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jokergoo · Oct 20, 2019 · 7abc442 · 7abc442
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diff --git a/NEWS b/NEWS
@@ -1,7 +1,7 @@
 CHANGES in VERSION 2.1.1
 
 * `Heatmap()`: give error when heatmap has empty string as its name.
-* `anno_mark()`: text positions are correctly calcualted now with rotations.
+* `anno_mark()`: text positions are correctly calculated now with rotations.
 
 ========================
 

diff --git a/man/AdditiveUnit-class.Rd b/man/AdditiveUnit-class.Rd
@@ -15,4 +15,5 @@ method and the \code{\%v\%v} method so that above three classes can be appended
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/AdditiveUnit.Rd b/man/AdditiveUnit.Rd
@@ -26,4 +26,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/AnnotationFunction-class.Rd b/man/AnnotationFunction-class.Rd
@@ -22,4 +22,5 @@ See \code{\link{AnnotationFunction}} constructor for details.
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/ColorMapping-class.Rd b/man/ColorMapping-class.Rd
@@ -26,4 +26,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/ComplexHeatmap-package.Rd b/man/ComplexHeatmap-package.Rd
@@ -40,4 +40,5 @@ The complete reference of ComplexHeatmap package is available at \url{http://jok
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/Heatmap-class.Rd b/man/Heatmap-class.Rd
@@ -30,4 +30,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/Heatmap.Rd b/man/Heatmap.Rd
@@ -206,4 +206,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/HeatmapAnnotation-class.Rd b/man/HeatmapAnnotation-class.Rd
@@ -25,4 +25,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/HeatmapAnnotation.Rd b/man/HeatmapAnnotation.Rd
@@ -80,4 +80,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/HeatmapList-class.Rd b/man/HeatmapList-class.Rd
@@ -27,4 +27,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/HeatmapList.Rd b/man/HeatmapList.Rd
@@ -26,4 +26,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/Legends.Rd b/man/Legends.Rd
@@ -26,4 +26,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/SingleAnnotation-class.Rd b/man/SingleAnnotation-class.Rd
@@ -28,4 +28,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/add.AdditiveUnit.Rd b/man/add.AdditiveUnit.Rd
@@ -40,4 +40,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/add_heatmap-Heatmap-method.Rd b/man/add_heatmap-Heatmap-method.Rd
@@ -28,4 +28,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/add_heatmap-HeatmapAnnotation-method.Rd b/man/add_heatmap-HeatmapAnnotation-method.Rd
@@ -28,4 +28,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/add_heatmap-HeatmapList-method.Rd b/man/add_heatmap-HeatmapList-method.Rd
@@ -28,4 +28,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/adjust_heatmap_list-HeatmapList-method.Rd b/man/adjust_heatmap_list-HeatmapList-method.Rd
@@ -1,5 +1,6 @@
 \name{adjust_heatmap_list-HeatmapList-method}
 \alias{adjust_heatmap_list,HeatmapList-method}
+\alias{adjust_heatmap_list}
 \title{
 Adjust Heatmap List
 }
@@ -23,8 +24,8 @@ This function is only for internal use.
 \author{
 Zuguang Gu <z.gu@dkfz.de>
 }
-\alias{adjust_heatmap_list}
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/anno_link.Rd b/man/anno_link.Rd
@@ -20,4 +20,5 @@ anno_link(...)
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/anno_mark.Rd b/man/anno_mark.Rd
@@ -10,7 +10,7 @@ Link annotation with labels
 anno_mark(at, labels, which = c("column", "row"),
     side = ifelse(which == "column", "top", "right"),
     lines_gp = gpar(), labels_gp = gpar(),
-    labels_rot = ifelse(which == "column", 90, 0), padding = 0.5,
+    labels_rot = ifelse(which == "column", 90, 0), padding = unit(1, "mm"),
     link_width = unit(5, "mm"), link_height = link_width,
     link_gp = lines_gp,
     extend = unit(0, "mm"))

diff --git a/man/anno_oncoprint_barplot.Rd b/man/anno_oncoprint_barplot.Rd
@@ -34,4 +34,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/annotation_legend_size-HeatmapList-method.Rd b/man/annotation_legend_size-HeatmapList-method.Rd
@@ -1,5 +1,6 @@
 \name{annotation_legend_size-HeatmapList-method}
 \alias{annotation_legend_size,HeatmapList-method}
+\alias{annotation_legend_size}
 \title{
 Size of the Annotation Legends
 }
@@ -27,8 +28,8 @@ A \code{\link[grid]{unit}} object.
 \author{
 Zuguang Gu <z.gu@dkfz.de>
 }
-\alias{annotation_legend_size}
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/color_mapping_legend-ColorMapping-method.Rd b/man/color_mapping_legend-ColorMapping-method.Rd
@@ -1,5 +1,6 @@
 \name{color_mapping_legend-ColorMapping-method}
 \alias{color_mapping_legend,ColorMapping-method}
+\alias{color_mapping_legend}
 \title{
 Draw Legend Based on Color Mapping
 }
@@ -65,8 +66,8 @@ A \code{\link{Legends-class}} object.
 \author{
 Zuguang Gu <z.gu@dkfz.de>
 }
-\alias{color_mapping_legend}
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/columnAnnotation.Rd b/man/columnAnnotation.Rd
@@ -29,4 +29,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/component_height-Heatmap-method.Rd b/man/component_height-Heatmap-method.Rd
@@ -31,4 +31,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/component_height-HeatmapList-method.Rd b/man/component_height-HeatmapList-method.Rd
@@ -24,4 +24,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/component_width-Heatmap-method.Rd b/man/component_width-Heatmap-method.Rd
@@ -30,4 +30,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/component_width-HeatmapList-method.Rd b/man/component_width-HeatmapList-method.Rd
@@ -27,4 +27,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/copy_all-AnnotationFunction-method.Rd b/man/copy_all-AnnotationFunction-method.Rd
@@ -26,4 +26,5 @@ The environment is at \code{object@var_env}.
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/copy_all-SingleAnnotation-method.Rd b/man/copy_all-SingleAnnotation-method.Rd
@@ -21,4 +21,5 @@ it calls \code{\link{copy_all,AnnotationFunction-method}} to hard copy the varia
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/decorate_column_dend.Rd b/man/decorate_column_dend.Rd
@@ -27,4 +27,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/decorate_column_names.Rd b/man/decorate_column_names.Rd
@@ -27,4 +27,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/decorate_column_title.Rd b/man/decorate_column_title.Rd
@@ -27,4 +27,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/decorate_row_dend.Rd b/man/decorate_row_dend.Rd
@@ -27,4 +27,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/decorate_row_names.Rd b/man/decorate_row_names.Rd
@@ -27,4 +27,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/decorate_row_title.Rd b/man/decorate_row_title.Rd
@@ -27,4 +27,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/default_get_type.Rd b/man/default_get_type.Rd
@@ -20,4 +20,5 @@ It recognizes following separators: \code{;:,|}.
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/dend_heights.Rd b/man/dend_heights.Rd
@@ -17,4 +17,5 @@ dend_heights(x)
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/dendrogramGrob.Rd b/man/dendrogramGrob.Rd
@@ -28,4 +28,5 @@ A \code{\link{grob}} object which is contructed by \code{\link[grid:grid.segment
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/dim.Heatmap.Rd b/man/dim.Heatmap.Rd
@@ -17,4 +17,5 @@ Dimension of the Heatmap
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/draw-AnnotationFunction-method.Rd b/man/draw-AnnotationFunction-method.Rd
@@ -28,4 +28,5 @@ which is generally for testing purpose.
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/draw-Heatmap-method.Rd b/man/draw-Heatmap-method.Rd
@@ -33,4 +33,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/draw-HeatmapAnnotation-method.Rd b/man/draw-HeatmapAnnotation-method.Rd
@@ -30,4 +30,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/draw-HeatmapList-method.Rd b/man/draw-HeatmapList-method.Rd
@@ -183,4 +183,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/draw-SingleAnnotation-method.Rd b/man/draw-SingleAnnotation-method.Rd
@@ -29,4 +29,5 @@ Zuguang Gu <[email protected]>
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/draw_annotation-Heatmap-method.Rd b/man/draw_annotation-Heatmap-method.Rd
@@ -1,5 +1,6 @@
 \name{draw_annotation-Heatmap-method}
 \alias{draw_annotation,Heatmap-method}
+\alias{draw_annotation}
 \title{
 Draw Heatmap Annotations on the Heatmap
 }
@@ -30,8 +31,8 @@ This function returns no value.
 \author{
 Zuguang Gu <z.gu@dkfz.de>
 }
-\alias{draw_annotation}
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/draw_annotation_legend-HeatmapList-method.Rd b/man/draw_annotation_legend-HeatmapList-method.Rd
@@ -1,5 +1,6 @@
 \name{draw_annotation_legend-HeatmapList-method}
 \alias{draw_annotation_legend,HeatmapList-method}
+\alias{draw_annotation_legend}
 \title{
 Draw legends for All Annotations
 }
@@ -31,8 +32,8 @@ This function returns no value.
 \author{
 Zuguang Gu <z.gu@dkfz.de>
 }
-\alias{draw_annotation_legend}
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/draw_dend-Heatmap-method.Rd b/man/draw_dend-Heatmap-method.Rd
@@ -1,5 +1,6 @@
 \name{draw_dend-Heatmap-method}
 \alias{draw_dend,Heatmap-method}
+\alias{draw_dend}
 \title{
 Draw Heatmap Dendrograms
 }
@@ -33,8 +34,8 @@ This function returns no value.
 \author{
 Zuguang Gu <z.gu@dkfz.de>
 }
-\alias{draw_dend}
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/draw_dimnames-Heatmap-method.Rd b/man/draw_dimnames-Heatmap-method.Rd
@@ -1,5 +1,6 @@
 \name{draw_dimnames-Heatmap-method}
 \alias{draw_dimnames,Heatmap-method}
+\alias{draw_dimnames}
 \title{
 Draw row names or column names
 }
@@ -29,8 +30,8 @@ This function returns no value.
 \author{
 Zuguang Gu <z.gu@dkfz.de>
 }
-\alias{draw_dimnames}
 \examples{
 # There is no example
 NULL
+
 }
diff --git a/man/draw_heatmap_body-Heatmap-method.Rd b/man/draw_heatmap_body-Heatmap-method.Rd
@@ -1,5 +1,6 @@
 \name{draw_heatmap_body-Heatmap-method}
 \alias{draw_heatmap_body,Heatmap-method}
+\alias{draw_heatmap_body}
 \title{
 Draw Heatmap Body
 }
@@ -28,8 +29,8 @@ This function returns no value.
 \author{
 Zuguang Gu <z.gu@dkfz.de>
 }
-\alias{draw_heatmap_body}
 \examples{
 # There is no example
 NULL
+
 }
-Original file line number
+Diff line change
@@ Expand Up @@
     \examples{
     # There is no example
     NULL
     }