
if(!is.null(alter_fun$background)) alter_fun$background(x, y, w, h) |
| 188 | 188 |
|
| 189 | 189 |
alter_fun = alter_fun[names(alter_fun) != "background"] |
| 190 | 190 |
|
| 191 | 191 |
if(sum(v)) {
|
| 192 | 192 |
for(nm in names(alter_fun)) {
|
| 193 |
- if(v[nm]) alter_fun[[nm]](x, y, w, h) |
|
| 193 |
+ if(v[nm]) {
|
|
| 194 |
+ if(length(formals(alter_fun[[nm]])) == 6) {
|
|
| 195 |
+ alter_fun[[nm]](x, y, w, h, j, i) |
|
| 196 |
+ } else {
|
|
| 197 |
+ alter_fun[[nm]](x, y, w, h) |
|
| 198 |
+ } |
|
| 199 |
+ } |
|
| 194 | 200 |
} |
| 195 | 201 |
} |
| 196 | 202 |
} |
| 197 | 203 |
} else {
|
| 198 |
- af = alter_fun |
|
| 204 |
+ if(length(formals(alter_fun)) == 7) {
|
|
| 205 |
+ af = function(x, y, w, h, v, j, i) {
|
|
| 206 |
+ alter_fun(x, y, w, h, v, j, i) |
|
| 207 |
+ } |
|
| 208 |
+ } else {
|
|
| 209 |
+ af = function(x, y, w, h, v, j, i) {
|
|
| 210 |
+ alter_fun(x, y, w, h, v) |
|
| 211 |
+ } |
|
| 212 |
+ } |
|
| 199 | 213 |
} |
| 200 | 214 |
|
| 201 | 215 |
col = col[intersect(names(col), all_type)] |
| ... | ... |
@@ -323,7 +337,7 @@ oncoPrint = function(mat, get_type = function(x) x, |
| 323 | 337 |
cell_fun = function(j, i, x, y, width, height, fill) {
|
| 324 | 338 |
z = arr[i, j, ] |
| 325 | 339 |
names(z) = dimnames(arr)[[3]] |
| 326 |
- af(x, y, width, height, z) |
|
| 340 |
+ af(x, y, width, height, z, j, i) |
|
| 327 | 341 |
}, |
| 328 | 342 |
top_annotation = top_annotation, |
| 329 | 343 |
top_annotation_height = top_annotation_height, |
