updat docs

jokergoo · Apr 13, 2020 · 175d97c · 175d97c
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commit 175d97c
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Showing 4 changed files with 8 additions and 2 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: ComplexHeatmap
 Type: Package
 Title: Make Complex Heatmaps
 Version: 2.3.4
-Date: 2020-04-03
+Date: 2020-04-13
 Author: Zuguang Gu
 Maintainer: Zuguang Gu <[email protected]>
 Depends: R (>= 3.1.2), methods, grid, graphics, stats, grDevices

diff --git a/NEWS b/NEWS
@@ -3,6 +3,7 @@ CHANGES in VERSION 2.3.4
 * add `alter_graphic()` to automatically generate alteration graphic functions.
 * add `label`/`annotation_label` argument in `SingleAnnotation()` and `HeatmapAnnotation()`.
 * improved the subsetting methods for `comb_mat` class
+* rewrite `smartAlign2()`
 
 ========================
 

diff --git a/man/anno_zoom.Rd b/man/anno_zoom.Rd
@@ -11,7 +11,7 @@ anno_zoom(align_to, panel_fun = function(index, nm = NULL) { grid.rect() },
     which = c("column", "row"), side = ifelse(which == "column", "top", "right"),
     size = NULL, gap = unit(1, "mm"),
     link_width = unit(5, "mm"), link_height = link_width, link_gp = gpar(),
-    extend = unit(0, "mm"), width = NULL, height = NULL)
+    extend = unit(0, "mm"), width = NULL, height = NULL, internal_line = TRUE)
 }
 \arguments{
 
@@ -27,6 +27,7 @@ anno_zoom(align_to, panel_fun = function(index, nm = NULL) { grid.rect() },
   \item{extend}{By default, the region for the labels has the same width (if it is a column annotation) or same height (if it is a row annotation) as the heatmap. The size can be extended by this options. The value can be a proportion number or  a \code{\link[grid]{unit}} object. The length can be either one or two.}
   \item{width}{Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.}
   \item{height}{Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.}
+  \item{internal_line}{Internally used.}
 
 }
 \details{

diff --git a/tests/test-AnnotationFunction.R b/tests/test-AnnotationFunction.R
@@ -486,6 +486,10 @@ panel_fun = function(index, nm) {
 anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun)
 draw(anno, index = 1:100, test = "anno_zoom")
 
+anno = anno_zoom(align_to = list(a = which(fa == "a")), which = "row", panel_fun = panel_fun)
+draw(anno, index = 1:100, test = "anno_zoom")
+
+
 panel_fun = function(index, nm) {
 	grid.rect(gp = gpar(fill = "grey", col = NA))
 	grid.text(nm)