zhewa authored on 16/09/2020 15:50:01
| ... | ... |
@@ -1973,16 +1973,7 @@ semiPheatmap <- function(mat, |
| 1973 | 1973 |
... |
| 1974 | 1974 |
) |
| 1975 | 1975 |
|
| 1976 |
- if (is.na(fileName) & !silent) {
|
|
| 1977 |
- grid.newpage() |
|
| 1978 |
- grid.draw(gt) |
|
| 1979 |
- } |
|
| 1980 |
- |
|
| 1981 |
- return(list( |
|
| 1982 |
- treeRow = treeRow, |
|
| 1983 |
- treeCol = treeCol, |
|
| 1984 |
- gtable = gt |
|
| 1985 |
- )) |
|
| 1976 |
+ return(gt) |
|
| 1986 | 1977 |
} |
| 1987 | 1978 |
|
| 1988 | 1979 |
|
Joshua D. Campbell authored on 06/04/2020 23:58:56
| ... | ... |
@@ -3,583 +3,660 @@ |
| 3 | 3 |
|
| 4 | 4 |
#' @importFrom gtable gtable |
| 5 | 5 |
.lo <- function(rown, |
| 6 |
- coln, |
|
| 7 |
- nrow, |
|
| 8 |
- ncol, |
|
| 9 |
- cellHeight = NA, |
|
| 10 |
- cellWidth = NA, |
|
| 11 |
- treeHeightCol, |
|
| 12 |
- treeHeightRow, |
|
| 13 |
- legend, |
|
| 14 |
- annotationRow, |
|
| 15 |
- annotationCol, |
|
| 16 |
- annotationColors, |
|
| 17 |
- annotationLegend, |
|
| 18 |
- annotationNamesRow, |
|
| 19 |
- annotationNamesCol, |
|
| 20 |
- main, |
|
| 21 |
- fontSize, |
|
| 22 |
- fontSizeRow, |
|
| 23 |
- fontSizeCol, |
|
| 24 |
- gapsRow, |
|
| 25 |
- gapsCol, |
|
| 26 |
- ...) {
|
|
| 27 |
- # Get height of colnames and length of rownames |
|
| 28 |
- if (!is.null(coln[1]) | |
|
| 29 |
- (!.is.na2(annotationRow) & annotationNamesRow)) {
|
|
| 30 |
- if (!is.null(coln[1])) {
|
|
| 31 |
- t <- coln |
|
| 32 |
- } else {
|
|
| 33 |
- t <- "" |
|
| 34 |
- } |
|
| 35 |
- tw <- strwidth(t, units = "in", cex = fontSizeCol / fontSize) |
|
| 36 |
- if (annotationNamesRow) {
|
|
| 37 |
- t <- c(t, colnames(annotationRow)) |
|
| 38 |
- tw <- c(tw, strwidth(colnames(annotationRow), units = "in")) |
|
| 39 |
- } |
|
| 40 |
- longestColn <- which.max(tw) |
|
| 41 |
- gp <- list(fontSize = ifelse(longestColn <= length(coln), |
|
| 42 |
- fontSizeCol, |
|
| 43 |
- fontSize), ...) |
|
| 44 |
- colnHeight <- unit(1, |
|
| 45 |
- "grobheight", |
|
| 46 |
- textGrob(t[longestColn], |
|
| 47 |
- rot = 90, |
|
| 48 |
- gp = do.call(gpar, gp))) + |
|
| 49 |
- unit(10, "bigpts") |
|
| 50 |
- } else {
|
|
| 51 |
- colnHeight <- unit(5, "bigpts") |
|
| 52 |
- } |
|
| 53 |
- |
|
| 54 |
- if (!is.null(rown[1])) {
|
|
| 55 |
- t <- rown |
|
| 56 |
- tw <- strwidth(t, units = "in", cex = fontSizeRow / fontSize) |
|
| 57 |
- if (annotationNamesCol) {
|
|
| 58 |
- t <- c(t, colnames(annotationCol)) |
|
| 59 |
- tw <- c(tw, strwidth(colnames(annotationCol), units = "in")) |
|
| 60 |
- } |
|
| 61 |
- longestRown <- which.max(tw) |
|
| 62 |
- gp <- list(fontSize = ifelse(longestRown <= length(rown), |
|
| 63 |
- fontSizeRow, |
|
| 64 |
- fontSize), ...) |
|
| 65 |
- rownWidth <- unit(1, |
|
| 66 |
- "grobwidth", |
|
| 67 |
- textGrob(t[longestRown], |
|
| 68 |
- gp = do.call(gpar, gp))) + |
|
| 69 |
- unit(10, "bigpts") |
|
| 70 |
- } else {
|
|
| 71 |
- rownWidth <- unit(5, "bigpts") |
|
| 72 |
- } |
|
| 73 |
- |
|
| 74 |
- gp <- list(fontSize = fontSize, ...) |
|
| 75 |
- # Legend position |
|
| 76 |
- if (!.is.na2(legend)) {
|
|
| 77 |
- longestBreak <- which.max(nchar(names(legend))) |
|
| 78 |
- longestBreak <- unit(1.1, |
|
| 79 |
- "grobwidth", |
|
| 80 |
- textGrob(as.character(names(legend))[longestBreak], |
|
| 81 |
- gp = do.call(gpar, gp))) |
|
| 82 |
- titleLength <- unit(1.1, |
|
| 83 |
- "grobwidth", |
|
| 84 |
- textGrob("Scale",
|
|
| 85 |
- gp = gpar(fontface = "bold", |
|
| 86 |
- ...))) |
|
| 87 |
- legendWidth <- unit(12, "bigpts") + longestBreak * 1.2 |
|
| 88 |
- legendWidth <- max(titleLength, legendWidth) |
|
| 89 |
- } else {
|
|
| 90 |
- legendWidth <- unit(0, "bigpts") |
|
| 91 |
- } |
|
| 92 |
- |
|
| 93 |
- # Set main title height |
|
| 94 |
- if (is.na(main)) {
|
|
| 95 |
- mainHeight <- unit(0, "npc") |
|
| 6 |
+ coln, |
|
| 7 |
+ nrow, |
|
| 8 |
+ ncol, |
|
| 9 |
+ cellHeight = NA, |
|
| 10 |
+ cellWidth = NA, |
|
| 11 |
+ treeHeightCol, |
|
| 12 |
+ treeHeightRow, |
|
| 13 |
+ legend, |
|
| 14 |
+ annotationRow, |
|
| 15 |
+ annotationCol, |
|
| 16 |
+ annotationColors, |
|
| 17 |
+ annotationLegend, |
|
| 18 |
+ annotationNamesRow, |
|
| 19 |
+ annotationNamesCol, |
|
| 20 |
+ main, |
|
| 21 |
+ fontSize, |
|
| 22 |
+ fontSizeRow, |
|
| 23 |
+ fontSizeCol, |
|
| 24 |
+ gapsRow, |
|
| 25 |
+ gapsCol, |
|
| 26 |
+ ...) {
|
|
| 27 |
+ # Get height of colnames and length of rownames |
|
| 28 |
+ if (!is.null(coln[1]) | |
|
| 29 |
+ (!.is.na2(annotationRow) & annotationNamesRow)) {
|
|
| 30 |
+ if (!is.null(coln[1])) {
|
|
| 31 |
+ t <- coln |
|
| 96 | 32 |
} else {
|
| 97 |
- mainHeight <- unit(1.5, |
|
| 98 |
- "grobheight", |
|
| 99 |
- textGrob(main, |
|
| 100 |
- gp = gpar(fontSize = 1.3 * fontSize, |
|
| 101 |
- ...))) |
|
| 33 |
+ t <- "" |
|
| 102 | 34 |
} |
| 103 |
- |
|
| 104 |
- # Column annotations |
|
| 105 |
- textheight <- unit(fontSize, "bigpts") |
|
| 106 |
- |
|
| 107 |
- if (!.is.na2(annotationCol)) {
|
|
| 108 |
- # Column annotation height |
|
| 109 |
- annotColHeight <- |
|
| 110 |
- ncol(annotationCol) * |
|
| 111 |
- (textheight + unit(2, "bigpts")) + |
|
| 112 |
- unit(2, "bigpts") |
|
| 113 |
- |
|
| 114 |
- # Width of the correponding legend |
|
| 115 |
- t <- c(as.vector(as.matrix(annotationCol)), colnames(annotationCol)) |
|
| 116 |
- annotColLegendWidth <- unit(1.2, |
|
| 117 |
- "grobwidth", |
|
| 118 |
- textGrob(t[which.max(nchar(t))], |
|
| 119 |
- gp = gpar(...))) + |
|
| 120 |
- unit(12, "bigpts") |
|
| 121 |
- if (!annotationLegend) {
|
|
| 122 |
- annotColLegendWidth <- unit(0, "npc") |
|
| 123 |
- } |
|
| 124 |
- } else {
|
|
| 125 |
- annotColHeight <- unit(0, "bigpts") |
|
| 126 |
- annotColLegendWidth <- unit(0, "bigpts") |
|
| 35 |
+ tw <- strwidth(t, units = "in", cex = fontSizeCol / fontSize) |
|
| 36 |
+ if (annotationNamesRow) {
|
|
| 37 |
+ t <- c(t, colnames(annotationRow)) |
|
| 38 |
+ tw <- c(tw, strwidth(colnames(annotationRow), units = "in")) |
|
| 127 | 39 |
} |
| 128 |
- |
|
| 129 |
- # Row annotations |
|
| 130 |
- if (!.is.na2(annotationRow)) {
|
|
| 131 |
- # Row annotation width |
|
| 132 |
- annotRowWidth <- ncol(annotationRow) * |
|
| 133 |
- (textheight + unit(2, "bigpts")) + |
|
| 134 |
- unit(2, "bigpts") |
|
| 135 |
- |
|
| 136 |
- # Width of the correponding legend |
|
| 137 |
- t <- c(as.vector(as.matrix(annotationRow)), |
|
| 138 |
- colnames(annotationRow)) |
|
| 139 |
- annotRowLegendWidth <- unit(1.2, |
|
| 140 |
- "grobwidth", |
|
| 141 |
- textGrob(t[which.max(nchar(t))], |
|
| 142 |
- gp = gpar(...))) + |
|
| 143 |
- unit(12, |
|
| 144 |
- "bigpts") |
|
| 145 |
- |
|
| 146 |
- if (!annotationLegend) {
|
|
| 147 |
- annotRowLegendWidth <- unit(0, "npc") |
|
| 148 |
- } |
|
| 149 |
- } else {
|
|
| 150 |
- annotRowWidth <- unit(0, "bigpts") |
|
| 151 |
- annotRowLegendWidth <- unit(0, "bigpts") |
|
| 40 |
+ longestColn <- which.max(tw) |
|
| 41 |
+ gp <- list(fontSize = ifelse(longestColn <= length(coln), |
|
| 42 |
+ fontSizeCol, |
|
| 43 |
+ fontSize |
|
| 44 |
+ ), ...) |
|
| 45 |
+ colnHeight <- unit( |
|
| 46 |
+ 1, |
|
| 47 |
+ "grobheight", |
|
| 48 |
+ textGrob(t[longestColn], |
|
| 49 |
+ rot = 90, |
|
| 50 |
+ gp = do.call(gpar, gp) |
|
| 51 |
+ ) |
|
| 52 |
+ ) + |
|
| 53 |
+ unit(10, "bigpts") |
|
| 54 |
+ } else {
|
|
| 55 |
+ colnHeight <- unit(5, "bigpts") |
|
| 56 |
+ } |
|
| 57 |
+ |
|
| 58 |
+ if (!is.null(rown[1])) {
|
|
| 59 |
+ t <- rown |
|
| 60 |
+ tw <- strwidth(t, units = "in", cex = fontSizeRow / fontSize) |
|
| 61 |
+ if (annotationNamesCol) {
|
|
| 62 |
+ t <- c(t, colnames(annotationCol)) |
|
| 63 |
+ tw <- c(tw, strwidth(colnames(annotationCol), units = "in")) |
|
| 152 | 64 |
} |
| 153 |
- |
|
| 154 |
- annotLegendWidth <- max(annotRowLegendWidth, annotColLegendWidth) |
|
| 155 |
- |
|
| 156 |
- # Tree height |
|
| 157 |
- treeHeightCol <- unit(treeHeightCol, "bigpts") + unit(5, "bigpts") |
|
| 158 |
- treeHeightRow <- unit(treeHeightRow, "bigpts") + unit(5, "bigpts") |
|
| 159 |
- |
|
| 160 |
- # Set cell sizes |
|
| 161 |
- if (is.na(cellWidth)) {
|
|
| 162 |
- matWidth <- unit(1, "npc") - |
|
| 163 |
- rownWidth - |
|
| 164 |
- legendWidth - |
|
| 165 |
- treeHeightRow - |
|
| 166 |
- annotRowWidth - |
|
| 167 |
- annotLegendWidth |
|
| 168 |
- } else {
|
|
| 169 |
- matWidth <- unit(cellWidth * ncol, "bigpts") + |
|
| 170 |
- length(gapsCol) * |
|
| 171 |
- unit(0, "bigpts") |
|
| 65 |
+ longestRown <- which.max(tw) |
|
| 66 |
+ gp <- list(fontSize = ifelse(longestRown <= length(rown), |
|
| 67 |
+ fontSizeRow, |
|
| 68 |
+ fontSize |
|
| 69 |
+ ), ...) |
|
| 70 |
+ rownWidth <- unit( |
|
| 71 |
+ 1, |
|
| 72 |
+ "grobwidth", |
|
| 73 |
+ textGrob(t[longestRown], |
|
| 74 |
+ gp = do.call(gpar, gp) |
|
| 75 |
+ ) |
|
| 76 |
+ ) + |
|
| 77 |
+ unit(10, "bigpts") |
|
| 78 |
+ } else {
|
|
| 79 |
+ rownWidth <- unit(5, "bigpts") |
|
| 80 |
+ } |
|
| 81 |
+ |
|
| 82 |
+ gp <- list(fontSize = fontSize, ...) |
|
| 83 |
+ # Legend position |
|
| 84 |
+ if (!.is.na2(legend)) {
|
|
| 85 |
+ longestBreak <- which.max(nchar(names(legend))) |
|
| 86 |
+ longestBreak <- unit( |
|
| 87 |
+ 1.1, |
|
| 88 |
+ "grobwidth", |
|
| 89 |
+ textGrob(as.character(names(legend))[longestBreak], |
|
| 90 |
+ gp = do.call(gpar, gp) |
|
| 91 |
+ ) |
|
| 92 |
+ ) |
|
| 93 |
+ titleLength <- unit( |
|
| 94 |
+ 1.1, |
|
| 95 |
+ "grobwidth", |
|
| 96 |
+ textGrob("Scale",
|
|
| 97 |
+ gp = gpar( |
|
| 98 |
+ fontface = "bold", |
|
| 99 |
+ ... |
|
| 100 |
+ ) |
|
| 101 |
+ ) |
|
| 102 |
+ ) |
|
| 103 |
+ legendWidth <- unit(12, "bigpts") + longestBreak * 1.2 |
|
| 104 |
+ legendWidth <- max(titleLength, legendWidth) |
|
| 105 |
+ } else {
|
|
| 106 |
+ legendWidth <- unit(0, "bigpts") |
|
| 107 |
+ } |
|
| 108 |
+ |
|
| 109 |
+ # Set main title height |
|
| 110 |
+ if (is.na(main)) {
|
|
| 111 |
+ mainHeight <- unit(0, "npc") |
|
| 112 |
+ } else {
|
|
| 113 |
+ mainHeight <- unit( |
|
| 114 |
+ 1.5, |
|
| 115 |
+ "grobheight", |
|
| 116 |
+ textGrob(main, |
|
| 117 |
+ gp = gpar( |
|
| 118 |
+ fontSize = 1.3 * fontSize, |
|
| 119 |
+ ... |
|
| 120 |
+ ) |
|
| 121 |
+ ) |
|
| 122 |
+ ) |
|
| 123 |
+ } |
|
| 124 |
+ |
|
| 125 |
+ # Column annotations |
|
| 126 |
+ textheight <- unit(fontSize, "bigpts") |
|
| 127 |
+ |
|
| 128 |
+ if (!.is.na2(annotationCol)) {
|
|
| 129 |
+ # Column annotation height |
|
| 130 |
+ annotColHeight <- |
|
| 131 |
+ ncol(annotationCol) * |
|
| 132 |
+ (textheight + unit(2, "bigpts")) + |
|
| 133 |
+ unit(2, "bigpts") |
|
| 134 |
+ |
|
| 135 |
+ # Width of the correponding legend |
|
| 136 |
+ t <- c(as.vector(as.matrix(annotationCol)), colnames(annotationCol)) |
|
| 137 |
+ annotColLegendWidth <- unit( |
|
| 138 |
+ 1.2, |
|
| 139 |
+ "grobwidth", |
|
| 140 |
+ textGrob(t[which.max(nchar(t))], |
|
| 141 |
+ gp = gpar(...) |
|
| 142 |
+ ) |
|
| 143 |
+ ) + |
|
| 144 |
+ unit(12, "bigpts") |
|
| 145 |
+ if (!annotationLegend) {
|
|
| 146 |
+ annotColLegendWidth <- unit(0, "npc") |
|
| 172 | 147 |
} |
| 173 |
- |
|
| 174 |
- if (is.na(cellHeight)) {
|
|
| 175 |
- matHeight <- unit(1, "npc") - |
|
| 176 |
- mainHeight - |
|
| 177 |
- colnHeight - |
|
| 178 |
- treeHeightCol - |
|
| 179 |
- annotColHeight |
|
| 180 |
- } else {
|
|
| 181 |
- matHeight <- unit(cellHeight * nrow, "bigpts") + |
|
| 182 |
- length(gapsRow) * |
|
| 183 |
- unit(0, "bigpts") |
|
| 148 |
+ } else {
|
|
| 149 |
+ annotColHeight <- unit(0, "bigpts") |
|
| 150 |
+ annotColLegendWidth <- unit(0, "bigpts") |
|
| 151 |
+ } |
|
| 152 |
+ |
|
| 153 |
+ # Row annotations |
|
| 154 |
+ if (!.is.na2(annotationRow)) {
|
|
| 155 |
+ # Row annotation width |
|
| 156 |
+ annotRowWidth <- ncol(annotationRow) * |
|
| 157 |
+ (textheight + unit(2, "bigpts")) + |
|
| 158 |
+ unit(2, "bigpts") |
|
| 159 |
+ |
|
| 160 |
+ # Width of the correponding legend |
|
| 161 |
+ t <- c( |
|
| 162 |
+ as.vector(as.matrix(annotationRow)), |
|
| 163 |
+ colnames(annotationRow) |
|
| 164 |
+ ) |
|
| 165 |
+ annotRowLegendWidth <- unit( |
|
| 166 |
+ 1.2, |
|
| 167 |
+ "grobwidth", |
|
| 168 |
+ textGrob(t[which.max(nchar(t))], |
|
| 169 |
+ gp = gpar(...) |
|
| 170 |
+ ) |
|
| 171 |
+ ) + |
|
| 172 |
+ unit( |
|
| 173 |
+ 12, |
|
| 174 |
+ "bigpts" |
|
| 175 |
+ ) |
|
| 176 |
+ |
|
| 177 |
+ if (!annotationLegend) {
|
|
| 178 |
+ annotRowLegendWidth <- unit(0, "npc") |
|
| 184 | 179 |
} |
| 185 |
- |
|
| 186 |
- # Produce gtable |
|
| 187 |
- gt <- gtable::gtable(widths = unit.c(treeHeightRow, |
|
| 188 |
- annotRowWidth, |
|
| 189 |
- matWidth, |
|
| 190 |
- rownWidth, |
|
| 191 |
- legendWidth, |
|
| 192 |
- annotLegendWidth), |
|
| 193 |
- heights = unit.c(mainHeight, |
|
| 194 |
- treeHeightCol, |
|
| 195 |
- annotColHeight, |
|
| 196 |
- matHeight, |
|
| 197 |
- colnHeight), |
|
| 198 |
- vp = viewport(gp = do.call(gpar, gp))) |
|
| 199 |
- |
|
| 200 |
- cw <- convertWidth(matWidth - |
|
| 201 |
- (length(gapsCol) * unit(0, "bigpts")), |
|
| 202 |
- "bigpts", valueOnly = TRUE) / ncol |
|
| 203 |
- ch <- convertHeight(matHeight - |
|
| 204 |
- (length(gapsRow) * unit(0, "bigpts")), |
|
| 205 |
- "bigpts", valueOnly = TRUE) / nrow |
|
| 206 |
- |
|
| 207 |
- # Return minimal cell dimension in bigpts to decide if borders are drawn |
|
| 208 |
- mindim <- min(cw, ch) |
|
| 209 |
- |
|
| 210 |
- res <- list(gt = gt, mindim = mindim) |
|
| 211 |
- |
|
| 212 |
- return(res) |
|
| 180 |
+ } else {
|
|
| 181 |
+ annotRowWidth <- unit(0, "bigpts") |
|
| 182 |
+ annotRowLegendWidth <- unit(0, "bigpts") |
|
| 183 |
+ } |
|
| 184 |
+ |
|
| 185 |
+ annotLegendWidth <- max(annotRowLegendWidth, annotColLegendWidth) |
|
| 186 |
+ |
|
| 187 |
+ # Tree height |
|
| 188 |
+ treeHeightCol <- unit(treeHeightCol, "bigpts") + unit(5, "bigpts") |
|
| 189 |
+ treeHeightRow <- unit(treeHeightRow, "bigpts") + unit(5, "bigpts") |
|
| 190 |
+ |
|
| 191 |
+ # Set cell sizes |
|
| 192 |
+ if (is.na(cellWidth)) {
|
|
| 193 |
+ matWidth <- unit(1, "npc") - |
|
| 194 |
+ rownWidth - |
|
| 195 |
+ legendWidth - |
|
| 196 |
+ treeHeightRow - |
|
| 197 |
+ annotRowWidth - |
|
| 198 |
+ annotLegendWidth |
|
| 199 |
+ } else {
|
|
| 200 |
+ matWidth <- unit(cellWidth * ncol, "bigpts") + |
|
| 201 |
+ length(gapsCol) * |
|
| 202 |
+ unit(0, "bigpts") |
|
| 203 |
+ } |
|
| 204 |
+ |
|
| 205 |
+ if (is.na(cellHeight)) {
|
|
| 206 |
+ matHeight <- unit(1, "npc") - |
|
| 207 |
+ mainHeight - |
|
| 208 |
+ colnHeight - |
|
| 209 |
+ treeHeightCol - |
|
| 210 |
+ annotColHeight |
|
| 211 |
+ } else {
|
|
| 212 |
+ matHeight <- unit(cellHeight * nrow, "bigpts") + |
|
| 213 |
+ length(gapsRow) * |
|
| 214 |
+ unit(0, "bigpts") |
|
| 215 |
+ } |
|
| 216 |
+ |
|
| 217 |
+ # Produce gtable |
|
| 218 |
+ gt <- gtable::gtable( |
|
| 219 |
+ widths = unit.c( |
|
| 220 |
+ treeHeightRow, |
|
| 221 |
+ annotRowWidth, |
|
| 222 |
+ matWidth, |
|
| 223 |
+ rownWidth, |
|
| 224 |
+ legendWidth, |
|
| 225 |
+ annotLegendWidth |
|
| 226 |
+ ), |
|
| 227 |
+ heights = unit.c( |
|
| 228 |
+ mainHeight, |
|
| 229 |
+ treeHeightCol, |
|
| 230 |
+ annotColHeight, |
|
| 231 |
+ matHeight, |
|
| 232 |
+ colnHeight |
|
| 233 |
+ ), |
|
| 234 |
+ vp = viewport(gp = do.call(gpar, gp)) |
|
| 235 |
+ ) |
|
| 236 |
+ |
|
| 237 |
+ cw <- convertWidth(matWidth - |
|
| 238 |
+ (length(gapsCol) * unit(0, "bigpts")), |
|
| 239 |
+ "bigpts", |
|
| 240 |
+ valueOnly = TRUE |
|
| 241 |
+ ) / ncol |
|
| 242 |
+ ch <- convertHeight(matHeight - |
|
| 243 |
+ (length(gapsRow) * unit(0, "bigpts")), |
|
| 244 |
+ "bigpts", |
|
| 245 |
+ valueOnly = TRUE |
|
| 246 |
+ ) / nrow |
|
| 247 |
+ |
|
| 248 |
+ # Return minimal cell dimension in bigpts to decide if borders are drawn |
|
| 249 |
+ mindim <- min(cw, ch) |
|
| 250 |
+ |
|
| 251 |
+ res <- list(gt = gt, mindim = mindim) |
|
| 252 |
+ |
|
| 253 |
+ return(res) |
|
| 213 | 254 |
} |
| 214 | 255 |
|
| 215 | 256 |
.findCoordinates <- function(n, gaps, m = seq(1, n)) {
|
| 216 |
- if (length(gaps) == 0) {
|
|
| 217 |
- return(list( |
|
| 218 |
- coord = unit(m / n, "npc"), |
|
| 219 |
- size = unit(1 / n, "npc"))) |
|
| 220 |
- } |
|
| 257 |
+ if (length(gaps) == 0) {
|
|
| 258 |
+ return(list( |
|
| 259 |
+ coord = unit(m / n, "npc"), |
|
| 260 |
+ size = unit(1 / n, "npc") |
|
| 261 |
+ )) |
|
| 262 |
+ } |
|
| 221 | 263 |
|
| 222 |
- if (max(gaps) > n) {
|
|
| 223 |
- stop("Gaps do not match with matrix size")
|
|
| 224 |
- } |
|
| 225 |
- |
|
| 226 |
- size <- (1 / n) * |
|
| 227 |
- (unit(1, "npc") - length(gaps) * unit("0", "bigpts"))
|
|
| 264 |
+ if (max(gaps) > n) {
|
|
| 265 |
+ stop("Gaps do not match with matrix size")
|
|
| 266 |
+ } |
|
| 228 | 267 |
|
| 229 |
- gaps2 <- base::apply(vapply(gaps, |
|
| 230 |
- function(gap, x) {
|
|
| 231 |
- x > gap |
|
| 232 |
- }, |
|
| 233 |
- integer(n), m), 1, sum) |
|
| 234 |
- coord <- m * size + (gaps2 * unit("0", "bigpts"))
|
|
| 268 |
+ size <- (1 / n) * |
|
| 269 |
+ (unit(1, "npc") - length(gaps) * unit("0", "bigpts"))
|
|
| 235 | 270 |
|
| 236 |
- return(list(coord = coord, size = size)) |
|
| 271 |
+ gaps2 <- base::apply(vapply( |
|
| 272 |
+ gaps, |
|
| 273 |
+ function(gap, x) {
|
|
| 274 |
+ x > gap |
|
| 275 |
+ }, |
|
| 276 |
+ integer(n), m |
|
| 277 |
+ ), 1, sum) |
|
| 278 |
+ coord <- m * size + (gaps2 * unit("0", "bigpts"))
|
|
| 279 |
+ |
|
| 280 |
+ return(list(coord = coord, size = size)) |
|
| 237 | 281 |
} |
| 238 | 282 |
|
| 239 | 283 |
.drawDendrogram <- function(hc, gaps, horizontal = TRUE) {
|
| 240 |
- h <- hc$height / max(hc$height) / 1.05 |
|
| 241 |
- m <- hc$merge |
|
| 242 |
- o <- hc$order |
|
| 243 |
- n <- length(o) |
|
| 244 |
- |
|
| 245 |
- m[m > 0] <- n + m[m > 0] |
|
| 246 |
- m[m < 0] <- abs(m[m < 0]) |
|
| 247 |
- |
|
| 248 |
- dist <- matrix(0, |
|
| 249 |
- nrow = 2 * n - 1, |
|
| 250 |
- ncol = 2, |
|
| 251 |
- dimnames = list(NULL, c("x", "y")))
|
|
| 252 |
- dist[seq(1, n), 1] <- 1 / n / 2 + (1 / n) * |
|
| 253 |
- (match(seq(1, n), o) - 1) |
|
| 254 |
- |
|
| 255 |
- for (i in seq(1, nrow(m))) {
|
|
| 256 |
- dist[n + i, 1] <- (dist[m[i, 1], 1] + dist[m[i, 2], 1]) / 2 |
|
| 257 |
- dist[n + i, 2] <- h[i] |
|
| 258 |
- } |
|
| 259 |
- |
|
| 260 |
- drawConnection <- function(x1, x2, y1, y2, y) {
|
|
| 261 |
- res <- list(x = c(x1, x1, x2, x2), |
|
| 262 |
- y = c(y1, y, y, y2)) |
|
| 263 |
- |
|
| 264 |
- return(res) |
|
| 265 |
- } |
|
| 266 |
- |
|
| 267 |
- x <- rep(NA, nrow(m) * 4) |
|
| 268 |
- y <- rep(NA, nrow(m) * 4) |
|
| 269 |
- id <- rep(seq(nrow(m)), rep(4, nrow(m))) |
|
| 270 |
- |
|
| 271 |
- for (i in seq(1, nrow(m))) {
|
|
| 272 |
- c <- drawConnection(dist[m[i, 1], 1], |
|
| 273 |
- dist[m[i, 2], 1], |
|
| 274 |
- dist[m[i, 1], 2], |
|
| 275 |
- dist[m[i, 2], 2], |
|
| 276 |
- h[i]) |
|
| 277 |
- k <- (i - 1) * 4 + 1 |
|
| 278 |
- x[seq(k, k + 3)] <- c$x |
|
| 279 |
- y[seq(k, k + 3)] <- c$y |
|
| 280 |
- } |
|
| 281 |
- |
|
| 282 |
- x <- .findCoordinates(n, gaps, x * n)$coord |
|
| 283 |
- y <- unit(y, "npc") |
|
| 284 |
- |
|
| 285 |
- if (!horizontal) {
|
|
| 286 |
- a <- x |
|
| 287 |
- x <- unit(1, "npc") - y |
|
| 288 |
- y <- unit(1, "npc") - a |
|
| 289 |
- } |
|
| 290 |
- res <- polylineGrob(x = x, y = y, id = id) |
|
| 284 |
+ h <- hc$height / max(hc$height) / 1.05 |
|
| 285 |
+ m <- hc$merge |
|
| 286 |
+ o <- hc$order |
|
| 287 |
+ n <- length(o) |
|
| 288 |
+ |
|
| 289 |
+ m[m > 0] <- n + m[m > 0] |
|
| 290 |
+ m[m < 0] <- abs(m[m < 0]) |
|
| 291 |
+ |
|
| 292 |
+ dist <- matrix(0, |
|
| 293 |
+ nrow = 2 * n - 1, |
|
| 294 |
+ ncol = 2, |
|
| 295 |
+ dimnames = list(NULL, c("x", "y"))
|
|
| 296 |
+ ) |
|
| 297 |
+ dist[seq(1, n), 1] <- 1 / n / 2 + (1 / n) * |
|
| 298 |
+ (match(seq(1, n), o) - 1) |
|
| 299 |
+ |
|
| 300 |
+ for (i in seq(1, nrow(m))) {
|
|
| 301 |
+ dist[n + i, 1] <- (dist[m[i, 1], 1] + dist[m[i, 2], 1]) / 2 |
|
| 302 |
+ dist[n + i, 2] <- h[i] |
|
| 303 |
+ } |
|
| 304 |
+ |
|
| 305 |
+ drawConnection <- function(x1, x2, y1, y2, y) {
|
|
| 306 |
+ res <- list( |
|
| 307 |
+ x = c(x1, x1, x2, x2), |
|
| 308 |
+ y = c(y1, y, y, y2) |
|
| 309 |
+ ) |
|
| 291 | 310 |
|
| 292 | 311 |
return(res) |
| 312 |
+ } |
|
| 313 |
+ |
|
| 314 |
+ x <- rep(NA, nrow(m) * 4) |
|
| 315 |
+ y <- rep(NA, nrow(m) * 4) |
|
| 316 |
+ id <- rep(seq(nrow(m)), rep(4, nrow(m))) |
|
| 317 |
+ |
|
| 318 |
+ for (i in seq(1, nrow(m))) {
|
|
| 319 |
+ c <- drawConnection( |
|
| 320 |
+ dist[m[i, 1], 1], |
|
| 321 |
+ dist[m[i, 2], 1], |
|
| 322 |
+ dist[m[i, 1], 2], |
|
| 323 |
+ dist[m[i, 2], 2], |
|
| 324 |
+ h[i] |
|
| 325 |
+ ) |
|
| 326 |
+ k <- (i - 1) * 4 + 1 |
|
| 327 |
+ x[seq(k, k + 3)] <- c$x |
|
| 328 |
+ y[seq(k, k + 3)] <- c$y |
|
| 329 |
+ } |
|
| 330 |
+ |
|
| 331 |
+ x <- .findCoordinates(n, gaps, x * n)$coord |
|
| 332 |
+ y <- unit(y, "npc") |
|
| 333 |
+ |
|
| 334 |
+ if (!horizontal) {
|
|
| 335 |
+ a <- x |
|
| 336 |
+ x <- unit(1, "npc") - y |
|
| 337 |
+ y <- unit(1, "npc") - a |
|
| 338 |
+ } |
|
| 339 |
+ res <- polylineGrob(x = x, y = y, id = id) |
|
| 340 |
+ |
|
| 341 |
+ return(res) |
|
| 293 | 342 |
} |
| 294 | 343 |
|
| 295 | 344 |
.drawMatrix <- function(matrix, |
| 296 |
- borderColor, |
|
| 297 |
- gapsRows, |
|
| 298 |
- gapsCols, |
|
| 299 |
- fmat, |
|
| 300 |
- fontSizeNumber, |
|
| 301 |
- numberColor) {
|
|
| 302 |
- |
|
| 303 |
- n <- nrow(matrix) |
|
| 304 |
- m <- ncol(matrix) |
|
| 305 |
- |
|
| 306 |
- coordX <- .findCoordinates(m, gapsCols) |
|
| 307 |
- coordY <- .findCoordinates(n, gapsRows) |
|
| 308 |
- |
|
| 309 |
- x <- coordX$coord - |
|
| 310 |
- 0.5 * coordX$size |
|
| 311 |
- y <- unit(1, "npc") - |
|
| 312 |
- (coordY$coord - 0.5 * coordY$size) |
|
| 313 |
- |
|
| 314 |
- coord <- expand.grid(y = y, x = x) |
|
| 315 |
- |
|
| 316 |
- res <- gList() |
|
| 317 |
- |
|
| 318 |
- res[["rect"]] <- rectGrob(x = coord$x, |
|
| 319 |
- y = coord$y, |
|
| 320 |
- width = coordX$size, |
|
| 321 |
- height = coordY$size, |
|
| 322 |
- gp = gpar(fill = matrix, col = borderColor)) |
|
| 323 |
- |
|
| 324 |
- if (attr(fmat, "draw")) {
|
|
| 325 |
- res[["text"]] <- textGrob(x = coord$x, |
|
| 326 |
- y = coord$y, |
|
| 327 |
- label = fmat, |
|
| 328 |
- gp = gpar(col = numberColor, fontSize = fontSizeNumber)) |
|
| 329 |
- } |
|
| 330 |
- |
|
| 331 |
- res <- gTree(children = res) |
|
| 332 |
- |
|
| 333 |
- return(res) |
|
| 345 |
+ borderColor, |
|
| 346 |
+ gapsRows, |
|
| 347 |
+ gapsCols, |
|
| 348 |
+ fmat, |
|
| 349 |
+ fontSizeNumber, |
|
| 350 |
+ numberColor) {
|
|
| 351 |
+ n <- nrow(matrix) |
|
| 352 |
+ m <- ncol(matrix) |
|
| 353 |
+ |
|
| 354 |
+ coordX <- .findCoordinates(m, gapsCols) |
|
| 355 |
+ coordY <- .findCoordinates(n, gapsRows) |
|
| 356 |
+ |
|
| 357 |
+ x <- coordX$coord - |
|
| 358 |
+ 0.5 * coordX$size |
|
| 359 |
+ y <- unit(1, "npc") - |
|
| 360 |
+ (coordY$coord - 0.5 * coordY$size) |
|
| 361 |
+ |
|
| 362 |
+ coord <- expand.grid(y = y, x = x) |
|
| 363 |
+ |
|
| 364 |
+ res <- gList() |
|
| 365 |
+ |
|
| 366 |
+ res[["rect"]] <- rectGrob( |
|
| 367 |
+ x = coord$x, |
|
| 368 |
+ y = coord$y, |
|
| 369 |
+ width = coordX$size, |
|
| 370 |
+ height = coordY$size, |
|
| 371 |
+ gp = gpar(fill = matrix, col = borderColor) |
|
| 372 |
+ ) |
|
| 373 |
+ |
|
| 374 |
+ if (attr(fmat, "draw")) {
|
|
| 375 |
+ res[["text"]] <- textGrob( |
|
| 376 |
+ x = coord$x, |
|
| 377 |
+ y = coord$y, |
|
| 378 |
+ label = fmat, |
|
| 379 |
+ gp = gpar(col = numberColor, fontSize = fontSizeNumber) |
|
| 380 |
+ ) |
|
| 381 |
+ } |
|
| 382 |
+ |
|
| 383 |
+ res <- gTree(children = res) |
|
| 384 |
+ |
|
| 385 |
+ return(res) |
|
| 334 | 386 |
} |
| 335 | 387 |
|
| 336 | 388 |
.drawColnames <- function(coln, gaps, ...) {
|
| 337 |
- coord <- .findCoordinates(length(coln), gaps) |
|
| 338 |
- x <- coord$coord - 0.5 * coord$size |
|
| 339 |
- |
|
| 340 |
- res <- textGrob(coln, |
|
| 341 |
- x = x, |
|
| 342 |
- y = unit(1, "npc") - |
|
| 343 |
- unit(3, "bigpts"), |
|
| 344 |
- vjust = 0.5, |
|
| 345 |
- hjust = 0, |
|
| 346 |
- rot = 270, |
|
| 347 |
- gp = gpar(...)) |
|
| 348 |
- |
|
| 349 |
- return(res) |
|
| 389 |
+ coord <- .findCoordinates(length(coln), gaps) |
|
| 390 |
+ x <- coord$coord - 0.5 * coord$size |
|
| 391 |
+ |
|
| 392 |
+ res <- textGrob(coln, |
|
| 393 |
+ x = x, |
|
| 394 |
+ y = unit(1, "npc") - |
|
| 395 |
+ unit(3, "bigpts"), |
|
| 396 |
+ vjust = 0.5, |
|
| 397 |
+ hjust = 0, |
|
| 398 |
+ rot = 270, |
|
| 399 |
+ gp = gpar(...) |
|
| 400 |
+ ) |
|
| 401 |
+ |
|
| 402 |
+ return(res) |
|
| 350 | 403 |
} |
| 351 | 404 |
|
| 352 | 405 |
.drawRownames <- function(rown, gaps, ...) {
|
| 353 |
- coord <- .findCoordinates(length(rown), gaps) |
|
| 354 |
- y <- unit(1, "npc") - (coord$coord - 0.5 * coord$size) |
|
| 355 |
- |
|
| 356 |
- res <- textGrob(rown, |
|
| 357 |
- x = unit(3, "bigpts"), |
|
| 358 |
- y = y, |
|
| 359 |
- vjust = 0.5, |
|
| 360 |
- hjust = 0, |
|
| 361 |
- gp = gpar(...)) |
|
| 362 |
- |
|
| 363 |
- return(res) |
|
| 406 |
+ coord <- .findCoordinates(length(rown), gaps) |
|
| 407 |
+ y <- unit(1, "npc") - (coord$coord - 0.5 * coord$size) |
|
| 408 |
+ |
|
| 409 |
+ res <- textGrob(rown, |
|
| 410 |
+ x = unit(3, "bigpts"), |
|
| 411 |
+ y = y, |
|
| 412 |
+ vjust = 0.5, |
|
| 413 |
+ hjust = 0, |
|
| 414 |
+ gp = gpar(...) |
|
| 415 |
+ ) |
|
| 416 |
+ |
|
| 417 |
+ return(res) |
|
| 364 | 418 |
} |
| 365 | 419 |
|
| 366 | 420 |
.drawLegend <- function(color, breaks, legend, ...) {
|
| 367 |
- height <- min(unit(1, "npc"), unit(150, "bigpts")) |
|
| 421 |
+ height <- min(unit(1, "npc"), unit(150, "bigpts")) |
|
| 368 | 422 |
|
| 369 |
- legendPos <- (legend - min(breaks)) / (max(breaks) - min(breaks)) |
|
| 370 |
- legendPos <- height * legendPos + (unit(1, "npc") - height) |
|
| 423 |
+ legendPos <- (legend - min(breaks)) / (max(breaks) - min(breaks)) |
|
| 424 |
+ legendPos <- height * legendPos + (unit(1, "npc") - height) |
|
| 371 | 425 |
|
| 372 |
- breaks <- (breaks - min(breaks)) / (max(breaks) - min(breaks)) |
|
| 373 |
- breaks <- height * breaks + (unit(1, "npc") - height) |
|
| 426 |
+ breaks <- (breaks - min(breaks)) / (max(breaks) - min(breaks)) |
|
| 427 |
+ breaks <- height * breaks + (unit(1, "npc") - height) |
|
| 374 | 428 |
|
| 375 |
- h <- breaks[-1] - breaks[-length(breaks)] |
|
| 429 |
+ h <- breaks[-1] - breaks[-length(breaks)] |
|
| 376 | 430 |
|
| 377 |
- rect <- rectGrob(x = 0, |
|
| 378 |
- y = breaks[-length(breaks)], |
|
| 379 |
- width = unit(10, "bigpts"), |
|
| 380 |
- height = h, |
|
| 381 |
- hjust = 0, |
|
| 382 |
- vjust = 0, |
|
| 383 |
- gp = gpar(fill = color, col = "#FFFFFF00")) |
|
| 431 |
+ rect <- rectGrob( |
|
| 432 |
+ x = 0, |
|
| 433 |
+ y = breaks[-length(breaks)], |
|
| 434 |
+ width = unit(10, "bigpts"), |
|
| 435 |
+ height = h, |
|
| 436 |
+ hjust = 0, |
|
| 437 |
+ vjust = 0, |
|
| 438 |
+ gp = gpar(fill = color, col = "#FFFFFF00") |
|
| 439 |
+ ) |
|
| 384 | 440 |
|
| 385 |
- text <- textGrob(names(legend), |
|
| 386 |
- x = unit(14, "bigpts"), |
|
| 387 |
- y = legendPos, |
|
| 388 |
- hjust = 0, |
|
| 389 |
- gp = gpar(...)) |
|
| 441 |
+ text <- textGrob(names(legend), |
|
| 442 |
+ x = unit(14, "bigpts"), |
|
| 443 |
+ y = legendPos, |
|
| 444 |
+ hjust = 0, |
|
| 445 |
+ gp = gpar(...) |
|
| 446 |
+ ) |
|
| 390 | 447 |
|
| 391 |
- res <- grobTree(rect, text) |
|
| 448 |
+ res <- grobTree(rect, text) |
|
| 392 | 449 |
|
| 393 |
- return(res) |
|
| 450 |
+ return(res) |
|
| 394 | 451 |
} |
| 395 | 452 |
|
| 396 | 453 |
.convertAnnotations <- function(annotation, annotationColors) {
|
| 397 |
- new <- annotation |
|
| 398 |
- for (i in seq(ncol(annotation))) {
|
|
| 399 |
- a <- annotation[, i] |
|
| 400 |
- b <- annotationColors[[colnames(annotation)[i]]] |
|
| 401 |
- if (is.character(a) | is.factor(a)) {
|
|
| 402 |
- a <- as.character(a) |
|
| 403 |
- |
|
| 404 |
- if (length(setdiff(setdiff(a, NA), names(b))) > 0) {
|
|
| 405 |
- stop(sprintf("Factor levels on variable %s do not match
|
|
| 454 |
+ new <- annotation |
|
| 455 |
+ for (i in seq(ncol(annotation))) {
|
|
| 456 |
+ a <- annotation[, i] |
|
| 457 |
+ b <- annotationColors[[colnames(annotation)[i]]] |
|
| 458 |
+ if (is.character(a) | is.factor(a)) {
|
|
| 459 |
+ a <- as.character(a) |
|
| 460 |
+ |
|
| 461 |
+ if (length(setdiff(setdiff(a, NA), names(b))) > 0) {
|
|
| 462 |
+ stop(sprintf( |
|
| 463 |
+ "Factor levels on variable %s do not match |
|
| 406 | 464 |
with annotationColors", |
| 407 |
- colnames(annotation)[i])) |
|
| 408 |
- } |
|
| 409 |
- new[, i] <- b[a] |
|
| 410 |
- } else {
|
|
| 411 |
- a <- cut(a, breaks = 100) |
|
| 412 |
- new[, i] <- colorRampPalette(b)(100)[a] |
|
| 413 |
- } |
|
| 465 |
+ colnames(annotation)[i] |
|
| 466 |
+ )) |
|
| 467 |
+ } |
|
| 468 |
+ new[, i] <- b[a] |
|
| 469 |
+ } else {
|
|
| 470 |
+ a <- cut(a, breaks = 100) |
|
| 471 |
+ new[, i] <- colorRampPalette(b)(100)[a] |
|
| 414 | 472 |
} |
| 415 |
- return(as.matrix(new)) |
|
| 473 |
+ } |
|
| 474 |
+ return(as.matrix(new)) |
|
| 416 | 475 |
} |
| 417 | 476 |
|
| 418 | 477 |
.drawAnnotations <- function(convertedAnnotations, |
| 419 |
- borderColor, |
|
| 420 |
- gaps, |
|
| 421 |
- fontSize, |
|
| 422 |
- horizontal) {
|
|
| 423 |
- |
|
| 424 |
- n <- ncol(convertedAnnotations) |
|
| 425 |
- m <- nrow(convertedAnnotations) |
|
| 426 |
- |
|
| 427 |
- coordX <- .findCoordinates(m, gaps) |
|
| 428 |
- |
|
| 429 |
- x <- coordX$coord - 0.5 * coordX$size |
|
| 430 |
- |
|
| 431 |
- # y = cumsum(rep(fontSize, n)) - 4 + cumsum(rep(2, n)) |
|
| 432 |
- y <- cumsum(rep(fontSize, n)) + |
|
| 433 |
- cumsum(rep(2, n)) - |
|
| 434 |
- fontSize / 2 + 1 |
|
| 435 |
- y <- unit(y, "bigpts") |
|
| 478 |
+ borderColor, |
|
| 479 |
+ gaps, |
|
| 480 |
+ fontSize, |
|
| 481 |
+ horizontal) {
|
|
| 482 |
+ n <- ncol(convertedAnnotations) |
|
| 483 |
+ m <- nrow(convertedAnnotations) |
|
| 484 |
+ |
|
| 485 |
+ coordX <- .findCoordinates(m, gaps) |
|
| 486 |
+ |
|
| 487 |
+ x <- coordX$coord - 0.5 * coordX$size |
|
| 488 |
+ |
|
| 489 |
+ # y = cumsum(rep(fontSize, n)) - 4 + cumsum(rep(2, n)) |
|
| 490 |
+ y <- cumsum(rep(fontSize, n)) + |
|
| 491 |
+ cumsum(rep(2, n)) - |
|
| 492 |
+ fontSize / 2 + 1 |
|
| 493 |
+ y <- unit(y, "bigpts") |
|
| 494 |
+ |
|
| 495 |
+ if (horizontal) {
|
|
| 496 |
+ coord <- expand.grid(x = x, y = y) |
|
| 497 |
+ res <- rectGrob( |
|
| 498 |
+ x = coord$x, |
|
| 499 |
+ y = coord$y, |
|
| 500 |
+ width = coordX$size, |
|
| 501 |
+ height = unit(fontSize, "bigpts"), |
|