From c94e524a23998d739077e3d031c6ea97fb14a4fc Mon Sep 17 00:00:00 2001 From: Zuguang Gu Date: Wed, 15 Jun 2022 12:42:56 +0200 Subject: [PATCH] add max_density argument --- R/00_S4_generic_methods.R | 46 +++++++++---------- R/AnnotationFunction-function.R | 25 ++++++++-- man/AdditiveUnit-class.Rd | 1 + man/AdditiveUnit.Rd | 1 + man/AnnotationFunction-class.Rd | 1 + man/ColorMapping-class.Rd | 1 + man/ComplexHeatmap-package.Rd | 1 + man/Extract.gridtext.Rd | 1 + man/Heatmap-class.Rd | 1 + man/Heatmap.Rd | 1 + man/HeatmapAnnotation-class.Rd | 1 + man/HeatmapAnnotation.Rd | 1 + man/HeatmapList-class.Rd | 1 + man/HeatmapList.Rd | 1 + man/Legends.Rd | 1 + man/SingleAnnotation-class.Rd | 1 + man/add.AdditiveUnit.Rd | 1 + man/add_heatmap-Heatmap-method.Rd | 1 + man/add_heatmap-HeatmapAnnotation-method.Rd | 1 + man/add_heatmap-HeatmapList-method.Rd | 1 + man/adjust_heatmap_list-HeatmapList-method.Rd | 3 +- man/anno_density.Rd | 3 +- man/anno_link.Rd | 1 + man/anno_oncoprint_barplot.Rd | 1 + man/anno_textbox.Rd | 2 +- ...notation_legend_size-HeatmapList-method.Rd | 3 +- man/attach_annotation-Heatmap-method.Rd | 2 +- man/bin_genome.Rd | 1 + ...olor_mapping_legend-ColorMapping-method.Rd | 3 +- man/columnAnnotation.Rd | 1 + man/complement_size.Rd | 1 + man/component_height-Heatmap-method.Rd | 1 + man/component_height-HeatmapList-method.Rd | 1 + man/component_width-Heatmap-method.Rd | 1 + man/component_width-HeatmapList-method.Rd | 1 + man/component_width-dispatch.Rd | 2 +- man/copy_all-AnnotationFunction-method.Rd | 1 + man/copy_all-SingleAnnotation-method.Rd | 1 + man/decorate_column_dend.Rd | 1 + man/decorate_column_names.Rd | 1 + man/decorate_column_title.Rd | 1 + man/decorate_row_dend.Rd | 1 + man/decorate_row_names.Rd | 1 + man/decorate_row_title.Rd | 1 + man/default_get_type.Rd | 1 + man/dend_heights.Rd | 1 + man/dendrogramGrob.Rd | 1 + man/dim.Heatmap.Rd | 1 + man/draw-AnnotationFunction-method.Rd | 1 + man/draw-Heatmap-method.Rd | 1 + man/draw-HeatmapAnnotation-method.Rd | 1 + man/draw-HeatmapList-method.Rd | 1 + man/draw-SingleAnnotation-method.Rd | 1 + man/draw-dispatch.Rd | 6 +-- man/draw_annotation-Heatmap-method.Rd | 3 +- ...aw_annotation_legend-HeatmapList-method.Rd | 3 +- man/draw_dend-Heatmap-method.Rd | 3 +- man/draw_dimnames-Heatmap-method.Rd | 3 +- man/draw_heatmap_body-Heatmap-method.Rd | 3 +- man/draw_heatmap_legend-HeatmapList-method.Rd | 3 +- man/draw_heatmap_list-HeatmapList-method.Rd | 3 +- man/draw_title-Heatmap-method.Rd | 1 + man/draw_title-HeatmapList-method.Rd | 1 + ...r_mapping_list-HeatmapAnnotation-method.Rd | 3 +- ...end_param_list-HeatmapAnnotation-method.Rd | 3 +- man/grid.textbox.Rd | 1 + man/heatmap_legend_size-HeatmapList-method.Rd | 3 +- man/height.Heatmap.Rd | 1 + man/height.HeatmapAnnotation.Rd | 1 + man/height.HeatmapList.Rd | 1 + man/height.SingleAnnotation.Rd | 1 + man/heightAssign.AnnotationFunction.Rd | 1 + man/heightAssign.HeatmapAnnotation.Rd | 1 + man/heightAssign.SingleAnnotation.Rd | 1 + man/heightDetails.annotation_axis.Rd | 1 + man/heightDetails.legend.Rd | 1 + man/heightDetails.legend_body.Rd | 1 + man/heightDetails.packed_legends.Rd | 1 + man/heightDetails.textbox.Rd | 1 + man/ht_global_opt.Rd | 1 + man/ht_size.Rd | 1 + man/length.HeatmapAnnotation.Rd | 1 + man/length.HeatmapList.Rd | 1 + man/list_components.Rd | 1 + man/make_column_cluster-Heatmap-method.Rd | 3 +- man/make_layout-Heatmap-method.Rd | 1 + man/make_layout-HeatmapList-method.Rd | 1 + man/make_row_cluster-Heatmap-method.Rd | 3 +- man/map_to_colors-ColorMapping-method.Rd | 2 +- man/names.HeatmapList.Rd | 1 + man/ncol.Heatmap.Rd | 1 + man/nobs.HeatmapAnnotation.Rd | 1 + man/nobs.SingleAnnotation.Rd | 1 + man/normalize_comb_mat.Rd | 1 + man/nrow.Heatmap.Rd | 1 + man/oncoPrint.Rd | 1 + man/order.comb_mat.Rd | 1 + man/pct_v_pct.Rd | 1 + man/pheatmap.Rd | 1 + man/plot.Heatmap.Rd | 1 + man/plot.HeatmapAnnotation.Rd | 1 + man/plot.HeatmapList.Rd | 1 + man/prepare-Heatmap-method.Rd | 3 +- man/print.comb_mat.Rd | 1 + man/re_size-HeatmapAnnotation-method.Rd | 3 +- man/rowAnnotation.Rd | 1 + man/row_anno_barplot.Rd | 1 + man/row_anno_boxplot.Rd | 1 + man/row_anno_density.Rd | 1 + man/row_anno_histogram.Rd | 1 + man/row_anno_points.Rd | 1 + man/row_anno_text.Rd | 1 + man/set_component_height-Heatmap-method.Rd | 3 +- man/set_component_width-Heatmap-method.Rd | 3 +- man/show-AnnotationFunction-method.Rd | 1 + man/show-ColorMapping-method.Rd | 1 + man/show-Heatmap-method.Rd | 1 + man/show-HeatmapAnnotation-method.Rd | 1 + man/show-HeatmapList-method.Rd | 1 + man/show-SingleAnnotation-method.Rd | 1 + man/show-dispatch.Rd | 6 +-- man/size.HeatmapAnnotation.Rd | 1 + man/size.SingleAnnotation.Rd | 1 + man/sizeAssign.HeatmapAnnotation.Rd | 1 + man/sizeAssign.SingleAnnotation.Rd | 1 + man/str.comb_mat.Rd | 1 + man/subset_matrix_by_row.Rd | 1 + man/subset_no.Rd | 1 + man/subset_vector.Rd | 1 + man/summary.Heatmap.Rd | 1 + man/summary.HeatmapList.Rd | 1 + man/unify_mat_list.Rd | 1 + man/upset_left_annotation.Rd | 1 + man/upset_right_annotation.Rd | 1 + man/upset_top_annotation.Rd | 1 + man/width.Heatmap.Rd | 1 + man/width.HeatmapAnnotation.Rd | 1 + man/width.HeatmapList.Rd | 1 + man/width.SingleAnnotation.Rd | 1 + man/widthAssign.AnnotationFunction.Rd | 1 + man/widthAssign.HeatmapAnnotation.Rd | 1 + man/widthAssign.SingleAnnotation.Rd | 1 + man/widthDetails.annotation_axis.Rd | 1 + man/widthDetails.legend.Rd | 1 + man/widthDetails.legend_body.Rd | 1 + man/widthDetails.packed_legends.Rd | 1 + man/widthDetails.textbox.Rd | 1 + 147 files changed, 212 insertions(+), 58 deletions(-) diff --git a/R/00_S4_generic_methods.R b/R/00_S4_generic_methods.R index 822839f1..b15fdd85 100755 --- a/R/00_S4_generic_methods.R +++ b/R/00_S4_generic_methods.R @@ -1,32 +1,32 @@ -setGeneric('re_size', function(object, ...) standardGeneric('re_size')) -setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list')) -setGeneric('component_height', function(object, ...) standardGeneric('component_height')) -setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster')) -setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend')) -setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation')) -setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list')) setGeneric('draw_title', function(object, ...) standardGeneric('draw_title')) +setGeneric('row_order', function(object, ...) standardGeneric('row_order')) +setGeneric('row_dend', function(object, ...) standardGeneric('row_dend')) +setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body')) setGeneric('make_layout', function(object, ...) standardGeneric('make_layout')) +setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list')) +setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend')) +setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend')) setGeneric('draw', function(object, ...) standardGeneric('draw')) setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend')) +setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend')) +setGeneric('prepare', function(object, ...) standardGeneric('prepare')) +setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list')) +setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster')) +setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation')) +setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster')) +setGeneric('component_height', function(object, ...) standardGeneric('component_height')) +setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap')) +setGeneric('column_order', function(object, ...) standardGeneric('column_order')) +setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width')) +setGeneric('component_width', function(object, ...) standardGeneric('component_width')) +setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames')) setGeneric('column_dend', function(object, ...) standardGeneric('column_dend')) +setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation')) +setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list')) +setGeneric('copy_all', function(object, ...) standardGeneric('copy_all')) +setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height')) setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size')) -setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body')) setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors')) -setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster')) +setGeneric('re_size', function(object, ...) standardGeneric('re_size')) setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size')) -setGeneric('component_width', function(object, ...) standardGeneric('component_width')) -setGeneric('copy_all', function(object, ...) standardGeneric('copy_all')) -setGeneric('column_order', function(object, ...) standardGeneric('column_order')) -setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list')) -setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend')) -setGeneric('prepare', function(object, ...) standardGeneric('prepare')) -setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames')) setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list')) -setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height')) -setGeneric('row_order', function(object, ...) standardGeneric('row_order')) -setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation')) -setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend')) -setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width')) -setGeneric('row_dend', function(object, ...) standardGeneric('row_dend')) -setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap')) diff --git a/R/AnnotationFunction-function.R b/R/AnnotationFunction-function.R index e07aa09e..f2565891 100644 --- a/R/AnnotationFunction-function.R +++ b/R/AnnotationFunction-function.R @@ -1958,6 +1958,8 @@ anno_histogram = function(x, which = c("column", "row"), n_breaks = 11, # -type Type of graphics to represent density distribution. "lines" for normal density plot; "violine" for violin plot # and "heatmap" for heatmap visualization of density distribution. # -xlim Range on x-axis. +# -max_density Maximal density values in the plot. Normally you don't need to manually set it, but when you have multiple density annotations +# and you want to compare between them, you should manually set this argument to make density distributions are in a same scale. # -heatmap_colors A vector of colors for interpolating density values. # -joyplot_scale Relative height of density distribution. A value higher than 1 increases the height of the density # distribution and the plot will represented as so-called "joyplot". @@ -1986,7 +1988,7 @@ anno_histogram = function(x, which = c("column", "row"), n_breaks = 11, # heatmap_colors = c("white", "orange")) # draw(anno, test = "heatmap, colors") anno_density = function(x, which = c("column", "row"), - type = c("lines", "violin", "heatmap"), xlim = NULL, + type = c("lines", "violin", "heatmap"), xlim = NULL, max_density = NULL, heatmap_colors = rev(brewer.pal(name = "RdYlBu", n = 11)), joyplot_scale = 1, border = TRUE, gp = gpar(fill = "#CCCCCC"), axis = TRUE, axis_param = default_axis_param(which), @@ -2044,16 +2046,29 @@ anno_density = function(x, which = c("column", "row"), if(type == "lines") { xscale = xscale + c(-0.025, 0.025)*(xscale[2] - xscale[1]) - yscale = c(0, max(unlist(density_y))) + if(is.null(max_density)) { + yscale = c(0, max(unlist(density_y))) + } else { + yscale = c(0, max_density) + } yscale[2] = yscale[2]*1.05 } else if(type == "violin") { xscale = xscale + c(-0.025, 0.025)*(xscale[2] - xscale[1]) - yscale = max(unlist(density_y)) + if(is.null(max_density)) { + yscale = max(unlist(density_y)) + } else { + yscale = max_density + } yscale = c(-yscale*1.05, yscale*1.05) } else if(type == "heatmap") { yscale = c(0, 1) - min_y = min(unlist(density_y)) - max_y = max(unlist(density_y)) + if(is.null(max_density)) { + min_y = min(unlist(density_y)) + max_y = max(unlist(density_y)) + } else { + min_y = 0 + max_y = max_density + } col_fun = colorRamp2(seq(min_y, max_y, length.out = length(heatmap_colors)), heatmap_colors) } diff --git a/man/AdditiveUnit-class.Rd b/man/AdditiveUnit-class.Rd index dbf27962..807d82dc 100644 --- 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 index d2fa1bab..31bd2bd7 100644 --- a/man/AdditiveUnit.Rd +++ b/man/AdditiveUnit.Rd @@ -26,4 +26,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/AnnotationFunction-class.Rd b/man/AnnotationFunction-class.Rd index 9125bec9..f053cfe8 100644 --- 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 index 64b92ef5..0f4da901 100644 --- a/man/ColorMapping-class.Rd +++ b/man/ColorMapping-class.Rd @@ -26,4 +26,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/ComplexHeatmap-package.Rd b/man/ComplexHeatmap-package.Rd index 7f21420e..387073bc 100644 --- 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/Extract.gridtext.Rd b/man/Extract.gridtext.Rd index 29257edc..61a7f27d 100644 --- a/man/Extract.gridtext.Rd +++ b/man/Extract.gridtext.Rd @@ -22,4 +22,5 @@ Internally used. \examples{ # There is no example NULL + } diff --git a/man/Heatmap-class.Rd b/man/Heatmap-class.Rd index 4feff7f6..b3161770 100644 --- a/man/Heatmap-class.Rd +++ b/man/Heatmap-class.Rd @@ -30,4 +30,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/Heatmap.Rd b/man/Heatmap.Rd index d27be4a4..d222242a 100644 --- a/man/Heatmap.Rd +++ b/man/Heatmap.Rd @@ -212,4 +212,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/HeatmapAnnotation-class.Rd b/man/HeatmapAnnotation-class.Rd index a975dde1..f1fbd84d 100644 --- a/man/HeatmapAnnotation-class.Rd +++ b/man/HeatmapAnnotation-class.Rd @@ -25,4 +25,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/HeatmapAnnotation.Rd b/man/HeatmapAnnotation.Rd index fa7d119b..a0501872 100644 --- a/man/HeatmapAnnotation.Rd +++ b/man/HeatmapAnnotation.Rd @@ -84,4 +84,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/HeatmapList-class.Rd b/man/HeatmapList-class.Rd index 80d00025..40241060 100644 --- a/man/HeatmapList-class.Rd +++ b/man/HeatmapList-class.Rd @@ -27,4 +27,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/HeatmapList.Rd b/man/HeatmapList.Rd index b7844f15..8c4e504a 100644 --- a/man/HeatmapList.Rd +++ b/man/HeatmapList.Rd @@ -26,4 +26,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/Legends.Rd b/man/Legends.Rd index 05fa9028..64ad1e93 100644 --- a/man/Legends.Rd +++ b/man/Legends.Rd @@ -26,4 +26,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/SingleAnnotation-class.Rd b/man/SingleAnnotation-class.Rd index c58f52ce..e788fa34 100644 --- a/man/SingleAnnotation-class.Rd +++ b/man/SingleAnnotation-class.Rd @@ -28,4 +28,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/add.AdditiveUnit.Rd b/man/add.AdditiveUnit.Rd index f5a550d4..c96c7791 100644 --- a/man/add.AdditiveUnit.Rd +++ b/man/add.AdditiveUnit.Rd @@ -40,4 +40,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/add_heatmap-Heatmap-method.Rd b/man/add_heatmap-Heatmap-method.Rd index a9b95ee9..b41a1191 100644 --- a/man/add_heatmap-Heatmap-method.Rd +++ b/man/add_heatmap-Heatmap-method.Rd @@ -28,4 +28,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/add_heatmap-HeatmapAnnotation-method.Rd b/man/add_heatmap-HeatmapAnnotation-method.Rd index 83d56644..bf7f3db3 100644 --- a/man/add_heatmap-HeatmapAnnotation-method.Rd +++ b/man/add_heatmap-HeatmapAnnotation-method.Rd @@ -28,4 +28,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/add_heatmap-HeatmapList-method.Rd b/man/add_heatmap-HeatmapList-method.Rd index 302482df..006f0750 100644 --- a/man/add_heatmap-HeatmapList-method.Rd +++ b/man/add_heatmap-HeatmapList-method.Rd @@ -28,4 +28,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/adjust_heatmap_list-HeatmapList-method.Rd b/man/adjust_heatmap_list-HeatmapList-method.Rd index 3289eb88..e7fecfca 100644 --- 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 } -\alias{adjust_heatmap_list} \examples{ # There is no example NULL + } diff --git a/man/anno_density.Rd b/man/anno_density.Rd index 6338d3f8..f1b8cd46 100644 --- a/man/anno_density.Rd +++ b/man/anno_density.Rd @@ -8,7 +8,7 @@ Density Annotation } \usage{ anno_density(x, which = c("column", "row"), - type = c("lines", "violin", "heatmap"), xlim = NULL, + type = c("lines", "violin", "heatmap"), xlim = NULL, max_density = NULL, heatmap_colors = rev(brewer.pal(name = "RdYlBu", n = 11)), joyplot_scale = 1, border = TRUE, gp = gpar(fill = "#CCCCCC"), axis = TRUE, axis_param = default_axis_param(which), @@ -20,6 +20,7 @@ anno_density(x, which = c("column", "row"), \item{which}{Whether it is a column annotation or a row annotation?} \item{type}{Type of graphics to represent density distribution. "lines" for normal density plot; "violine" for violin plot and "heatmap" for heatmap visualization of density distribution.} \item{xlim}{Range on x-axis.} + \item{max_density}{Maximal density values in the plot. Normally you don't need to manually set it, but when you have multiple density annotations and you want to compare between them, you should manually set this argument to make density distributions are in a same scale.} \item{heatmap_colors}{A vector of colors for interpolating density values.} \item{joyplot_scale}{Relative height of density distribution. A value higher than 1 increases the height of the density distribution and the plot will represented as so-called "joyplot".} \item{border}{Wether draw borders of the annotation region?} diff --git a/man/anno_link.Rd b/man/anno_link.Rd index 598e2b0b..c8b7643f 100644 --- a/man/anno_link.Rd +++ b/man/anno_link.Rd @@ -20,4 +20,5 @@ This function is the same as \code{\link{anno_zoom}}. It links subsets of rows o \examples{ # There is no example NULL + } diff --git a/man/anno_oncoprint_barplot.Rd b/man/anno_oncoprint_barplot.Rd index 3377e1f3..8ffa2d99 100644 --- a/man/anno_oncoprint_barplot.Rd +++ b/man/anno_oncoprint_barplot.Rd @@ -36,4 +36,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/anno_textbox.Rd b/man/anno_textbox.Rd index 5926e124..8e6454e8 100644 --- a/man/anno_textbox.Rd +++ b/man/anno_textbox.Rd @@ -12,7 +12,7 @@ anno_textbox(align_to, text, background_gp = gpar(fill = "#DDDDDD", col = "#AAAA } \arguments{ - \item{align_to}{It controls how the text boxes are aligned to the heatmap rows. The value can be a categorical vector which have the same length as heatmap rows, or a list of row indices.} + \item{align_to}{It controls how the text boxes are aligned to the heatmap rows. The value can be a categorical vector which have the same length as heatmap rows, or a list of row indices. It does not necessarily include all row indices.} \item{text}{The corresponding texts. The value should be a list of texts. To control graphics parameters of texts in the boxes, The value of \code{text} can also be set as a list of data frames where the first column contains the text, from the second column contains graphics parameters for each text. The column names should be "col", "fontsize", "fontfamily" and "fontface".} \item{background_gp}{Graphics for the background.} \item{which}{Only "row" is allowed.} diff --git a/man/annotation_legend_size-HeatmapList-method.Rd b/man/annotation_legend_size-HeatmapList-method.Rd index 7f3002e2..1de0f7c0 100644 --- 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 } -\alias{annotation_legend_size} \examples{ # There is no example NULL + } diff --git a/man/attach_annotation-Heatmap-method.Rd b/man/attach_annotation-Heatmap-method.Rd index 8b69339f..cd554608 100644 --- a/man/attach_annotation-Heatmap-method.Rd +++ b/man/attach_annotation-Heatmap-method.Rd @@ -1,5 +1,6 @@ \name{attach_annotation-Heatmap-method} \alias{attach_annotation,Heatmap-method} +\alias{attach_annotation} \title{ Attach heatmap annotations to the heatmap } @@ -28,4 +29,3 @@ ha2 = HeatmapAnnotation(bar = letters[1:10]) ht = attach_annotation(ht, ha2) ht } -\alias{attach_annotation} diff --git a/man/bin_genome.Rd b/man/bin_genome.Rd index 6e78c507..8bc52c73 100644 --- a/man/bin_genome.Rd +++ b/man/bin_genome.Rd @@ -23,4 +23,5 @@ A \code{\link[GenomicRanges:GRanges-class]{GRanges}} object of the genomic bins. \examples{ # There is no example NULL + } diff --git a/man/color_mapping_legend-ColorMapping-method.Rd b/man/color_mapping_legend-ColorMapping-method.Rd index f9a88bff..0b206a65 100644 --- 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 } @@ -69,8 +70,8 @@ A \code{\link{Legends-class}} object. \author{ Zuguang Gu } -\alias{color_mapping_legend} \examples{ # There is no example NULL + } diff --git a/man/columnAnnotation.Rd b/man/columnAnnotation.Rd index d3f94203..ff0474bb 100644 --- a/man/columnAnnotation.Rd +++ b/man/columnAnnotation.Rd @@ -29,4 +29,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/complement_size.Rd b/man/complement_size.Rd index 0fa1082d..e335f830 100644 --- a/man/complement_size.Rd +++ b/man/complement_size.Rd @@ -20,4 +20,5 @@ If there is no complement set, it returns zero. \examples{ # There is no example NULL + } diff --git a/man/component_height-Heatmap-method.Rd b/man/component_height-Heatmap-method.Rd index 8f0880a6..bbad76e2 100644 --- a/man/component_height-Heatmap-method.Rd +++ b/man/component_height-Heatmap-method.Rd @@ -31,4 +31,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/component_height-HeatmapList-method.Rd b/man/component_height-HeatmapList-method.Rd index 02bb44ff..5bdb6cb3 100644 --- a/man/component_height-HeatmapList-method.Rd +++ b/man/component_height-HeatmapList-method.Rd @@ -24,4 +24,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/component_width-Heatmap-method.Rd b/man/component_width-Heatmap-method.Rd index 80ba5db3..22d7583f 100644 --- a/man/component_width-Heatmap-method.Rd +++ b/man/component_width-Heatmap-method.Rd @@ -30,4 +30,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/component_width-HeatmapList-method.Rd b/man/component_width-HeatmapList-method.Rd index 9e2e7e91..b2150ac0 100644 --- a/man/component_width-HeatmapList-method.Rd +++ b/man/component_width-HeatmapList-method.Rd @@ -27,4 +27,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/component_width-dispatch.Rd b/man/component_width-dispatch.Rd index f1ae2f46..ebab483f 100644 --- a/man/component_width-dispatch.Rd +++ b/man/component_width-dispatch.Rd @@ -10,8 +10,8 @@ Method dispatch page for \code{component_width}. \code{component_width} can be dispatched on following classes: \itemize{ -\item \code{\link{component_width,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method \item \code{\link{component_width,Heatmap-method}}, \code{\link{Heatmap-class}} class method +\item \code{\link{component_width,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method } } \examples{ diff --git a/man/copy_all-AnnotationFunction-method.Rd b/man/copy_all-AnnotationFunction-method.Rd index c1733cba..c24c4d10 100644 --- 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 index 0e01307c..d4bf7054 100644 --- 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 index e8119b83..2f6d014a 100644 --- a/man/decorate_column_dend.Rd +++ b/man/decorate_column_dend.Rd @@ -27,4 +27,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/decorate_column_names.Rd b/man/decorate_column_names.Rd index 2a2d5198..0774b107 100644 --- a/man/decorate_column_names.Rd +++ b/man/decorate_column_names.Rd @@ -27,4 +27,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/decorate_column_title.Rd b/man/decorate_column_title.Rd index ab6ea341..01b4464a 100644 --- a/man/decorate_column_title.Rd +++ b/man/decorate_column_title.Rd @@ -27,4 +27,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/decorate_row_dend.Rd b/man/decorate_row_dend.Rd index 3b6c6bde..75a2febf 100644 --- a/man/decorate_row_dend.Rd +++ b/man/decorate_row_dend.Rd @@ -27,4 +27,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/decorate_row_names.Rd b/man/decorate_row_names.Rd index 6b656109..499c00e5 100644 --- a/man/decorate_row_names.Rd +++ b/man/decorate_row_names.Rd @@ -27,4 +27,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/decorate_row_title.Rd b/man/decorate_row_title.Rd index 6c4f2a19..7e3c2e0e 100644 --- a/man/decorate_row_title.Rd +++ b/man/decorate_row_title.Rd @@ -27,4 +27,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/default_get_type.Rd b/man/default_get_type.Rd index da6b22cf..e822e95c 100644 --- 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 index 35439e08..7e760617 100644 --- 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 index 4495fdef..3a824805 100644 --- 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 index 0fa8e730..b34150a0 100644 --- 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 index 8c6cb33f..4718b0d4 100644 --- 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 index b791a3fb..1b29c05a 100644 --- a/man/draw-Heatmap-method.Rd +++ b/man/draw-Heatmap-method.Rd @@ -33,4 +33,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/draw-HeatmapAnnotation-method.Rd b/man/draw-HeatmapAnnotation-method.Rd index b332f2a9..b1c8714b 100644 --- a/man/draw-HeatmapAnnotation-method.Rd +++ b/man/draw-HeatmapAnnotation-method.Rd @@ -30,4 +30,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/draw-HeatmapList-method.Rd b/man/draw-HeatmapList-method.Rd index 6f093d24..13d2e454 100644 --- a/man/draw-HeatmapList-method.Rd +++ b/man/draw-HeatmapList-method.Rd @@ -209,4 +209,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/draw-SingleAnnotation-method.Rd b/man/draw-SingleAnnotation-method.Rd index 28b66a74..d8e3b8b0 100644 --- a/man/draw-SingleAnnotation-method.Rd +++ b/man/draw-SingleAnnotation-method.Rd @@ -29,4 +29,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/draw-dispatch.Rd b/man/draw-dispatch.Rd index 019f09d8..5de7a65f 100644 --- a/man/draw-dispatch.Rd +++ b/man/draw-dispatch.Rd @@ -10,12 +10,12 @@ Method dispatch page for \code{draw}. \code{draw} can be dispatched on following classes: \itemize{ -\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method -\item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method -\item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method \item \code{\link{draw,Legends-method}}, \code{\link{Legends-class}} class method \item \code{\link{draw,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method \item \code{\link{draw,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method +\item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method +\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method +\item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method } } \examples{ diff --git a/man/draw_annotation-Heatmap-method.Rd b/man/draw_annotation-Heatmap-method.Rd index a2e52510..fbf957fb 100644 --- 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 } -\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 index 0754ce58..030cc9f7 100644 --- 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 } -\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 index aaa8f33e..762046dc 100644 --- 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 } -\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 index 00a34581..b2afe6e9 100644 --- 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 } -\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 index 395277d6..715626b4 100644 --- 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 } -\alias{draw_heatmap_body} \examples{ # There is no example NULL + } diff --git a/man/draw_heatmap_legend-HeatmapList-method.Rd b/man/draw_heatmap_legend-HeatmapList-method.Rd index 0d11751d..d8b98a5d 100644 --- a/man/draw_heatmap_legend-HeatmapList-method.Rd +++ b/man/draw_heatmap_legend-HeatmapList-method.Rd @@ -1,5 +1,6 @@ \name{draw_heatmap_legend-HeatmapList-method} \alias{draw_heatmap_legend,HeatmapList-method} +\alias{draw_heatmap_legend} \title{ Draw legends for All Heatmaps } @@ -32,8 +33,8 @@ This function returns no value. \author{ Zuguang Gu } -\alias{draw_heatmap_legend} \examples{ # There is no example NULL + } diff --git a/man/draw_heatmap_list-HeatmapList-method.Rd b/man/draw_heatmap_list-HeatmapList-method.Rd index 2b8bc139..9d009965 100644 --- a/man/draw_heatmap_list-HeatmapList-method.Rd +++ b/man/draw_heatmap_list-HeatmapList-method.Rd @@ -1,5 +1,6 @@ \name{draw_heatmap_list-HeatmapList-method} \alias{draw_heatmap_list,HeatmapList-method} +\alias{draw_heatmap_list} \title{ Draw the List of Heatmaps } @@ -25,8 +26,8 @@ This function returns no value. \author{ Zuguang Gu } -\alias{draw_heatmap_list} \examples{ # There is no example NULL + } diff --git a/man/draw_title-Heatmap-method.Rd b/man/draw_title-Heatmap-method.Rd index 6702399d..2bb60fad 100644 --- a/man/draw_title-Heatmap-method.Rd +++ b/man/draw_title-Heatmap-method.Rd @@ -32,4 +32,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/draw_title-HeatmapList-method.Rd b/man/draw_title-HeatmapList-method.Rd index 59600ddd..6648a097 100644 --- a/man/draw_title-HeatmapList-method.Rd +++ b/man/draw_title-HeatmapList-method.Rd @@ -30,4 +30,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/get_color_mapping_list-HeatmapAnnotation-method.Rd b/man/get_color_mapping_list-HeatmapAnnotation-method.Rd index 3320bc12..be483545 100644 --- a/man/get_color_mapping_list-HeatmapAnnotation-method.Rd +++ b/man/get_color_mapping_list-HeatmapAnnotation-method.Rd @@ -1,5 +1,6 @@ \name{get_color_mapping_list-HeatmapAnnotation-method} \alias{get_color_mapping_list,HeatmapAnnotation-method} +\alias{get_color_mapping_list} \title{ Get a List of ColorMapping objects } @@ -25,8 +26,8 @@ A list of \code{\link{ColorMapping-class}} objects or an empty list. \author{ Zuguang Gu } -\alias{get_color_mapping_list} \examples{ # There is no example NULL + } diff --git a/man/get_legend_param_list-HeatmapAnnotation-method.Rd b/man/get_legend_param_list-HeatmapAnnotation-method.Rd index 3e0c68e9..d0f80254 100644 --- a/man/get_legend_param_list-HeatmapAnnotation-method.Rd +++ b/man/get_legend_param_list-HeatmapAnnotation-method.Rd @@ -1,5 +1,6 @@ \name{get_legend_param_list-HeatmapAnnotation-method} \alias{get_legend_param_list,HeatmapAnnotation-method} +\alias{get_legend_param_list} \title{ Get a List of Annotation Legend Parameters } @@ -25,8 +26,8 @@ A list. \author{ Zuguang Gu } -\alias{get_legend_param_list} \examples{ # There is no example NULL + } diff --git a/man/grid.textbox.Rd b/man/grid.textbox.Rd index 3d1acff5..71720c0b 100644 --- a/man/grid.textbox.Rd +++ b/man/grid.textbox.Rd @@ -24,4 +24,5 @@ All details can be found in the help page of \code{\link{textbox_grob}}. \examples{ # There is no example NULL + } diff --git a/man/heatmap_legend_size-HeatmapList-method.Rd b/man/heatmap_legend_size-HeatmapList-method.Rd index 587a240b..da8b2af0 100644 --- a/man/heatmap_legend_size-HeatmapList-method.Rd +++ b/man/heatmap_legend_size-HeatmapList-method.Rd @@ -1,5 +1,6 @@ \name{heatmap_legend_size-HeatmapList-method} \alias{heatmap_legend_size,HeatmapList-method} +\alias{heatmap_legend_size} \title{ Size of the Heatmap Legends } @@ -27,8 +28,8 @@ A \code{\link[grid]{unit}} object. \author{ Zuguang Gu } -\alias{heatmap_legend_size} \examples{ # There is no example NULL + } diff --git a/man/height.Heatmap.Rd b/man/height.Heatmap.Rd index 2a5ab323..289f5f0a 100644 --- a/man/height.Heatmap.Rd +++ b/man/height.Heatmap.Rd @@ -18,4 +18,5 @@ Height of the Heatmap \examples{ # There is no example NULL + } diff --git a/man/height.HeatmapAnnotation.Rd b/man/height.HeatmapAnnotation.Rd index 098f74f0..13807944 100644 --- a/man/height.HeatmapAnnotation.Rd +++ b/man/height.HeatmapAnnotation.Rd @@ -21,4 +21,5 @@ Internally used. \examples{ # There is no example NULL + } diff --git a/man/height.HeatmapList.Rd b/man/height.HeatmapList.Rd index 38938e35..7ade1068 100644 --- a/man/height.HeatmapList.Rd +++ b/man/height.HeatmapList.Rd @@ -18,4 +18,5 @@ Height of the Heatmap List \examples{ # There is no example NULL + } diff --git a/man/height.SingleAnnotation.Rd b/man/height.SingleAnnotation.Rd index 074cc597..84ec7732 100644 --- a/man/height.SingleAnnotation.Rd +++ b/man/height.SingleAnnotation.Rd @@ -21,4 +21,5 @@ Internally used. \examples{ # There is no example NULL + } diff --git a/man/heightAssign.AnnotationFunction.Rd b/man/heightAssign.AnnotationFunction.Rd index feabb869..ea6c78a7 100644 --- a/man/heightAssign.AnnotationFunction.Rd +++ b/man/heightAssign.AnnotationFunction.Rd @@ -23,4 +23,5 @@ Internally used. \examples{ # There is no example NULL + } diff --git a/man/heightAssign.HeatmapAnnotation.Rd b/man/heightAssign.HeatmapAnnotation.Rd index 0e7e6732..640f5654 100644 --- a/man/heightAssign.HeatmapAnnotation.Rd +++ b/man/heightAssign.HeatmapAnnotation.Rd @@ -23,4 +23,5 @@ Internally used. \examples{ # There is no example NULL + } diff --git a/man/heightAssign.SingleAnnotation.Rd b/man/heightAssign.SingleAnnotation.Rd index e9681dee..aefc9e42 100644 --- a/man/heightAssign.SingleAnnotation.Rd +++ b/man/heightAssign.SingleAnnotation.Rd @@ -23,4 +23,5 @@ Internally used. \examples{ # There is no example NULL + } diff --git a/man/heightDetails.annotation_axis.Rd b/man/heightDetails.annotation_axis.Rd index e9fd4bc9..a0b19507 100644 --- a/man/heightDetails.annotation_axis.Rd +++ b/man/heightDetails.annotation_axis.Rd @@ -20,4 +20,5 @@ The physical height of the grob can be get by \code{convertWidth(grobHeight(axis \examples{ # There is no example NULL + } diff --git a/man/heightDetails.legend.Rd b/man/heightDetails.legend.Rd index 716864e3..6c0bd601 100644 --- a/man/heightDetails.legend.Rd +++ b/man/heightDetails.legend.Rd @@ -17,4 +17,5 @@ Grob height for packed_legends \examples{ # There is no example NULL + } diff --git a/man/heightDetails.legend_body.Rd b/man/heightDetails.legend_body.Rd index c1ef66ad..5c35138c 100644 --- a/man/heightDetails.legend_body.Rd +++ b/man/heightDetails.legend_body.Rd @@ -17,4 +17,5 @@ Grob height for legend_body \examples{ # There is no example NULL + } diff --git a/man/heightDetails.packed_legends.Rd b/man/heightDetails.packed_legends.Rd index 44990531..6617ec1e 100644 --- a/man/heightDetails.packed_legends.Rd +++ b/man/heightDetails.packed_legends.Rd @@ -17,4 +17,5 @@ Grob height for packed_legends \examples{ # There is no example NULL + } diff --git a/man/heightDetails.textbox.Rd b/man/heightDetails.textbox.Rd index f963ceaf..2dfcff8a 100644 --- a/man/heightDetails.textbox.Rd +++ b/man/heightDetails.textbox.Rd @@ -20,4 +20,5 @@ A \code{\link[grid]{unit}} object. \examples{ # There is no example NULL + } diff --git a/man/ht_global_opt.Rd b/man/ht_global_opt.Rd index 81226d29..57ee224c 100644 --- a/man/ht_global_opt.Rd +++ b/man/ht_global_opt.Rd @@ -25,4 +25,5 @@ will also be sychronized in \code{\link{ht_opt}}. \examples{ # There is no example NULL + } diff --git a/man/ht_size.Rd b/man/ht_size.Rd index 16ead9dc..8bf941d9 100644 --- a/man/ht_size.Rd +++ b/man/ht_size.Rd @@ -20,4 +20,5 @@ A list of two elements: width and height. \examples{ # There is no example NULL + } diff --git a/man/length.HeatmapAnnotation.Rd b/man/length.HeatmapAnnotation.Rd index 9c600289..fcbff61d 100644 --- a/man/length.HeatmapAnnotation.Rd +++ b/man/length.HeatmapAnnotation.Rd @@ -17,4 +17,5 @@ Number of Annotations \examples{ # There is no example NULL + } diff --git a/man/length.HeatmapList.Rd b/man/length.HeatmapList.Rd index 64510c7b..961cf9f6 100644 --- a/man/length.HeatmapList.Rd +++ b/man/length.HeatmapList.Rd @@ -17,4 +17,5 @@ Length of the HeatmapList object \examples{ # There is no example NULL + } diff --git a/man/list_components.Rd b/man/list_components.Rd index 8f5bd266..1909701a 100644 --- a/man/list_components.Rd +++ b/man/list_components.Rd @@ -20,4 +20,5 @@ A vector of viewport names. \examples{ # There is no example NULL + } diff --git a/man/make_column_cluster-Heatmap-method.Rd b/man/make_column_cluster-Heatmap-method.Rd index 7c545b57..a35149b5 100644 --- a/man/make_column_cluster-Heatmap-method.Rd +++ b/man/make_column_cluster-Heatmap-method.Rd @@ -1,5 +1,6 @@ \name{make_column_cluster-Heatmap-method} \alias{make_column_cluster,Heatmap-method} +\alias{make_column_cluster} \title{ Make Cluster on Columns } @@ -28,8 +29,8 @@ A \code{\link{Heatmap-class}} object. \author{ Zuguang Gu } -\alias{make_column_cluster} \examples{ # There is no example NULL + } diff --git a/man/make_layout-Heatmap-method.Rd b/man/make_layout-Heatmap-method.Rd index 126fad38..13154698 100644 --- a/man/make_layout-Heatmap-method.Rd +++ b/man/make_layout-Heatmap-method.Rd @@ -32,4 +32,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/make_layout-HeatmapList-method.Rd b/man/make_layout-HeatmapList-method.Rd index 8a6c6865..94c5b28c 100644 --- a/man/make_layout-HeatmapList-method.Rd +++ b/man/make_layout-HeatmapList-method.Rd @@ -155,4 +155,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/make_row_cluster-Heatmap-method.Rd b/man/make_row_cluster-Heatmap-method.Rd index 5d246776..e4c53232 100644 --- a/man/make_row_cluster-Heatmap-method.Rd +++ b/man/make_row_cluster-Heatmap-method.Rd @@ -1,5 +1,6 @@ \name{make_row_cluster-Heatmap-method} \alias{make_row_cluster,Heatmap-method} +\alias{make_row_cluster} \title{ Make Cluster on Rows } @@ -27,8 +28,8 @@ A \code{\link{Heatmap-class}} object. \author{ Zuguang Gu } -\alias{make_row_cluster} \examples{ # There is no example NULL + } diff --git a/man/map_to_colors-ColorMapping-method.Rd b/man/map_to_colors-ColorMapping-method.Rd index e56109fb..18859158 100644 --- a/man/map_to_colors-ColorMapping-method.Rd +++ b/man/map_to_colors-ColorMapping-method.Rd @@ -1,5 +1,6 @@ \name{map_to_colors-ColorMapping-method} \alias{map_to_colors,ColorMapping-method} +\alias{map_to_colors} \title{ Map Values to Colors } @@ -34,4 +35,3 @@ col_fun = colorRamp2(c(0, 1), c("white", "red")) cm = ColorMapping(col_fun = col_fun) map_to_colors(cm, runif(10)) } -\alias{map_to_colors} diff --git a/man/names.HeatmapList.Rd b/man/names.HeatmapList.Rd index 5dc578ef..9106d390 100644 --- a/man/names.HeatmapList.Rd +++ b/man/names.HeatmapList.Rd @@ -17,4 +17,5 @@ Names of the heatmaps/annotations \examples{ # There is no example NULL + } diff --git a/man/ncol.Heatmap.Rd b/man/ncol.Heatmap.Rd index 6deed520..b214c8c7 100644 --- a/man/ncol.Heatmap.Rd +++ b/man/ncol.Heatmap.Rd @@ -17,4 +17,5 @@ Number of Columns in the Heatmap \examples{ # There is no example NULL + } diff --git a/man/nobs.HeatmapAnnotation.Rd b/man/nobs.HeatmapAnnotation.Rd index 723238e0..89d4a813 100644 --- a/man/nobs.HeatmapAnnotation.Rd +++ b/man/nobs.HeatmapAnnotation.Rd @@ -22,4 +22,5 @@ it returns \code{NA}. \examples{ # There is no example NULL + } diff --git a/man/nobs.SingleAnnotation.Rd b/man/nobs.SingleAnnotation.Rd index 7064daf1..2e34dc41 100644 --- a/man/nobs.SingleAnnotation.Rd +++ b/man/nobs.SingleAnnotation.Rd @@ -21,4 +21,5 @@ It returns the \code{n} slot of the annotaton function. If it does not exist, it \examples{ # There is no example NULL + } diff --git a/man/normalize_comb_mat.Rd b/man/normalize_comb_mat.Rd index 1bb37be0..753b339f 100644 --- a/man/normalize_comb_mat.Rd +++ b/man/normalize_comb_mat.Rd @@ -24,4 +24,5 @@ The sets (by \code{\link{set_name}}) from all combination matrice should be the \examples{ # There is no example NULL + } diff --git a/man/nrow.Heatmap.Rd b/man/nrow.Heatmap.Rd index 2d1b9148..4b29d347 100644 --- a/man/nrow.Heatmap.Rd +++ b/man/nrow.Heatmap.Rd @@ -17,4 +17,5 @@ Number of Rows in the Heatmap \examples{ # There is no example NULL + } diff --git a/man/oncoPrint.Rd b/man/oncoPrint.Rd index e304507e..b24776d4 100644 --- a/man/oncoPrint.Rd +++ b/man/oncoPrint.Rd @@ -95,4 +95,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/order.comb_mat.Rd b/man/order.comb_mat.Rd index 3fe83ff3..0a0c9755 100644 --- a/man/order.comb_mat.Rd +++ b/man/order.comb_mat.Rd @@ -23,4 +23,5 @@ by the combination matrix. \examples{ # There is no example NULL + } diff --git a/man/pct_v_pct.Rd b/man/pct_v_pct.Rd index 2280ed5b..dc98d8fe 100644 --- a/man/pct_v_pct.Rd +++ b/man/pct_v_pct.Rd @@ -39,4 +39,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/pheatmap.Rd b/man/pheatmap.Rd index f50257ef..25bfb543 100644 --- a/man/pheatmap.Rd +++ b/man/pheatmap.Rd @@ -148,4 +148,5 @@ A \code{\link{Heatmap-class}} object. \examples{ # There is no example NULL + } diff --git a/man/plot.Heatmap.Rd b/man/plot.Heatmap.Rd index 85cfe7a4..50d17ddc 100644 --- a/man/plot.Heatmap.Rd +++ b/man/plot.Heatmap.Rd @@ -18,4 +18,5 @@ Draw heatmap \examples{ # There is no example NULL + } diff --git a/man/plot.HeatmapAnnotation.Rd b/man/plot.HeatmapAnnotation.Rd index 6c8472c7..ad967202 100644 --- a/man/plot.HeatmapAnnotation.Rd +++ b/man/plot.HeatmapAnnotation.Rd @@ -18,4 +18,5 @@ Draw heatmap annotations \examples{ # There is no example NULL + } diff --git a/man/plot.HeatmapList.Rd b/man/plot.HeatmapList.Rd index c864ab43..f8bf93d5 100644 --- a/man/plot.HeatmapList.Rd +++ b/man/plot.HeatmapList.Rd @@ -18,4 +18,5 @@ Draw heatmap \examples{ # There is no example NULL + } diff --git a/man/prepare-Heatmap-method.Rd b/man/prepare-Heatmap-method.Rd index cbe75aa6..a1031ce4 100644 --- a/man/prepare-Heatmap-method.Rd +++ b/man/prepare-Heatmap-method.Rd @@ -1,5 +1,6 @@ \name{prepare-Heatmap-method} \alias{prepare,Heatmap-method} +\alias{prepare} \title{ Prepare the Heatmap } @@ -33,8 +34,8 @@ The \code{\link{Heatmap-class}} object. \author{ Zuguang Gu } -\alias{prepare} \examples{ # There is no example NULL + } diff --git a/man/print.comb_mat.Rd b/man/print.comb_mat.Rd index c8c99d0a..c85f5faf 100644 --- a/man/print.comb_mat.Rd +++ b/man/print.comb_mat.Rd @@ -18,4 +18,5 @@ Print the comb_mat Object \examples{ # There is no example NULL + } diff --git a/man/re_size-HeatmapAnnotation-method.Rd b/man/re_size-HeatmapAnnotation-method.Rd index cff1bf38..e6f2bee1 100644 --- a/man/re_size-HeatmapAnnotation-method.Rd +++ b/man/re_size-HeatmapAnnotation-method.Rd @@ -1,5 +1,6 @@ \name{re_size-HeatmapAnnotation-method} \alias{re_size,HeatmapAnnotation-method} +\alias{re_size} \title{ Resize the Width or Height of Heatmap Annotations } @@ -41,8 +42,8 @@ The basic rules are (take \code{height} and \code{annotation_height} for example and \code{simple_anno_size} is disabled. 6. If \code{simple_anno_size_adjust} is \code{FALSE}, the size of the simple annotations will not change. } -\alias{re_size} \examples{ # There is no example NULL + } diff --git a/man/rowAnnotation.Rd b/man/rowAnnotation.Rd index 9465b74d..9acc2fdb 100644 --- a/man/rowAnnotation.Rd +++ b/man/rowAnnotation.Rd @@ -29,4 +29,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/row_anno_barplot.Rd b/man/row_anno_barplot.Rd index 3ef9a033..34c0e4bf 100644 --- a/man/row_anno_barplot.Rd +++ b/man/row_anno_barplot.Rd @@ -25,4 +25,5 @@ See help page of \code{\link{anno_barplot}}. \examples{ # There is no example NULL + } diff --git a/man/row_anno_boxplot.Rd b/man/row_anno_boxplot.Rd index 0f231a1d..7d7ecab5 100644 --- a/man/row_anno_boxplot.Rd +++ b/man/row_anno_boxplot.Rd @@ -25,4 +25,5 @@ See help page of \code{\link{anno_boxplot}}. \examples{ # There is no example NULL + } diff --git a/man/row_anno_density.Rd b/man/row_anno_density.Rd index 076b7aed..10e78863 100644 --- a/man/row_anno_density.Rd +++ b/man/row_anno_density.Rd @@ -25,4 +25,5 @@ See help page of \code{\link{anno_density}}. \examples{ # There is no example NULL + } diff --git a/man/row_anno_histogram.Rd b/man/row_anno_histogram.Rd index 9c587ba4..2eb4a6d0 100644 --- a/man/row_anno_histogram.Rd +++ b/man/row_anno_histogram.Rd @@ -25,4 +25,5 @@ See help page of \code{\link{anno_histogram}}. \examples{ # There is no example NULL + } diff --git a/man/row_anno_points.Rd b/man/row_anno_points.Rd index 5eabb8cb..bed8f4bd 100644 --- a/man/row_anno_points.Rd +++ b/man/row_anno_points.Rd @@ -25,4 +25,5 @@ See help page of \code{\link{anno_points}}. \examples{ # There is no example NULL + } diff --git a/man/row_anno_text.Rd b/man/row_anno_text.Rd index b86a3a30..e2c385d6 100644 --- a/man/row_anno_text.Rd +++ b/man/row_anno_text.Rd @@ -25,4 +25,5 @@ See help page of \code{\link{anno_text}}. \examples{ # There is no example NULL + } diff --git a/man/set_component_height-Heatmap-method.Rd b/man/set_component_height-Heatmap-method.Rd index c23b70eb..d5ef5478 100644 --- a/man/set_component_height-Heatmap-method.Rd +++ b/man/set_component_height-Heatmap-method.Rd @@ -1,5 +1,6 @@ \name{set_component_height-Heatmap-method} \alias{set_component_height,Heatmap-method} +\alias{set_component_height} \title{ Set Height of Heatmap Component } @@ -29,8 +30,8 @@ The \code{\link{Heatmap-class}} object. \author{ Zuguang Gu } -\alias{set_component_height} \examples{ # There is no example NULL + } diff --git a/man/set_component_width-Heatmap-method.Rd b/man/set_component_width-Heatmap-method.Rd index 852dd83b..7cf4869d 100644 --- a/man/set_component_width-Heatmap-method.Rd +++ b/man/set_component_width-Heatmap-method.Rd @@ -1,5 +1,6 @@ \name{set_component_width-Heatmap-method} \alias{set_component_width,Heatmap-method} +\alias{set_component_width} \title{ Set Width of Heatmap Component } @@ -28,8 +29,8 @@ The \code{\link{Heatmap-class}} object. \author{ Zuguang Gu } -\alias{set_component_width} \examples{ # There is no example NULL + } diff --git a/man/show-AnnotationFunction-method.Rd b/man/show-AnnotationFunction-method.Rd index cc633a4a..0150b04b 100644 --- a/man/show-AnnotationFunction-method.Rd +++ b/man/show-AnnotationFunction-method.Rd @@ -17,4 +17,5 @@ Print the AnnotationFunction Object \examples{ # There is no example NULL + } diff --git a/man/show-ColorMapping-method.Rd b/man/show-ColorMapping-method.Rd index 65abc2b5..a89400cb 100644 --- a/man/show-ColorMapping-method.Rd +++ b/man/show-ColorMapping-method.Rd @@ -23,4 +23,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/show-Heatmap-method.Rd b/man/show-Heatmap-method.Rd index 363b7af0..ca1ce84c 100644 --- a/man/show-Heatmap-method.Rd +++ b/man/show-Heatmap-method.Rd @@ -27,4 +27,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/show-HeatmapAnnotation-method.Rd b/man/show-HeatmapAnnotation-method.Rd index 3f2ade1d..d6ba8fa7 100644 --- a/man/show-HeatmapAnnotation-method.Rd +++ b/man/show-HeatmapAnnotation-method.Rd @@ -23,4 +23,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/show-HeatmapList-method.Rd b/man/show-HeatmapList-method.Rd index 2cb351fc..2b40e7a0 100644 --- a/man/show-HeatmapList-method.Rd +++ b/man/show-HeatmapList-method.Rd @@ -24,4 +24,5 @@ This function returns no value. \examples{ # There is no example NULL + } diff --git a/man/show-SingleAnnotation-method.Rd b/man/show-SingleAnnotation-method.Rd index c3e39de8..e5ba81ca 100644 --- a/man/show-SingleAnnotation-method.Rd +++ b/man/show-SingleAnnotation-method.Rd @@ -23,4 +23,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/show-dispatch.Rd b/man/show-dispatch.Rd index a996f8a5..4ab41050 100644 --- a/man/show-dispatch.Rd +++ b/man/show-dispatch.Rd @@ -10,12 +10,12 @@ Method dispatch page for \code{show}. \code{show} can be dispatched on following classes: \itemize{ -\item \code{\link{show,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method +\item \code{\link{show,Heatmap-method}}, \code{\link{Heatmap-class}} class method \item \code{\link{show,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method +\item \code{\link{show,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method \item \code{\link{show,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method -\item \code{\link{show,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method \item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method -\item \code{\link{show,Heatmap-method}}, \code{\link{Heatmap-class}} class method +\item \code{\link{show,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method } } \examples{ diff --git a/man/size.HeatmapAnnotation.Rd b/man/size.HeatmapAnnotation.Rd index 1b387416..1eeaa4f6 100644 --- a/man/size.HeatmapAnnotation.Rd +++ b/man/size.HeatmapAnnotation.Rd @@ -23,4 +23,5 @@ Internally used. \examples{ # There is no example NULL + } diff --git a/man/size.SingleAnnotation.Rd b/man/size.SingleAnnotation.Rd index 69ee3b25..84811bff 100644 --- a/man/size.SingleAnnotation.Rd +++ b/man/size.SingleAnnotation.Rd @@ -23,4 +23,5 @@ Internally used. \examples{ # There is no example NULL + } diff --git a/man/sizeAssign.HeatmapAnnotation.Rd b/man/sizeAssign.HeatmapAnnotation.Rd index f3e73acb..3c72e637 100644 --- a/man/sizeAssign.HeatmapAnnotation.Rd +++ b/man/sizeAssign.HeatmapAnnotation.Rd @@ -25,4 +25,5 @@ Internally used. \examples{ # There is no example NULL + } diff --git a/man/sizeAssign.SingleAnnotation.Rd b/man/sizeAssign.SingleAnnotation.Rd index 3dcea415..0c5f667b 100644 --- a/man/sizeAssign.SingleAnnotation.Rd +++ b/man/sizeAssign.SingleAnnotation.Rd @@ -25,4 +25,5 @@ Internally used. \examples{ # There is no example NULL + } diff --git a/man/str.comb_mat.Rd b/man/str.comb_mat.Rd index 8e133a62..4ffb51cd 100644 --- a/man/str.comb_mat.Rd +++ b/man/str.comb_mat.Rd @@ -18,4 +18,5 @@ str method \examples{ # There is no example NULL + } diff --git a/man/subset_matrix_by_row.Rd b/man/subset_matrix_by_row.Rd index 2d58f576..160167b4 100644 --- a/man/subset_matrix_by_row.Rd +++ b/man/subset_matrix_by_row.Rd @@ -21,4 +21,5 @@ Mainly used for constructing the \code{\link{AnnotationFunction-class}} object. \examples{ # There is no example NULL + } diff --git a/man/subset_no.Rd b/man/subset_no.Rd index 8960a48c..fb061c66 100644 --- a/man/subset_no.Rd +++ b/man/subset_no.Rd @@ -21,4 +21,5 @@ Mainly used for constructing the \code{\link{AnnotationFunction-class}} object. \examples{ # There is no example NULL + } diff --git a/man/subset_vector.Rd b/man/subset_vector.Rd index 0909ba69..2a1dbf33 100644 --- a/man/subset_vector.Rd +++ b/man/subset_vector.Rd @@ -21,4 +21,5 @@ Mainly used for constructing the \code{\link{AnnotationFunction-class}} object. \examples{ # There is no example NULL + } diff --git a/man/summary.Heatmap.Rd b/man/summary.Heatmap.Rd index 97ae58c4..df34407e 100644 --- a/man/summary.Heatmap.Rd +++ b/man/summary.Heatmap.Rd @@ -18,4 +18,5 @@ Print the Summary of a Heatmap \examples{ # There is no example NULL + } diff --git a/man/summary.HeatmapList.Rd b/man/summary.HeatmapList.Rd index 0841f26c..2bab6887 100644 --- a/man/summary.HeatmapList.Rd +++ b/man/summary.HeatmapList.Rd @@ -18,4 +18,5 @@ Summary of a Heatmap List \examples{ # There is no example NULL + } diff --git a/man/unify_mat_list.Rd b/man/unify_mat_list.Rd index 9f6ae3d2..785e4f1c 100644 --- a/man/unify_mat_list.Rd +++ b/man/unify_mat_list.Rd @@ -27,4 +27,5 @@ Zuguang Gu \examples{ # There is no example NULL + } diff --git a/man/upset_left_annotation.Rd b/man/upset_left_annotation.Rd index 6c487358..62444279 100644 --- a/man/upset_left_annotation.Rd +++ b/man/upset_left_annotation.Rd @@ -35,4 +35,5 @@ upset_left_annotation(m, \examples{ # There is no example NULL + } diff --git a/man/upset_right_annotation.Rd b/man/upset_right_annotation.Rd index 45b119da..0301e0ff 100644 --- a/man/upset_right_annotation.Rd +++ b/man/upset_right_annotation.Rd @@ -41,4 +41,5 @@ and if under the union mode, it is \code{union_size}. \examples{ # There is no example NULL + } diff --git a/man/upset_top_annotation.Rd b/man/upset_top_annotation.Rd index dbfe8d9d..e6cdc866 100644 --- a/man/upset_top_annotation.Rd +++ b/man/upset_top_annotation.Rd @@ -41,4 +41,5 @@ and if under the union mode, it is \code{union_size}. \examples{ # There is no example NULL + } diff --git a/man/width.Heatmap.Rd b/man/width.Heatmap.Rd index 353ec24a..1126da1a 100644 --- a/man/width.Heatmap.Rd +++ b/man/width.Heatmap.Rd @@ -18,4 +18,5 @@ Width of the Heatmap \examples{ # There is no example NULL + } diff --git a/man/width.HeatmapAnnotation.Rd b/man/width.HeatmapAnnotation.Rd index 979887d0..2d9ab332 100644 --- a/man/width.HeatmapAnnotation.Rd +++ b/man/width.HeatmapAnnotation.Rd @@ -21,4 +21,5 @@ Internally used. \examples{ # There is no example NULL + } diff --git a/man/width.HeatmapList.Rd b/man/width.HeatmapList.Rd index 36f5fd00..9209a66f 100644 --- a/man/width.HeatmapList.Rd +++ b/man/width.HeatmapList.Rd @@ -18,4 +18,5 @@ Width of the Heatmap List \examples{ # There is no example NULL + } diff --git a/man/width.SingleAnnotation.Rd b/man/width.SingleAnnotation.Rd index b48901c0..6ebf1fec 100644 --- a/man/width.SingleAnnotation.Rd +++ b/man/width.SingleAnnotation.Rd @@ -21,4 +21,5 @@ Internally used. \examples{ # There is no example NULL + } diff --git a/man/widthAssign.AnnotationFunction.Rd b/man/widthAssign.AnnotationFunction.Rd index da9cd7fc..a08a8954 100644 --- a/man/widthAssign.AnnotationFunction.Rd +++ b/man/widthAssign.AnnotationFunction.Rd @@ -23,4 +23,5 @@ Internally used. \examples{ # There is no example NULL + } diff --git a/man/widthAssign.HeatmapAnnotation.Rd b/man/widthAssign.HeatmapAnnotation.Rd index 1902b0b0..e6834971 100644 --- a/man/widthAssign.HeatmapAnnotation.Rd +++ b/man/widthAssign.HeatmapAnnotation.Rd @@ -23,4 +23,5 @@ Internally used. \examples{ # There is no example NULL + } diff --git a/man/widthAssign.SingleAnnotation.Rd b/man/widthAssign.SingleAnnotation.Rd index a9cacec9..5a615b7f 100644 --- a/man/widthAssign.SingleAnnotation.Rd +++ b/man/widthAssign.SingleAnnotation.Rd @@ -23,4 +23,5 @@ Internally used. \examples{ # There is no example NULL + } diff --git a/man/widthDetails.annotation_axis.Rd b/man/widthDetails.annotation_axis.Rd index cc6fe7f8..4d7a0037 100644 --- a/man/widthDetails.annotation_axis.Rd +++ b/man/widthDetails.annotation_axis.Rd @@ -20,4 +20,5 @@ The physical width of the grob can be get by \code{convertWidth(grobWidth(axis_g \examples{ # There is no example NULL + } diff --git a/man/widthDetails.legend.Rd b/man/widthDetails.legend.Rd index 00bc5f24..cae8ebdc 100644 --- a/man/widthDetails.legend.Rd +++ b/man/widthDetails.legend.Rd @@ -17,4 +17,5 @@ Grob width for packed_legends \examples{ # There is no example NULL + } diff --git a/man/widthDetails.legend_body.Rd b/man/widthDetails.legend_body.Rd index 650a8f21..7e8014ad 100644 --- a/man/widthDetails.legend_body.Rd +++ b/man/widthDetails.legend_body.Rd @@ -17,4 +17,5 @@ Grob width for legend_body \examples{ # There is no example NULL + } diff --git a/man/widthDetails.packed_legends.Rd b/man/widthDetails.packed_legends.Rd index 21e16753..9249f61d 100644 --- a/man/widthDetails.packed_legends.Rd +++ b/man/widthDetails.packed_legends.Rd @@ -17,4 +17,5 @@ Grob width for packed_legends \examples{ # There is no example NULL + } diff --git a/man/widthDetails.textbox.Rd b/man/widthDetails.textbox.Rd index 255a0178..72da5484 100644 --- a/man/widthDetails.textbox.Rd +++ b/man/widthDetails.textbox.Rd @@ -20,4 +20,5 @@ A \code{\link[grid]{unit}} object. \examples{ # There is no example NULL + }