add fontsize settings in circos.genomicInitialize()

jokergoo · Jun 15, 2018 · a748c97 · a748c97
1 parent ad33704
commit a748c97
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Showing 5 changed files with 20 additions and 13 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,4 +1,7 @@
-export('$.CELL_META')
+S3method("$", CELL_META)
+export("$.CELL_META")
+S3method("print", CELL_META)
+export("print.CELL_META")
 export('circos.arrow')
 export('circos.axis')
 export('circos.clear')
@@ -52,7 +55,6 @@ export('highlight.chromosome')
 export('highlight.sector')
 export('posTransform.default')
 export('posTransform.text')
-export('print.CELL_META')
 export('read.chromInfo')
 export('read.cytoband')
 export('reverse.circlize')
@@ -83,8 +85,6 @@ export(uh)
 export(ux)
 export(uy)
 
-S3method("$", CELL_META)
-S3method(print, CELL_META)
 import(graphics)
 importFrom("GlobalOptions", setGlobalOptions)
 importFrom("colorspace", HLS)

diff --git a/NEWS b/NEWS
@@ -1,11 +1,11 @@
 Changes in version 0.4.5
--------------------------------------------------------------------------
-
-* update denpendency of GlobalOptions package
+------------------------------------------------------------------------
+* add `axis.labels.cex` and `labels.cex` in `circos.genomicInitialize()`.
 
 Changes in version 0.4.4
 -------------------------------------------------------------------------
 
+* update denpendency of GlobalOptions package
 * `genomicDensity()`: add `chr.len` argument.
 
 Changes in version 0.4.3

diff --git a/R/genomic.R b/R/genomic.R
@@ -134,6 +134,8 @@ circos.genomicIdeogram = function(cytoband = system.file(package = "circlize",
 # -plotType     If it is not ``NULL``, there will create a new track containing axis and names for sectors.
 #               This argument controls which part should be drawn, ``axis`` for genomic axis and ``labels`` for chromosome names
 # -tickLabelsStartFromZero Whether axis tick labels start from 0? This will only affect the axis labels while not affect x-values in cells.
+# -axis.labels.cex the font size for the axis tick labels.
+# -labels.cex   the font size for the labels.
 # -track.height If ``PlotType`` is not ``NULL``, height of the annotation track.
 # -...          Pass to `circos.initialize`
 #
@@ -146,7 +148,8 @@ circos.genomicIdeogram = function(cytoband = system.file(package = "circlize",
 #
 # For more details on initializing genomic plot, please refer to the vignettes.
 circos.genomicInitialize = function(data, sector.names = NULL, major.by = NULL,
-	plotType = c("axis", "labels"), tickLabelsStartFromZero = TRUE, 
+	plotType = c("axis", "labels"), tickLabelsStartFromZero = TRUE,
+	axis.labels.cex = 0.4*par("cex"), labels.cex = par("cex"), 
 	track.height = convert_height(3, "mm"), ...) {
 
 	if(is.factor(data[[1]])) {
@@ -217,12 +220,12 @@ circos.genomicInitialize = function(data, sector.names = NULL, major.by = NULL,
 
 
 				if(all(c("axis", "labels") %in% plotType)) {
-					circos.axis(h = 0, major.at = major.at, labels = major.tick.labels, labels.cex = 0.4*par("cex"))
-					circos.text(mean(xlim), 1.3, labels = sector.names[sector.index], cex = par("cex"), adj = c(0.5, 0), niceFacing = TRUE)
+					circos.axis(h = 0, major.at = major.at, labels = major.tick.labels, labels.cex = axis.labels.cex)
+					circos.text(mean(xlim), 1.3, labels = sector.names[sector.index], cex = labels.cex, adj = c(0.5, 0), niceFacing = TRUE)
 				} else if("labels" %in% plotType) {
-					circos.text(mean(xlim), 0, labels = sector.names[sector.index], cex = par("cex"), adj = c(0.5, 0), niceFacing = TRUE)
+					circos.text(mean(xlim), 0, labels = sector.names[sector.index], cex = labels.cex, adj = c(0.5, 0), niceFacing = TRUE)
 				} else if("axis" %in% plotType) {
-					circos.axis(h = 0, major.at = major.at, labels = major.tick.labels, labels.cex = 0.4*par("cex"))
+					circos.axis(h = 0, major.at = major.at, labels = major.tick.labels, labels.cex = axis.labels.cex)
 				}
  			}
 		)

diff --git a/man/circos.genomicInitialize.rd b/man/circos.genomicInitialize.rd
@@ -9,6 +9,7 @@ Initialize circular plot with any genomic data
 \usage{
 circos.genomicInitialize(data, sector.names = NULL, major.by = NULL,
     plotType = c("axis", "labels"), tickLabelsStartFromZero = TRUE,
+    axis.labels.cex = 0.4*par("cex"), labels.cex = par("cex"),
     track.height = convert_height(3, "mm"), ...)
 }
 \arguments{
@@ -18,6 +19,8 @@ circos.genomicInitialize(data, sector.names = NULL, major.by = NULL,
   \item{major.by}{Increment of major ticks. It is calculated automatically if the value is not set (about every 10 degrees there is a major tick).}
   \item{plotType}{If it is not \code{NULL}, there will create a new track containing axis and names for sectors. This argument controls which part should be drawn, \code{axis} for genomic axis and \code{labels} for chromosome names}
   \item{tickLabelsStartFromZero}{Whether axis tick labels start from 0? This will only affect the axis labels while not affect x-values in cells.}
+  \item{axis.labels.cex}{the font size for the axis tick labels.}
+  \item{labels.cex}{the font size for the labels.}
   \item{track.height}{If \code{PlotType} is not \code{NULL}, height of the annotation track.}
   \item{...}{Pass to \code{\link{circos.initialize}}}
 

diff --git a/man/circos.par.rd b/man/circos.par.rd
@@ -15,7 +15,8 @@ circos.par(..., RESET = FALSE, READ.ONLY = NULL, LOCAL = FALSE, ADD = FALSE)
   \item{RESET}{reset to default values}
   \item{READ.ONLY}{please ignore}
   \item{LOCAL}{please ignore}
-  \item{ADD}{please ignore}
+  \item{ADD}{please ignore}
+
 }
 \details{
 Global parameters for the circular layout. Currently supported parameters are: