deleted file mode 100644

@@ -1,99 +0,0 @@

-\name{densityHeatmap}

-\alias{densityHeatmap}

-\title{

-Visualize Density Distribution by Heatmap

-}

-\description{

-Visualize Density Distribution by Heatmap

-}

-\usage{

-densityHeatmap(data,

-    density_param = list(na.rm = TRUE),

-    

-    col = rev(brewer.pal(11, "Spectral")),

-    color_space = "LAB",

-    ylab = deparse(substitute(data)),

-    column_title = paste0("Density heatmap of ", deparse(substitute(data))),

-    title = column_title,

-    ylim = NULL,

-    range = ylim,

-    

-    title_gp = gpar(fontsize = 14),

-    ylab_gp = gpar(fontsize = 12),

-    tick_label_gp = gpar(fontsize = 10),

-    quantile_gp = gpar(fontsize = 10),

-    show_quantiles = TRUE,

-    

-    column_order = NULL,

-    column_names_side = "bottom",

-    show_column_names = TRUE,

-    column_names_max_height = unit(6, "cm"),

-    column_names_gp = gpar(fontsize = 12),

-    column_names_rot = 90,

-    

-    cluster_columns = FALSE,

-    clustering_distance_columns = "ks",

-    clustering_method_columns = "complete",

-    mc.cores = 1,

-    

-    ...)

-}

-\arguments{

-

-  \item{data}{A matrix or a list. If it is a matrix, density is calculated by columns.}

-  \item{density_param}{Parameters send to \code{\link[stats]{density}}, \code{na.rm} is enforced to be \code{TRUE}.}

-  \item{col}{A vector of colors that density values are mapped to.}

-  \item{color_space}{The color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}

-  \item{ylab}{Label on y-axis.}

-  \item{column_title}{Title of the heatmap.}

-  \item{title}{Same as \code{column_title}.}

-  \item{ylim}{Ranges on the y-axis.}

-  \item{range}{Same as \code{ylim}.}

-  \item{title_gp}{Graphic parameters for title.}

-  \item{ylab_gp}{Graphic parameters for y-labels.}

-  \item{tick_label_gp}{Graphic parameters for y-ticks.}

-  \item{quantile_gp}{Graphic parameters for the quantiles.}

-  \item{show_quantiles}{Whether show quantile lines.}

-  \item{column_order}{Order of columns.}

-  \item{column_names_side}{Pass to \code{\link{Heatmap}}.}

-  \item{show_column_names}{Pass to \code{\link{Heatmap}}.}

-  \item{column_names_max_height}{Pass to \code{\link{Heatmap}}.}

-  \item{column_names_gp}{Pass to \code{\link{Heatmap}}.}

-  \item{column_names_rot}{Pass to \code{\link{Heatmap}}.}

-  \item{cluster_columns}{Whether cluster columns?}

-  \item{clustering_distance_columns}{There is a specific distance method \code{ks} which is the Kolmogorov-Smirnov statistic between two distributions. For other methods, the distance is calculated on the density matrix.}

-  \item{clustering_method_columns}{Pass to \code{\link{Heatmap}}.}

-  \item{mc.cores}{Multiple cores for calculating ks distance.}

-  \item{...}{Pass to \code{\link{Heatmap}}.}

-

-}

-\details{

-To visualize data distribution in a matrix or in a list, we normally use

-boxplot or violinplot. We can also use colors to map the density values and

-visualize distribution of values through a heatmap. It is useful if you have

-huge number of columns in \code{data} to visualize.

-

-The density matrix is generated with 500 rows ranging between the maximun

-and minimal values in all densities.

-}

-\value{

-A \code{\link{Heatmap-class}} object. It can oly add other heatmaps/annotations vertically.

-}

-\seealso{

-\url{https://jokergoo.github.io/ComplexHeatmap-reference/book/other-high-level-plots.html#density-heatmap}

-}

-\author{

-Zuguang Gu <z.gu@dkfz.de>

-}

-\examples{

-matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10]

-densityHeatmap(matrix)

-

-lt = list(rnorm(10), rnorm(10))

-densityHeatmap(lt)

-

-ha = HeatmapAnnotation(points = anno_points(runif(10)),

-    anno = rep(c("A", "B"), each = 5), col = list(anno = c("A" = "red", "B" = "blue")))

-densityHeatmap(matrix, top_annotation = ha)

-densityHeatmap(matrix, top_annotation = ha) \%v\% Heatmap(matrix, height = unit(6, "cm"))

-}

@@ -15,7 +15,7 @@ densityHeatmap(data,

     ylab = deparse(substitute(data)),

     column_title = paste0("Density heatmap of ", deparse(substitute(data))),

     title = column_title,

-    ylim = c(-Inf, Inf),

+    ylim = NULL,

     range = ylim,

     title_gp = gpar(fontsize = 14),

@@ -22,6 +22,7 @@ densityHeatmap(data,

     ylab_gp = gpar(fontsize = 12),

     tick_label_gp = gpar(fontsize = 10),

     quantile_gp = gpar(fontsize = 10),

+    show_quantiles = TRUE,

     column_order = NULL,

     column_names_side = "bottom",

@@ -52,6 +53,7 @@ densityHeatmap(data,

   \item{ylab_gp}{Graphic parameters for y-labels.}

   \item{tick_label_gp}{Graphic parameters for y-ticks.}

   \item{quantile_gp}{Graphic parameters for the quantiles.}

+  \item{show_quantiles}{Whether show quantile lines.}

   \item{column_order}{Order of columns.}

   \item{column_names_side}{Pass to \code{\link{Heatmap}}.}

   \item{show_column_names}{Pass to \code{\link{Heatmap}}.}

@@ -33,6 +33,7 @@ densityHeatmap(data,

     cluster_columns = FALSE,

     clustering_distance_columns = "ks",

     clustering_method_columns = "complete",

+    mc.cores = 1,

     ...)

 }

@@ -60,6 +61,7 @@ densityHeatmap(data,

   \item{cluster_columns}{Whether cluster columns?}

   \item{clustering_distance_columns}{There is a specific distance method \code{ks} which is the Kolmogorov-Smirnov statistic between two distributions. For other methods, the distance is calculated on the density matrix.}

   \item{clustering_method_columns}{Pass to \code{\link{Heatmap}}.}

+  \item{mc.cores}{Multiple cores for calculating ks distance.}

   \item{...}{Pass to \code{\link{Heatmap}}.}

 }

@@ -45,22 +45,22 @@ densityHeatmap(data,

   \item{ylab}{Label on y-axis.}

   \item{column_title}{Title of the heatmap.}

   \item{title}{Same as \code{column_title}.}

-  \item{ylim}{Ranges on the y-axis. By default the range is between 1th quantile and 99th quantile of the data.}

+  \item{ylim}{Ranges on the y-axis.}

   \item{range}{Same as \code{ylim}.}

-  \item{title_gp}{= gpar(fontsize = 14),}

-  \item{ylab_gp}{= gpar(fontsize = 12),}

-  \item{tick_label_gp}{= gpar(fontsize = 10),}

-  \item{quantile_gp}{= gpar(fontsize = 10),}

-  \item{column_order}{column_order}

+  \item{title_gp}{Graphic parameters for title.}

+  \item{ylab_gp}{Graphic parameters for y-labels.}

+  \item{tick_label_gp}{Graphic parameters for y-ticks.}

+  \item{quantile_gp}{Graphic parameters for the quantiles.}

+  \item{column_order}{Order of columns.}

   \item{column_names_side}{Pass to \code{\link{Heatmap}}.}

   \item{show_column_names}{Pass to \code{\link{Heatmap}}.}

   \item{column_names_max_height}{Pass to \code{\link{Heatmap}}.}

   \item{column_names_gp}{Pass to \code{\link{Heatmap}}.}

   \item{column_names_rot}{Pass to \code{\link{Heatmap}}.}

-  \item{cluster_columns}{Whether cluster columns (here clustered by density values)? Normally we don't cluster columns.}

-  \item{clustering_distance_columns}{-clustering_distance_columns}

-  \item{clustering_method_columns}{-clustering_method_columns}

-  \item{...}{pass to \code{\link{Heatmap}}.}

+  \item{cluster_columns}{Whether cluster columns?}

+  \item{clustering_distance_columns}{There is a specific distance method \code{ks} which is the Kolmogorov-Smirnov statistic between two distributions. For other methods, the distance is calculated on the density matrix.}

+  \item{clustering_method_columns}{Pass to \code{\link{Heatmap}}.}

+  \item{...}{Pass to \code{\link{Heatmap}}.}

 }

 \details{

@@ -70,12 +70,13 @@ visualize distribution of values through a heatmap. It is useful if you have

 huge number of columns in \code{data} to visualize.

 The density matrix is generated with 500 rows ranging between the maximun

-and minimal values in all densities. The density values in each row are

-linearly intepolated between the two density values at the two nearest

-bounds.

+and minimal values in all densities.

 }

 \value{

-A \code{\link{HeatmapList-class}} object with only one heatmap, but it can only add other heatmaps/annotations vertically.

+A \code{\link{Heatmap-class}} object. It can oly add other heatmaps/annotations vertically.

+}

+\seealso{

+\url{https://jokergoo.github.io/ComplexHeatmap-reference/book/other-high-level-plots.html#density-heatmap}

 }

 \author{

 Zuguang Gu <z.gu@dkfz.de>

@@ -90,5 +91,5 @@ densityHeatmap(lt)

 ha = HeatmapAnnotation(points = anno_points(runif(10)),

     anno = rep(c("A", "B"), each = 5), col = list(anno = c("A" = "red", "B" = "blue")))

 densityHeatmap(matrix, top_annotation = ha)

-densityHeatmap(matrix, top_annotation = ha) %v% Heatmap(matrix, height = unit(6, "cm"))

+densityHeatmap(matrix, top_annotation = ha) \%v\% Heatmap(matrix, height = unit(6, "cm"))

 }

@@ -57,7 +57,8 @@ densityHeatmap(data,

   \item{column_names_max_height}{Pass to \code{\link{Heatmap}}.}

   \item{column_names_gp}{Pass to \code{\link{Heatmap}}.}

   \item{column_names_rot}{Pass to \code{\link{Heatmap}}.}

-  \item{cluster_columns}{Whether cluster columns (here clustered by density values)? Normally we don't cluster columns. - clustering_distance_columns}

+  \item{cluster_columns}{Whether cluster columns (here clustered by density values)? Normally we don't cluster columns.}

+  \item{clustering_distance_columns}{-clustering_distance_columns}

   \item{clustering_method_columns}{-clustering_method_columns}

   \item{...}{pass to \code{\link{Heatmap}}.}

@@ -31,6 +31,9 @@ densityHeatmap(data,

     column_names_rot = 90,

     cluster_columns = FALSE,

+    clustering_distance_columns = "ks",

+    clustering_method_columns = "complete",

+    

     ...)

 }

 \arguments{

@@ -54,7 +57,8 @@ densityHeatmap(data,

   \item{column_names_max_height}{Pass to \code{\link{Heatmap}}.}

   \item{column_names_gp}{Pass to \code{\link{Heatmap}}.}

   \item{column_names_rot}{Pass to \code{\link{Heatmap}}.}

-  \item{cluster_columns}{Whether cluster columns (here clustered by density values)? Normally we don't cluster columns.}

+  \item{cluster_columns}{Whether cluster columns (here clustered by density values)? Normally we don't cluster columns. - clustering_distance_columns}

+  \item{clustering_method_columns}{-clustering_method_columns}

   \item{...}{pass to \code{\link{Heatmap}}.}

 }

@@ -35,7 +35,7 @@ densityHeatmap(data,

 }

 \arguments{

-  \item{data}{A matrix or a list. If it is a matrix, density will be calculated by columns.}

+  \item{data}{A matrix or a list. If it is a matrix, density is calculated by columns.}

   \item{density_param}{Parameters send to \code{\link[stats]{density}}, \code{na.rm} is enforced to be \code{TRUE}.}

   \item{col}{A vector of colors that density values are mapped to.}

   \item{color_space}{The color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}

@@ -47,7 +47,7 @@ densityHeatmap(data,

   \item{title_gp}{= gpar(fontsize = 14),}

   \item{ylab_gp}{= gpar(fontsize = 12),}

   \item{tick_label_gp}{= gpar(fontsize = 10),}

-  \item{quantile_gp}{= gpar(fontsize = 10),# -column_order Order of columns.}

+  \item{quantile_gp}{= gpar(fontsize = 10),}

   \item{column_order}{column_order}

   \item{column_names_side}{Pass to \code{\link{Heatmap}}.}

   \item{show_column_names}{Pass to \code{\link{Heatmap}}.}

@@ -59,13 +59,15 @@ densityHeatmap(data,

 }

 \details{

-To visualize data distribution in a matrix or in a list, sometimes we use boxplot or beanplot.

-Here we use colors to map the density values and visualize distribution of values

-in each column (or each vector in the list) through a heatmap. It is useful if you have huge number 

-of columns in \code{data} to visualize.

+To visualize data distribution in a matrix or in a list, we normally use

+boxplot or violinplot. We can also use colors to map the density values and

+visualize distribution of values through a heatmap. It is useful if you have

+huge number of columns in \code{data} to visualize.

-The density matrix is generated with 500 rows ranging between the maximun and minimal values in all densities.

-The density values in each row are linearly intepolated between the two density values at the two nearest bounds.

+The density matrix is generated with 500 rows ranging between the maximun

+and minimal values in all densities. The density values in each row are

+linearly intepolated between the two density values at the two nearest

+bounds.

 }

 \value{

 A \code{\link{HeatmapList-class}} object with only one heatmap, but it can only add other heatmaps/annotations vertically.

@@ -77,10 +79,11 @@ Zuguang Gu <z.gu@dkfz.de>

 matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10]

 densityHeatmap(matrix)

+lt = list(rnorm(10), rnorm(10))

+densityHeatmap(lt)

+

 ha = HeatmapAnnotation(points = anno_points(runif(10)),

     anno = rep(c("A", "B"), each = 5), col = list(anno = c("A" = "red", "B" = "blue")))

 densityHeatmap(matrix, top_annotation = ha)

-

-lt = list(rnorm(10), rnorm(10))

-densityHeatmap(lt)

+densityHeatmap(matrix, top_annotation = ha) %v% Heatmap(matrix, height = unit(6, "cm"))

 }

@@ -12,8 +12,6 @@ densityHeatmap(data,

     col = rev(brewer.pal(11, "Spectral")),

     color_space = "LAB",

-    top_annotation = NULL,

-    bottom_annotation = NULL,

     ylab = deparse(substitute(data)),

     column_title = paste0("Density heatmap of ", deparse(substitute(data))),

     title = column_title,

@@ -41,8 +39,6 @@ densityHeatmap(data,

   \item{density_param}{Parameters send to \code{\link[stats]{density}}, \code{na.rm} is enforced to be \code{TRUE}.}

   \item{col}{A vector of colors that density values are mapped to.}

   \item{color_space}{The color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}

-  \item{top_annotation}{A \code{\link{HeatmapAnnotation-class}} object which is put on top of the heatmap.}

-  \item{bottom_annotation}{A \code{\link{HeatmapAnnotation-class}} object which is put at bottom of the heatmap.}

   \item{ylab}{Label on y-axis.}

   \item{column_title}{Title of the heatmap.}

   \item{title}{Same as \code{column_title}.}

old mode 100755

new mode 100644

@@ -1,59 +1,65 @@

 \name{densityHeatmap}

 \alias{densityHeatmap}

 \title{

-Use colors to represent density distribution

+Visualize Density Distribution by Heatmap

 }

 \description{

-Use colors to represent density distribution

+Visualize Density Distribution by Heatmap

 }

 \usage{

 densityHeatmap(data,

-    col = rev(brewer.pal(11, "Spectral")),

     density_param = list(na.rm = TRUE),

+    

+    col = rev(brewer.pal(11, "Spectral")),

     color_space = "LAB",

-    anno = NULL,

+    top_annotation = NULL,

+    bottom_annotation = NULL,

     ylab = deparse(substitute(data)),

-    title = paste0("Density heatmap of ", deparse(substitute(data))),

-    range = c(-Inf, Inf),

-    cluster_columns = FALSE,

-    clustering_distance_columns = "euclidean",

-    clustering_method_columns = "complete",

-    column_dend_side = "top",

-    column_dend_height = unit(10, "mm"),

-    show_column_dend = FALSE,

-    column_dend_gp = gpar(),

-    column_dend_reorder = TRUE,

-    column_names_side = c("bottom", "top"),

+    column_title = paste0("Density heatmap of ", deparse(substitute(data))),

+    title = column_title,

+    ylim = c(-Inf, Inf),

+    range = ylim,

+    

+    title_gp = gpar(fontsize = 14),

+    ylab_gp = gpar(fontsize = 12),

+    tick_label_gp = gpar(fontsize = 10),

+    quantile_gp = gpar(fontsize = 10),

+    

+    column_order = NULL,

+    column_names_side = "bottom",

     show_column_names = TRUE,

-    column_names_max_height = unit(4, "cm"),

+    column_names_max_height = unit(6, "cm"),

     column_names_gp = gpar(fontsize = 12),

-    column_order = NULL,

+    column_names_rot = 90,

+    

+    cluster_columns = FALSE,

     ...)

 }

 \arguments{

-  \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns.}

-  \item{col}{a list of colors that density values are mapped to.}

-  \item{density_param}{parameters send to \code{\link[stats]{density}}, \code{na.rm} is enforced to \code{TRUE}.}

-  \item{color_space}{the color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}

-  \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame  and colors for annotations are randomly assigned. If you want to customize the annotation colors, use a \code{\link{HeatmapAnnotation-class}} object directly.}

-  \item{ylab}{label on y-axis in the plot}

-  \item{title}{title of the plot}

-  \item{range}{ranges on the y-axis. By default the range is between 1th quantile and 99th quantile of the data.}

-  \item{cluster_columns}{whether cluster columns (here cluster by density distributions)}

-  \item{clustering_distance_columns}{pass to \code{\link{Heatmap}}}

-  \item{clustering_method_columns}{pass to \code{\link{Heatmap}}}

-  \item{column_dend_side}{pass to \code{\link{Heatmap}}}

-  \item{column_dend_height}{pass to \code{\link{Heatmap}}}

-  \item{show_column_dend}{pass to \code{\link{Heatmap}}}

-  \item{column_dend_gp}{pass to \code{\link{Heatmap}}}

-  \item{column_dend_reorder}{pass to \code{\link{Heatmap}}}

-  \item{column_names_side}{pass to \code{\link{Heatmap}}}

-  \item{show_column_names}{pass to \code{\link{Heatmap}}}

-  \item{column_names_max_height}{pass to \code{\link{Heatmap}}}

-  \item{column_names_gp}{pass to \code{\link{Heatmap}}}

-  \item{column_order}{order of columns}

-  \item{...}{pass to \code{\link{draw,HeatmapList-method}}}

+  \item{data}{A matrix or a list. If it is a matrix, density will be calculated by columns.}

+  \item{density_param}{Parameters send to \code{\link[stats]{density}}, \code{na.rm} is enforced to be \code{TRUE}.}

+  \item{col}{A vector of colors that density values are mapped to.}

+  \item{color_space}{The color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}

+  \item{top_annotation}{A \code{\link{HeatmapAnnotation-class}} object which is put on top of the heatmap.}

+  \item{bottom_annotation}{A \code{\link{HeatmapAnnotation-class}} object which is put at bottom of the heatmap.}

+  \item{ylab}{Label on y-axis.}

+  \item{column_title}{Title of the heatmap.}

+  \item{title}{Same as \code{column_title}.}

+  \item{ylim}{Ranges on the y-axis. By default the range is between 1th quantile and 99th quantile of the data.}

+  \item{range}{Same as \code{ylim}.}

+  \item{title_gp}{= gpar(fontsize = 14),}

+  \item{ylab_gp}{= gpar(fontsize = 12),}

+  \item{tick_label_gp}{= gpar(fontsize = 10),}

+  \item{quantile_gp}{= gpar(fontsize = 10),# -column_order Order of columns.}

+  \item{column_order}{column_order}

+  \item{column_names_side}{Pass to \code{\link{Heatmap}}.}

+  \item{show_column_names}{Pass to \code{\link{Heatmap}}.}

+  \item{column_names_max_height}{Pass to \code{\link{Heatmap}}.}

+  \item{column_names_gp}{Pass to \code{\link{Heatmap}}.}

+  \item{column_names_rot}{Pass to \code{\link{Heatmap}}.}

+  \item{cluster_columns}{Whether cluster columns (here clustered by density values)? Normally we don't cluster columns.}

+  \item{...}{pass to \code{\link{Heatmap}}.}

 }

 \details{

@@ -66,7 +72,7 @@ The density matrix is generated with 500 rows ranging between the maximun and mi

 The density values in each row are linearly intepolated between the two density values at the two nearest bounds.

 }

 \value{

-No value is returned.

+A \code{\link{HeatmapList-class}} object with only one heatmap, but it can only add other heatmaps/annotations vertically.

 }

 \author{

 Zuguang Gu <z.gu@dkfz.de>

@@ -74,12 +80,10 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10]

 densityHeatmap(matrix)

-densityHeatmap(matrix, anno = rep(c("A", "B"), each = 5))

-densityHeatmap(matrix, col = c("white", "red"), anno = rep(c("A", "B"), each = 5))

 ha = HeatmapAnnotation(points = anno_points(runif(10)),

     anno = rep(c("A", "B"), each = 5), col = list(anno = c("A" = "red", "B" = "blue")))

-densityHeatmap(matrix, anno = ha)

+densityHeatmap(matrix, top_annotation = ha)

 lt = list(rnorm(10), rnorm(10))

 densityHeatmap(lt)

@@ -9,10 +9,7 @@ Use colors to represent density distribution

 \usage{

 densityHeatmap(data,

     col = rev(brewer.pal(11, "Spectral")),

-<<<<<<< HEAD

     density_param = list(na.rm = TRUE),

-=======

->>>>>>> bioc/master

     color_space = "LAB",

     anno = NULL,

     ylab = deparse(substitute(data)),

@@ -37,10 +34,7 @@ densityHeatmap(data,

   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns.}

   \item{col}{a list of colors that density values are mapped to.}

-<<<<<<< HEAD

   \item{density_param}{parameters send to \code{\link[stats]{density}}, \code{na.rm} is enforced to \code{TRUE}.}

-=======

->>>>>>> bioc/master

   \item{color_space}{the color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}

   \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame  and colors for annotations are randomly assigned. If you want to customize the annotation colors, use a \code{\link{HeatmapAnnotation-class}} object directly.}

   \item{ylab}{label on y-axis in the plot}

@@ -67,12 +61,9 @@ To visualize data distribution in a matrix or in a list, sometimes we use boxplo

 Here we use colors to map the density values and visualize distribution of values

 in each column (or each vector in the list) through a heatmap. It is useful if you have huge number 

 of columns in \code{data} to visualize.

-<<<<<<< HEAD

 The density matrix is generated with 500 rows ranging between the maximun and minimal values in all densities.

 The density values in each row are linearly intepolated between the two density values at the two nearest bounds.

-=======

->>>>>>> bioc/master

 }

 \value{

 No value is returned.

@@ -14,6 +14,18 @@ densityHeatmap(data,

     ylab = deparse(substitute(data)),

     title = paste0("Density heatmap of ", deparse(substitute(data))),

     range = c(-Inf, Inf),

+    cluster_columns = FALSE,

+    clustering_distance_columns = "euclidean",

+    clustering_method_columns = "complete",

+    column_dend_side = "top",

+    column_dend_height = unit(10, "mm"),

+    show_column_dend = FALSE,

+    column_dend_gp = gpar(),

+    column_dend_reorder = TRUE,

+    column_names_side = c("bottom", "top"),

+    show_column_names = TRUE,

+    column_names_max_height = unit(4, "cm"),

+    column_names_gp = gpar(fontsize = 12),

     column_order = NULL,

     ...)

 }

@@ -26,6 +38,18 @@ densityHeatmap(data,

   \item{ylab}{label on y-axis in the plot}

   \item{title}{title of the plot}

   \item{range}{ranges on the y-axis. By default the range is between 1th quantile and 99th quantile of the data.}

+  \item{cluster_columns}{whether cluster columns (here cluster by density distributions)}

+  \item{clustering_distance_columns}{pass to \code{\link{Heatmap}}}

+  \item{clustering_method_columns}{pass to \code{\link{Heatmap}}}

+  \item{column_dend_side}{pass to \code{\link{Heatmap}}}

+  \item{column_dend_height}{pass to \code{\link{Heatmap}}}

+  \item{show_column_dend}{pass to \code{\link{Heatmap}}}

+  \item{column_dend_gp}{pass to \code{\link{Heatmap}}}

+  \item{column_dend_reorder}{pass to \code{\link{Heatmap}}}

+  \item{column_names_side}{pass to \code{\link{Heatmap}}}

+  \item{show_column_names}{pass to \code{\link{Heatmap}}}

+  \item{column_names_max_height}{pass to \code{\link{Heatmap}}}

+  \item{column_names_gp}{pass to \code{\link{Heatmap}}}

   \item{column_order}{order of columns}

   \item{...}{pass to \code{\link{draw,HeatmapList-method}}}

@@ -50,7 +50,6 @@ densityHeatmap(data,

   \item{show_column_names}{pass to \code{\link{Heatmap}}}

   \item{column_names_max_height}{pass to \code{\link{Heatmap}}}

   \item{column_names_gp}{pass to \code{\link{Heatmap}}}

-  \item{column_order}{pass to \code{\link{Heatmap}}}

   \item{column_order}{order of columns}

   \item{...}{pass to \code{\link{draw,HeatmapList-method}}}

@@ -14,6 +14,18 @@ densityHeatmap(data,

     ylab = deparse(substitute(data)),

     title = paste0("Density heatmap of ", deparse(substitute(data))),

     range = c(-Inf, Inf),

+    cluster_columns = FALSE,

+    clustering_distance_columns = "euclidean",

+    clustering_method_columns = "complete",

+    column_dend_side = "top",

+    column_dend_height = unit(10, "mm"),

+    show_column_dend = FALSE,

+    column_dend_gp = gpar(),

+    column_dend_reorder = TRUE,

+    column_names_side = c("bottom", "top"),

+    show_column_names = TRUE,

+    column_names_max_height = unit(4, "cm"),

+    column_names_gp = gpar(fontsize = 12),

     column_order = NULL,

     ...)

 }

@@ -26,6 +38,19 @@ densityHeatmap(data,

   \item{ylab}{label on y-axis in the plot}

   \item{title}{title of the plot}

   \item{range}{ranges on the y-axis. By default the range is between 1th quantile and 99th quantile of the data.}

+  \item{cluster_columns}{whether cluster columns (here cluster by density distributions)}

+  \item{clustering_distance_columns}{pass to \code{\link{Heatmap}}}

+  \item{clustering_method_columns}{pass to \code{\link{Heatmap}}}

+  \item{column_dend_side}{pass to \code{\link{Heatmap}}}

+  \item{column_dend_height}{pass to \code{\link{Heatmap}}}

+  \item{show_column_dend}{pass to \code{\link{Heatmap}}}

+  \item{column_dend_gp}{pass to \code{\link{Heatmap}}}

+  \item{column_dend_reorder}{pass to \code{\link{Heatmap}}}

+  \item{column_names_side}{pass to \code{\link{Heatmap}}}

+  \item{show_column_names}{pass to \code{\link{Heatmap}}}

+  \item{column_names_max_height}{pass to \code{\link{Heatmap}}}

+  \item{column_names_gp}{pass to \code{\link{Heatmap}}}

+  \item{column_order}{pass to \code{\link{Heatmap}}}

   \item{column_order}{order of columns}

   \item{...}{pass to \code{\link{draw,HeatmapList-method}}}

@@ -14,6 +14,7 @@ densityHeatmap(data,

     ylab = deparse(substitute(data)),

     title = paste0("Density heatmap of ", deparse(substitute(data))),

     range = c(-Inf, Inf),

+    column_order = NULL,

     ...)

 }

 \arguments{

@@ -25,6 +26,7 @@ densityHeatmap(data,

   \item{ylab}{label on y-axis in the plot}

   \item{title}{title of the plot}

   \item{range}{ranges on the y-axis. By default the range is between 1th quantile and 99th quantile of the data.}

+  \item{column_order}{order of columns}

   \item{...}{pass to \code{\link{draw,HeatmapList-method}}}

 }

@@ -19,12 +19,12 @@ densityHeatmap(data,

 \arguments{

   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns.}

-  \item{col}{a list of colors that density values are scaled to.}

+  \item{col}{a list of colors that density values are mapped to.}

   \item{color_space}{the color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}

-  \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame.  It can also be a \code{\link{HeatmapAnnotation-class}} object.}

+  \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame  and colors for annotations are randomly assigned. If you want to customize the annotation colors, use a \code{\link{HeatmapAnnotation-class}} object directly.}

   \item{ylab}{label on y-axis in the plot}

   \item{title}{title of the plot}

-  \item{range}{ranges on the y-axis. The lower bound is the maximul value between \code{range[[1]]} and minimal value in the data and the upper bound is the minimal value between \code{range[[2]]} and maximul value in the data.}

+  \item{range}{ranges on the y-axis. By default the range is between 1th quantile and 99th quantile of the data.}

   \item{...}{pass to \code{\link{draw,HeatmapList-method}}}

 }

@@ -46,7 +46,8 @@ densityHeatmap(matrix)

 densityHeatmap(matrix, anno = rep(c("A", "B"), each = 5))

 densityHeatmap(matrix, col = c("white", "red"), anno = rep(c("A", "B"), each = 5))

-ha = HeatmapAnnotation(points = anno_points(runif(10)))

+ha = HeatmapAnnotation(points = anno_points(runif(10)),

+    anno = rep(c("A", "B"), each = 5), col = list(anno = c("A" = "red", "B" = "blue")))

 densityHeatmap(matrix, anno = ha)

 lt = list(rnorm(10), rnorm(10))

@@ -13,6 +13,7 @@ densityHeatmap(data,

     anno = NULL,

     ylab = deparse(substitute(data)),

     title = paste0("Density heatmap of ", deparse(substitute(data))),

+    range = c(-Inf, Inf),

     ...)

 }

 \arguments{

@@ -23,8 +24,7 @@ densityHeatmap(data,

   \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame.  It can also be a \code{\link{HeatmapAnnotation-class}} object.}

   \item{ylab}{label on y-axis in the plot}

   \item{title}{title of the plot}

-  \item{range}{ranges on the y-axis. The lower bound is the maximul value between \code{range[[1]]} and minimal value

-       in the data and the upper bound is the minimal value between \code{range[[2]]} and maximul value in the data.}

+  \item{range}{ranges on the y-axis. The lower bound is the maximul value between \code{range[[1]]} and minimal value in the data and the upper bound is the minimal value between \code{range[[2]]} and maximul value in the data.}

   \item{...}{pass to \code{\link{draw,HeatmapList-method}}}

 }

@@ -23,6 +23,8 @@ densityHeatmap(data,

   \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame.  It can also be a \code{\link{HeatmapAnnotation-class}} object.}

   \item{ylab}{label on y-axis in the plot}

   \item{title}{title of the plot}

+  \item{range}{ranges on the y-axis. The lower bound is the maximul value between \code{range[[1]]} and minimal value

+       in the data and the upper bound is the minimal value between \code{range[[2]]} and maximul value in the data.}

   \item{...}{pass to \code{\link{draw,HeatmapList-method}}}

 }

@@ -14,6 +14,7 @@ densityHeatmap(data,

     ylab = deparse(substitute(data)),

     title = paste0("Density heatmap of ", deparse(substitute(data))),

     range = c(-Inf, Inf),

+    column_order = NULL,

     ...)

 }

 \arguments{

@@ -25,6 +26,7 @@ densityHeatmap(data,

   \item{ylab}{label on y-axis in the plot}

   \item{title}{title of the plot}

   \item{range}{ranges on the y-axis. By default the range is between 1th quantile and 99th quantile of the data.}

+  \item{column_order}{order of columns}

   \item{...}{pass to \code{\link{draw,HeatmapList-method}}}

 }

@@ -19,12 +19,12 @@ densityHeatmap(data,

 \arguments{

   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns.}

-  \item{col}{a list of colors that density values are scaled to.}

+  \item{col}{a list of colors that density values are mapped to.}

   \item{color_space}{the color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}

-  \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame.  It can also be a \code{\link{HeatmapAnnotation-class}} object.}

+  \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame  and colors for annotations are randomly assigned. If you want to customize the annotation colors, use a \code{\link{HeatmapAnnotation-class}} object directly.}

   \item{ylab}{label on y-axis in the plot}

   \item{title}{title of the plot}

-  \item{range}{ranges on the y-axis. The lower bound is the maximul value between \code{range[[1]]} and minimal value in the data and the upper bound is the minimal value between \code{range[[2]]} and maximul value in the data.}

+  \item{range}{ranges on the y-axis. By default the range is between 1th quantile and 99th quantile of the data.}

   \item{...}{pass to \code{\link{draw,HeatmapList-method}}}

 }

@@ -46,7 +46,8 @@ densityHeatmap(matrix)

 densityHeatmap(matrix, anno = rep(c("A", "B"), each = 5))

 densityHeatmap(matrix, col = c("white", "red"), anno = rep(c("A", "B"), each = 5))

-ha = HeatmapAnnotation(points = anno_points(runif(10)))

+ha = HeatmapAnnotation(points = anno_points(runif(10)),

+    anno = rep(c("A", "B"), each = 5), col = list(anno = c("A" = "red", "B" = "blue")))

 densityHeatmap(matrix, anno = ha)

 lt = list(rnorm(10), rnorm(10))

@@ -13,6 +13,7 @@ densityHeatmap(data,

     anno = NULL,

     ylab = deparse(substitute(data)),

     title = paste0("Density heatmap of ", deparse(substitute(data))),

+    range = c(-Inf, Inf),

     ...)

 }

 \arguments{

@@ -23,8 +24,7 @@ densityHeatmap(data,

   \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame.  It can also be a \code{\link{HeatmapAnnotation-class}} object.}

   \item{ylab}{label on y-axis in the plot}

   \item{title}{title of the plot}

-  \item{range}{ranges on the y-axis. The lower bound is the maximul value between \code{range[[1]]} and minimal value

-       in the data and the upper bound is the minimal value between \code{range[[2]]} and maximul value in the data.}

+  \item{range}{ranges on the y-axis. The lower bound is the maximul value between \code{range[[1]]} and minimal value in the data and the upper bound is the minimal value between \code{range[[2]]} and maximul value in the data.}

   \item{...}{pass to \code{\link{draw,HeatmapList-method}}}

 }

@@ -23,6 +23,8 @@ densityHeatmap(data,

   \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame.  It can also be a \code{\link{HeatmapAnnotation-class}} object.}

   \item{ylab}{label on y-axis in the plot}

   \item{title}{title of the plot}

+  \item{range}{ranges on the y-axis. The lower bound is the maximul value between \code{range[[1]]} and minimal value

+       in the data and the upper bound is the minimal value between \code{range[[2]]} and maximul value in the data.}

   \item{...}{pass to \code{\link{draw,HeatmapList-method}}}

 }

@@ -12,7 +12,8 @@ densityHeatmap(data,

     color_space = "LAB",

     anno = NULL,

     ylab = deparse(substitute(data)),

-    title = paste0("Density heatmap of ", deparse(substitute(data))))

+    title = paste0("Density heatmap of ", deparse(substitute(data))),

+    ...)

 }

 \arguments{

@@ -22,6 +23,7 @@ densityHeatmap(data,

   \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame.  It can also be a \code{\link{HeatmapAnnotation-class}} object.}

   \item{ylab}{label on y-axis in the plot}

   \item{title}{title of the plot}

+  \item{...}{pass to \code{\link{draw,HeatmapList-method}}}

 }

 \details{

@@ -41,8 +43,10 @@ matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10]

 densityHeatmap(matrix)

 densityHeatmap(matrix, anno = rep(c("A", "B"), each = 5))

 densityHeatmap(matrix, col = c("white", "red"), anno = rep(c("A", "B"), each = 5))

+

 ha = HeatmapAnnotation(points = anno_points(runif(10)))

 densityHeatmap(matrix, anno = ha)

+

 lt = list(rnorm(10), rnorm(10))

 densityHeatmap(lt)

 }

@@ -12,7 +12,8 @@ densityHeatmap(data,

     color_space = "LAB",

     anno = NULL,

     ylab = deparse(substitute(data)),

-    title = paste0("Density heatmap of ", deparse(substitute(data))))

+    title = paste0("Density heatmap of ", deparse(substitute(data))),

+    ...)

 }

 \arguments{

@@ -22,6 +23,7 @@ densityHeatmap(data,

   \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame.  It can also be a \code{\link{HeatmapAnnotation-class}} object.}

   \item{ylab}{label on y-axis in the plot}

   \item{title}{title of the plot}

+  \item{...}{pass to \code{\link{draw,HeatmapList-method}}}

 }

 \details{

@@ -41,8 +43,10 @@ matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10]

 densityHeatmap(matrix)

 densityHeatmap(matrix, anno = rep(c("A", "B"), each = 5))

 densityHeatmap(matrix, col = c("white", "red"), anno = rep(c("A", "B"), each = 5))

+

 ha = HeatmapAnnotation(points = anno_points(runif(10)))

 densityHeatmap(matrix, anno = ha)

+

 lt = list(rnorm(10), rnorm(10))

 densityHeatmap(lt)

 }

@@ -19,7 +19,7 @@ densityHeatmap(data,

   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns.}

   \item{col}{a list of colors that density values are scaled to.}

   \item{color_space}{the color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}

-  \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame. It can also be a \code{\link{HeatmapAnnotation-class}} object.}

+  \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame.  It can also be a \code{\link{HeatmapAnnotation-class}} object.}

   \item{ylab}{label on y-axis in the plot}

   \item{title}{title of the plot}

@@ -19,7 +19,7 @@ densityHeatmap(data,

   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns.}

   \item{col}{a list of colors that density values are scaled to.}

   \item{color_space}{the color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}

-  \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame. It can also be a \code{\link{HeatmapAnnotation-class}} object.}

+  \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame.  It can also be a \code{\link{HeatmapAnnotation-class}} object.}

   \item{ylab}{label on y-axis in the plot}

   \item{title}{title of the plot}

old mode 100644

new mode 100755

old mode 100644

new mode 100755

@@ -7,8 +7,11 @@ Use colors to represent density distribution

 Use colors to represent density distribution

 }

 \usage{

-densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),

-    color_space = "RGB", anno = NULL, ylab = deparse(substitute(data)),

+densityHeatmap(data,

+    col = rev(brewer.pal(11, "Spectral")),

+    color_space = "LAB",

+    anno = NULL,

+    ylab = deparse(substitute(data)),

     title = paste0("Density heatmap of ", deparse(substitute(data))))

 }

 \arguments{

@@ -16,19 +19,23 @@ densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),

   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns.}

   \item{col}{a list of colors that density values are scaled to.}

   \item{color_space}{the color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}

-  \item{anno}{annotation for matrix columns or list. The value should be a vector or a data frame. It can also be a \code{\link{HeatmapAnnotation-class}} object.}

+  \item{anno}{annotation for the matrix columns or the list. The value should be a vector or a data frame. It can also be a \code{\link{HeatmapAnnotation-class}} object.}

   \item{ylab}{label on y-axis in the plot}

   \item{title}{title of the plot}

 }

 \details{

-To visualize distribution of columns in a matrix or in a list, sometimes we use boxplot or beanplot.

-Here we use colors to map to the density values and visualize distribution of values

-in each column (or each element in the list) through a heatmap. It is useful if you have huge number of columns in \code{data} to visualize.

+To visualize data distribution in a matrix or in a list, sometimes we use boxplot or beanplot.

+Here we use colors to map the density values and visualize distribution of values

+in each column (or each vector in the list) through a heatmap. It is useful if you have huge number 

+of columns in \code{data} to visualize.

 }

 \value{

 No value is returned.

 }

+\author{

+Zuguang Gu <z.gu@dkfz.de>

+}

 \examples{

 matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10]

 densityHeatmap(matrix)

@@ -7,8 +7,11 @@ Use colors to represent density distribution

 Use colors to represent density distribution

 }

 \usage{

-densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),

-    color_space = "RGB", anno = NULL, ylab = deparse(substitute(data)),

+densityHeatmap(data,

+    col = rev(brewer.pal(11, "Spectral")),

+    color_space = "LAB",

+    anno = NULL,