KB/MB -> kb/Mb

NAMESPACE

@@ -60,6 +60,9 @@ export("circos.updatePlotRegion")
 export("circos.violin")
 export("circos.xaxis")
 export("circos.yaxis")
+export("cm_h")
+export("cm_x")
+export("cm_y")
 export("col2value")
 export("colorRamp2")
 export("convert_height")
@@ -81,6 +84,15 @@ export("get.current.track.index")
 export("getI")
 export("highlight.chromosome")
 export("highlight.sector")
+export("inch_h")
+export("inch_x")
+export("inch_y")
+export("inches_h")
+export("inches_x")
+export("inches_y")
+export("mm_h")
+export("mm_x")
+export("mm_y")
 export("posTransform.default")
 export("posTransform.text")
 export("rainfallTransform")

NEWS

@@ -13,6 +13,8 @@ Changes in version 0.4.10
 * add `circos.boxplot()` and `circos.violin()`.
 * sector index are all enforced to be character.
 * `circos.nested()`: now the graphic parameters are reordered accordingly as the `correspondance`.
+* add `mm_x()`, `mm_y()`, `mm_h()`, `cm_x()`, `cm_y()`, `cm_h()`, `inches_x()`, `inches_y()`, `inches_h()`
+  functions
 
 Changes in version 0.4.9
 -----------------------------------------------------------------------

R/genomic.R

@@ -380,9 +380,9 @@ circos.genomicAxis = function(
 
 		if(is.null(labels)) {
 			if(major.by > 1e6) {
-				major.tick.labels = paste((major.at-offset)/1000000, "MB", sep = "")
+				major.tick.labels = paste((major.at-offset)/1000000, "Mb", sep = "")
 			} else if(major.by > 1e3) {
-				major.tick.labels = paste((major.at-offset)/1000, "KB", sep = "")
+				major.tick.labels = paste((major.at-offset)/1000, "kb", sep = "")
 			} else {
 				major.tick.labels = paste((major.at-offset), "bp", sep = "")
 			}

R/utils.R

@@ -575,6 +575,8 @@ col2value = function(r, g, b, col_fun) {
 # Since in the circular plot, the aspect ratio is always 1, it does not matter this conversion
 # is applied on x direction or y direction.
 #
+# This function is mainly used in the radical direction.
+#
 # == seealso
 # `convert_x` and `convert_y` convert absolute units into a data coordinate in a specified cell.
 #
@@ -630,6 +632,9 @@ convert_length = function(x, unit = c("mm", "cm", "inches")) {
 # This function is same as `convert_length`. The reason for naming this function
 # is `convert_length` is mostely used for defining the height of tracks and track margins.
 #
+# == seealso
+# For pre-defined units, users can use `cm_h`, `mm_h` and `inches_h`.
+#
 # == author
 # Zuguang Gu <[email protected]>
 #
@@ -731,6 +736,8 @@ convert_unit_in_data_coordinate = function(x, unit = c("mm", "cm", "inches", "ca
 # A vector of numeric values which are measured in the specified data coordinate
 #
 # == seealso
+# For pre-defined units, users can use `cm_x`, `mm_x` and `inches_x`.
+#
 # `convert_y` converts on y direction.
 #
 # https://jokergoo.github.io/circlize_book/book/circular-layout.html#convert-functions
@@ -742,21 +749,21 @@ convert_unit_in_data_coordinate = function(x, unit = c("mm", "cm", "inches", "ca
 # fa = letters[1:10]
 # circos.par(cell.padding = c(0, 0, 0, 0), track.margin = c(0, 0))
 # circos.initialize(fa, xlim = cbind(rep(0, 10), runif(10, 0.5, 1.5)))
-# circos.track(ylim = c(0, 1), track.height = convert_height(5, "mm"),
+# circos.track(ylim = c(0, 1), track.height = mm_h(5),
 #     panel.fun = function(x, y) {
-#         circos.lines(c(0, 0 + convert_x(5, "mm")), c(0.5, 0.5), col = "blue")
+#         circos.lines(c(0, 0 + mm_x(5)), c(0.5, 0.5), col = "blue")
 #     })
-# circos.par(track.margin = c(0, convert_height(2, "mm")))
+# circos.par(track.margin = c(0, mm_h(2)))
 # circos.track(ylim = c(0, 1), track.height = convert_height(1, "cm"),
 #     panel.fun = function(x, y) {
 #         xcenter = get.cell.meta.data("xcenter")
-#         circos.lines(c(xcenter, xcenter), c(0, convert_y(1, "cm")), col = "red")
+#         circos.lines(c(xcenter, xcenter), c(0, cm_y(1)), col = "red")
 #     })
-# circos.par(track.margin = c(0, convert_height(5, "mm")))
-# circos.track(ylim = c(0, 1), track.height = convert_height(1, "inches"),
+# circos.par(track.margin = c(0, mm_h(5)))
+# circos.track(ylim = c(0, 1), track.height = inch_h(1),
 #     panel.fun = function(x, y) {
-#         line_length_on_x = convert_x(1*sqrt(2)/2, "cm")
-#         line_length_on_y = convert_y(1*sqrt(2)/2, "cm")
+#         line_length_on_x = cm_x(1*sqrt(2)/2)
+#         line_length_on_y = cm_y(1*sqrt(2)/2)
 #         circos.lines(c(0, line_length_on_x), c(0, line_length_on_y), col = "orange")
 #     })
 # circos.clear()
@@ -803,6 +810,8 @@ ux = function(...) {
 # A vector of numeric values which are measured in the specified data coordinate
 #
 # == seealso
+# For pre-defined units, users can use `cm_y`, `mm_y` and `inches_y`.
+#
 # `convert_x` converts on x direction.
 #
 # https://jokergoo.github.io/circlize_book/book/circular-layout.html#convert-functions
@@ -867,6 +876,223 @@ convert_unit_in_canvas_coordinate = function(x, unit = c("mm", "cm", "inches"))
     return(len)
 }
 
+# == title
+# Convert unit on x direction in data coordinate
+#
+# == param
+# -... pass to `convert_x`
+#
+# == details
+# This function is same as `convert_x` in cm unit.
+#
+# == author
+# Zuguang Gu <[email protected]>
+#
+# == example
+# # see example in `convert_x` page
+# NULL
+cm_x = function(...) {
+    convert_x(..., unit = "cm")
+}
+# == title
+# Convert unit on y direction in data coordinate
+#
+# == param
+# -... pass to `convert_y`
+#
+# == details
+# This function is same as `convert_y` in cm unit.
+#
+# == author
+# Zuguang Gu <[email protected]>
+#
+# == example
+# # see example in `convert_y` page
+# NULL
+cm_y = function(...) {
+    convert_y(..., unit = "cm")
+}
+# == title
+# Convert units
+#
+# == param
+# -... pass to `convert_length`
+#
+# == details
+# This function is same as `convert_length` in cm unit.
+#
+# == author
+# Zuguang Gu <[email protected]>
+#
+# == example
+# # see example in `convert_length` page
+# NULL
+cm_h = function(...) {
+    convert_length(..., unit = "cm")
+}
+# == title
+# Convert unit on x direction in data coordinate
+#
+# == param
+# -... pass to `convert_x`
+#
+# == details
+# This function is same as `convert_x` in mm unit.
+#
+# == author
+# Zuguang Gu <[email protected]>
+#
+# == example
+# # see example in `convert_x` page
+# NULL
+mm_x = function(...) {
+    convert_x(..., unit = "mm")
+}
+# == title
+# Convert unit on y direction in data coordinate
+#
+# == param
+# -... pass to `convert_y`
+#
+# == details
+# This function is same as `convert_y` in mm unit.
+#
+# == author
+# Zuguang Gu <[email protected]>
+#
+# == example
+# # see example in `convert_y` page
+# NULL
+mm_y = function(...) {
+    convert_y(..., unit = "mm")
+}
+# == title
+# Convert units
+#
+# == param
+# -... pass to `convert_length`
+#
+# == details
+# This function is same as `convert_length` in mm unit.
+#
+# == author
+# Zuguang Gu <[email protected]>
+#
+# == example
+# # see example in `convert_length` page
+# NULL
+mm_h = function(...) {
+    convert_length(..., unit = "mm")
+}
+# == title
+# Convert unit on x direction in data coordinate
+#
+# == param
+# -... pass to `convert_x`
+#
+# == details
+# This function is same as `convert_x` in inch unit.
+#
+# == author
+# Zuguang Gu <[email protected]>
+#
+# == example
+# # see example in `convert_x` page
+# NULL
+inches_x = function(...) {
+    convert_x(..., unit = "inches")
+}
+# == title
+# Convert unit on y direction in data coordinate
+#
+# == param
+# -... pass to `convert_y`
+#
+# == details
+# This function is same as `convert_y` in inch unit.
+#
+# == author
+# Zuguang Gu <[email protected]>
+#
+# == example
+# # see example in `convert_y` page
+# NULL
+inches_y = function(...) {
+    convert_y(..., unit = "inches")
+}
+# == title
+# Convert units
+#
+# == param
+# -... pass to `convert_length`
+#
+# == details
+# This function is same as `convert_length` in inch unit.
+#
+# == author
+# Zuguang Gu <[email protected]>
+#
+# == example
+# # see example in `convert_length` page
+# NULL
+inches_h = function(...) {
+    convert_length(..., unit = "inches")
+}
+# == title
+# Convert unit on x direction in data coordinate
+#
+# == param
+# -... pass to `convert_x`
+#
+# == details
+# This function is same as `convert_x` in inch unit.
+#
+# == author
+# Zuguang Gu <[email protected]>
+#
+# == example
+# # see example in `convert_x` page
+# NULL
+inch_x = function(...) {
+    convert_x(..., unit = "inches")
+}
+# == title
+# Convert unit on y direction in data coordinate
+#
+# == param
+# -... pass to `convert_y`
+#
+# == details
+# This function is same as `convert_y` in inch unit.
+#
+# == author
+# Zuguang Gu <[email protected]>
+#
+# == example
+# # see example in `convert_y` page
+# NULL
+inch_y = function(...) {
+    convert_y(..., unit = "inches")
+}
+# == title
+# Convert units
+#
+# == param
+# -... pass to `convert_length`
+#
+# == details
+# This function is same as `convert_length` in inch unit.
+#
+# == author
+# Zuguang Gu <[email protected]>
+#
+# == example
+# # see example in `convert_length` page
+# NULL
+inch_h = function(...) {
+    convert_length(..., unit = "inches")
+}
+
 stop_wrap = function(...) {
     x = paste0(...)
     x = paste(strwrap(x), collapse = "\n")

man/circos.genomicDensity.Rd

@@ -51,7 +51,7 @@ This function is a high-level graphical function, and it will create a new track
 load(system.file(package = "circlize", "extdata", "DMR.RData"))
 
 # rainfall
-\dontrun{
+\donttest{
 circos.initializeWithIdeogram(plotType = c("axis", "labels"))
 
 bed_list = list(DMR_hyper, DMR_hypo)

man/circos.genomicHeatmap.Rd

@@ -52,7 +52,7 @@ for the heamtaps. The heatmaps always fill the whole track.
 \url{https://jokergoo.github.io/circlize_book/book/high-level-genomic-functions.html#genomic-heatmap}
 }
 \examples{
-\dontrun{
+\donttest{
 circos.initializeWithIdeogram(plotType = c("labels", "axis"))
 bed = generateRandomBed(nr = 100, nc = 4)
 col_fun = colorRamp2(c(-1, 0, 1), c("green", "black", "red"))

man/circos.genomicLink.Rd

@@ -42,7 +42,7 @@ If you want to have more controls on links, please use \code{\link{circos.link}}
 \url{https://jokergoo.github.io/circlize_book/book/genomic-plotting-region.html#genomic-links}
 }
 \examples{
-\dontrun{
+\donttest{
 set.seed(123)
 
 bed1 = generateRandomBed(nr = 100)

man/circos.genomicRainfall.Rd

@@ -42,7 +42,7 @@ On the plot, y-axis are log10-transformed.
 \url{https://jokergoo.github.io/circlize_book/book/high-level-genomic-functions.html#genomic-density-and-rainfall-plot}
 }
 \examples{
-\dontrun{
+\donttest{
 load(system.file(package = "circlize", "extdata", "DMR.RData"))
 
 # rainfall

man/circos.genomicRect.Rd

@@ -43,7 +43,7 @@ circos.genomicRect(
 The function is a low-level graphical function and usually is put in \code{panel.fun} when using \code{\link{circos.genomicTrackPlotRegion}}.
 }
 \examples{
-\dontrun{
+\donttest{
 ############################
 ### rect matrix
 circos.par("track.height" = 0.1, cell.padding = c(0, 0, 0, 0))

man/circos.initializeWithIdeogram.Rd

@@ -44,7 +44,7 @@ The style of ideogram is almost fixed, but you can customize it with your self-s
 \url{https://jokergoo.github.io/circlize_book/book/initialize-genomic-plot.html#initialize-cytoband}
 }
 \examples{
-\dontrun{
+\donttest{
 circos.initializeWithIdeogram()
 
 cytoband.file = system.file(package = "circlize",