add circos.labels()

jokergoo · Jan 7, 2021 · 4a95ffe · 4a95ffe
1 parent 9ba9dd8
commit 4a95ffe
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: circlize
 Type: Package
 Title: Circular Visualization
-Version: 0.4.12.1007
+Version: 0.4.12.1008
 Date: 2021-1-7
 Author: Zuguang Gu
 Maintainer: Zuguang Gu <[email protected]>

diff --git a/NAMESPACE b/NAMESPACE
@@ -42,6 +42,7 @@ export("circos.heatmap.link")
 export("circos.info")
 export("circos.initialize")
 export("circos.initializeWithIdeogram")
+export("circos.labels")
 export("circos.lines")
 export("circos.link")
 export("circos.nested")
@@ -139,3 +140,4 @@ importFrom("stats", rnorm)
 importFrom("stats", runif)
 importFrom("utils", download.file)
 importFrom("utils", read.table, packageDescription)
+
diff --git a/NEWS b/NEWS
@@ -14,6 +14,7 @@ Changes in version 0.4.12
 * add `circos.connect()` function.
 * `circos.heatmap()`: argument `cluster` can be a clustering object.
 * `circos.heatmap()`: add `cell_width` to control the relative width of heatmap cells.
+* add `circos.labels()`.
 
 Changes in version 0.4.11
 -----------------------------------------------------------------------

diff --git a/R/circos.heatmap.R b/R/circos.heatmap.R
@@ -181,16 +181,19 @@ circos.heatmap.initialize = function(mat, split = NULL, cluster = TRUE,
 
 	if(cluster_is_dendrogram) {
 		for(se in get.all.sector.index()) {
-			cw = cell_width_list[[se]][order.dendrogram(dend)]
-			add.sector.meta.data("cell_width", cw, sector.index = se)
-			add.sector.meta.data("cell_middle", cumsum(cw) - cw/2, sector.index = se)
-
 			dend = dend_list[[se]]
+
+			od = order.dendrogram(dend)
+			cw = cell_width_list[[se]][od]
+			od2 = order(od)
+			add.sector.meta.data("cell_width", cw[od2], sector.index = se)
+			add.sector.meta.data("cell_middle", (cumsum(cw) - cw/2)[od2], sector.index = se)
+
 			dend = ComplexHeatmap::adjust_dend_by_x(dend, cumsum(cw) - cw/2)
 			add.sector.meta.data("row_dend", dend, sector.index = se)
 			add.sector.meta.data("dend", dend, sector.index = se)
-			add.sector.meta.data("row_order", order.dendrogram(dend), sector.index = se)
-			add.sector.meta.data("order", order.dendrogram(dend), sector.index = se)
+			add.sector.meta.data("row_order", od, sector.index = se)
+			add.sector.meta.data("order", od, sector.index = se)
 			if(!is.null(subset_list)) {
 				add.sector.meta.data("subset", subset_list[[se]], sector.index = se)
 			}
@@ -210,16 +213,19 @@ circos.heatmap.initialize = function(mat, split = NULL, cluster = TRUE,
 			}
 
 			for(se in get.all.sector.index()) {
-				cw = cell_width_list[[se]][order.dendrogram(dend_list[[se]])]
-				add.sector.meta.data("cell_width", cw, sector.index = se)
-				add.sector.meta.data("cell_middle", cumsum(cw) - cw/2, sector.index = se)
-
 				dend = dend_list[[se]]
+
+				od = order.dendrogram(dend)
+				cw = cell_width_list[[se]][od]
+				od2 = order(od)
+				add.sector.meta.data("cell_width", cw[od2], sector.index = se)
+				add.sector.meta.data("cell_middle", (cumsum(cw) - cw/2)[od2], sector.index = se)
+
 				dend = ComplexHeatmap::adjust_dend_by_x(dend, cumsum(cw) - cw/2)
 				add.sector.meta.data("row_dend", dend, sector.index = se)
 				add.sector.meta.data("dend", dend, sector.index = se)
-				add.sector.meta.data("row_order", order.dendrogram(dend_list[[se]]), sector.index = se)
-				add.sector.meta.data("order", order.dendrogram(dend_list[[se]]), sector.index = se)
+				add.sector.meta.data("row_order", od, sector.index = se)
+				add.sector.meta.data("order", od, sector.index = se)
 				if(!is.null(subset_list)) {
 					add.sector.meta.data("subset", subset_list[[se]], sector.index = se)
 				}
@@ -412,7 +418,8 @@ circos.heatmap = function(mat, split = NULL, col, na.col = "grey",
 				    nr = nrow(m)
 
 				    if(!is.null(rownames(m))) {
-				    	circos.text(CELL_META$cell_middle, rep(0, nr), rownames(m)[od], cex = rownames.cex[CELL_META$subset][od], 
+				    	circos.text(CELL_META$cell_middle[od], rep(0, nr), rownames(m)[od], 
+				    		cex = rownames.cex[CELL_META$subset][od], 
 				    		font = rownames.font[CELL_META$subset][od], col = rownames.col[CELL_META$subset][od],
 				    		facing = "clockwise", niceFacing = TRUE, adj = c(0, 0.5))
 				    }
@@ -469,18 +476,18 @@ circos.heatmap = function(mat, split = NULL, col, na.col = "grey",
 	    		} else {
 	    			# qqcat("@{sum(l)} white rectangles are not drawn.\n")
 	    			circos.rect(
-	    				(CELL_META$cell_middle - CELL_META$cell_width/2)[!l], 
+	    				(CELL_META$cell_middle - CELL_META$cell_width/2)[od][!l], 
 	    				(rep(nc - i, nr))[!l], 
-			            (CELL_META$cell_middle + CELL_META$cell_width/2)[!l], 
+			            (CELL_META$cell_middle + CELL_META$cell_width/2)[od][!l], 
 			            (rep(nc - i + 1, nr))[!l], 
 			            border = col_mat[, i][!l], 
 			            col = col_mat[, i][!l])
 	    		}
 	    	} else {
 		        circos.rect(
-		        	CELL_META$cell_middle - CELL_META$cell_width/2, 
+		        	(CELL_META$cell_middle - CELL_META$cell_width/2)[od], 
 		        	rep(nc - i, nr), 
-		            CELL_META$cell_middle + CELL_META$cell_width/2, 
+		            (CELL_META$cell_middle + CELL_META$cell_width/2)[od], 
 		            rep(nc - i + 1, nr), 
 		            border = col_mat[, i], col = col_mat[, i])
 		       }
@@ -518,7 +525,7 @@ circos.heatmap = function(mat, split = NULL, col, na.col = "grey",
 				    nr = nrow(m)
 
 				    if(!is.null(rownames(m))) {
-				    	circos.text(CELL_META$cell_middle, rep(1, nr), rownames(m)[od], cex = rownames.cex[CELL_META$subset][od], 
+				    	circos.text(CELL_META$cell_middle[od], rep(1, nr), rownames(m)[od], cex = rownames.cex[CELL_META$subset][od], 
 				    		font = rownames.font[CELL_META$subset][od], col = rownames.col[CELL_META$subset][od],
 				    		facing = "clockwise", niceFacing = TRUE, adj = c(1, 0.5))
 				    }

diff --git a/R/genomic.R b/R/genomic.R
@@ -2474,7 +2474,7 @@ circos.genomicHeatmap = function(
 # -facing fFacing of the labels. The value can only be ``"clockwise"`` or ``"reverse.clockwise"``.
 # -niceFacing Whether automatically adjust the facing of the labels.
 # -col Color for the labels.
-# -cex Aize of the labels.
+# -cex Size of the labels.
 # -font Font of the labels.
 # -padding Padding of the labels, the value is the ratio to the height of the label.
 # -connection_height Height of the connection track.
@@ -2583,7 +2583,7 @@ circos.genomicLabels = function(
 
 	op = circos.par("points.overflow.warning")
 	circos.par("points.overflow.warning" = FALSE)
-	side = match.arg(side)[1]
+	labels.side = side = match.arg(side)[1]
 	if(labels.side == "inside") {
 		# an empty track
 		circos.genomicTrackPlotRegion(bed2, ylim = c(0, 1), 

diff --git a/R/low_level.R b/R/low_level.R
@@ -2596,3 +2596,65 @@ circos.connect = function(x0, y0, x1, y1,
         }
     }
 }
+
+
+# == title
+# Add a label track
+#
+# == param
+# -sectors A vector of sector names.
+# -x Positions of the labels.
+# -labels A vector of labels.
+# -facing fFacing of the labels. The value can only be ``"clockwise"`` or ``"reverse.clockwise"``.
+# -niceFacing Whether automatically adjust the facing of the labels.
+# -col Color for the labels.
+# -cex Size of the labels.
+# -font Font of the labels.
+# -padding Padding of the labels, the value is the ratio to the height of the label.
+# -connection_height Height of the connection track.
+# -line_col Color for the connection lines.
+# -line_lwd Line width for the connection lines.
+# -line_lty Line type for the connectioin lines.
+# -labels_height Height of the labels track.
+# -side Side of the labels track, is it in the inside of the track where the regions are marked?
+# -labels.side Same as ``side``. It will replace ``side`` in the future versions.
+# -track.margin Bottom and top margins.
+#
+# == details
+# This function creates two tracks, one for the connection lines and one for the labels.
+#
+# If two labels are too close and overlap, this function automatically adjusts the positions of neighouring labels.
+circos.labels = function(
+    sectors, x, labels, 
+    facing = "clockwise", 
+    niceFacing = TRUE,
+    col = par("col"), 
+    cex = 0.8, 
+    font = par("font"), 
+    padding = 0.4,
+    connection_height = mm_h(5), 
+    line_col = par("col"), 
+    line_lwd = par("lwd"), 
+    line_lty = par("lty"),
+    labels_height = min(c(cm_h(1.5), max(strwidth(labels, cex = cex, font = font)))),
+    side = c("inside", "outside"), 
+    labels.side = side,
+    track.margin = circos.par("track.margin")) {
+
+    if(missing(sectors) && missing(x)) {
+        env = circos.par("__tempenv__")
+        if(identical(env$circos.heatmap.initialized, TRUE)) {
+            subset = unlist(lapply(env$sector.meta.data, function(x) x$subset))
+            x = unlist(lapply(env$sector.meta.data, function(x) x$cell_middle))
+            labels = labels[subset]
+            sectors = rep(names(env$sector.meta.data), times = sapply(env$sector.meta.data, function(x) length(x$subset)))
+        }
+    }
+    bed = data.frame(sectors, x, x)
+
+    circos.genomicLabels(bed, labels = labels, facing = facing, niceFacing = niceFacing, col = col, cex = cex,
+        font = font, padding = padding, connection_height = connection_height, line_col = line_col,
+        line_lwd = line_lwd, line_lty = line_lty, labels_height = labels_height, side = side, labels.side = labels.side,
+        track.margin = track.margin)
+}
+
diff --git a/man/circos.boxplot.Rd b/man/circos.boxplot.Rd
@@ -18,7 +18,7 @@ circos.boxplot(value, pos, outline = TRUE, box_width = 0.6,
   \item{value}{A numeric vector, a matrix or a list. If it is a matrix, boxplots are made by columns (each column is a box).}
   \item{pos}{Positions of the boxes.}
   \item{outline}{Whether to draw outliers.}
-  \item{box_width}{Width of boxes. It assumes the bars locating at \code{x = 1, 2, ...}.}
+  \item{box_width}{Width of boxes.}
   \item{col}{Filled color of boxes.}
   \item{border}{Color for the border as well as the quantile lines.}
   \item{lwd}{Line width.}

diff --git a/man/circos.genomicLabels.Rd b/man/circos.genomicLabels.Rd
@@ -34,7 +34,7 @@ circos.genomicLabels(
   \item{facing}{fFacing of the labels. The value can only be \code{"clockwise"} or \code{"reverse.clockwise"}.}
   \item{niceFacing}{Whether automatically adjust the facing of the labels.}
   \item{col}{Color for the labels.}
-  \item{cex}{Aize of the labels.}
+  \item{cex}{Size of the labels.}
   \item{font}{Font of the labels.}
   \item{padding}{Padding of the labels, the value is the ratio to the height of the label.}
   \item{connection_height}{Height of the connection track.}

diff --git a/man/circos.labels.Rd b/man/circos.labels.Rd
@@ -0,0 +1,57 @@
+\name{circos.labels}
+\alias{circos.labels}
+\title{
+Add a label track
+}
+\description{
+Add a label track
+}
+\usage{
+circos.labels(
+    sectors, x, labels,
+    facing = "clockwise",
+    niceFacing = TRUE,
+    col = par("col"),
+    cex = 0.8,
+    font = par("font"),
+    padding = 0.4,
+    connection_height = mm_h(5),
+    line_col = par("col"),
+    line_lwd = par("lwd"),
+    line_lty = par("lty"),
+    labels_height = min(c(cm_h(1.5), max(strwidth(labels, cex = cex, font = font)))),
+    side = c("inside", "outside"),
+    labels.side = side,
+    track.margin = circos.par("track.margin"))
+}
+\arguments{
+
+  \item{sectors}{A vector of sector names.}
+  \item{x}{Positions of the labels.}
+  \item{labels}{A vector of labels.}
+  \item{facing}{fFacing of the labels. The value can only be \code{"clockwise"} or \code{"reverse.clockwise"}.}
+  \item{niceFacing}{Whether automatically adjust the facing of the labels.}
+  \item{col}{Color for the labels.}
+  \item{cex}{Size of the labels.}
+  \item{font}{Font of the labels.}
+  \item{padding}{Padding of the labels, the value is the ratio to the height of the label.}
+  \item{connection_height}{Height of the connection track.}
+  \item{line_col}{Color for the connection lines.}
+  \item{line_lwd}{Line width for the connection lines.}
+  \item{line_lty}{Line type for the connectioin lines.}
+  \item{labels_height}{Height of the labels track.}
+  \item{side}{Side of the labels track, is it in the inside of the track where the regions are marked?}
+  \item{labels.side}{Same as \code{side}. It will replace \code{side} in the future versions.}
+  \item{track.margin}{Bottom and top margins.}
+
+}
+\details{
+This function creates two tracks, one for the connection lines and one for the labels.
+
+If two labels are too close and overlap, this function automatically adjusts the positions of neighouring labels.
+}
+\examples{
+# There is no example
+NULL
+
+}