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R CMD check passed

Zuguang Gu authored on 20/09/2018 12:48:08
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-\name{plotDataFrame}
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-\alias{plotDataFrame}
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-\title{
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-Quickly visualize a data frame
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-}
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-\description{
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-Quickly visualize a data frame
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-}
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-\usage{
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-plotDataFrame(df, overlap = 0.25, nlevel = 30, show_row_names = TRUE,
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-    show_column_names = TRUE, group = NULL, group_names = names(group),
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-    main_heatmap = NULL, km = 1, split = NULL, cluster_rows = TRUE,
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-    cluster_columns = TRUE, row_order = NULL, ...)
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-}
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-\arguments{
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-
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-  \item{df}{a data frame.}
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-  \item{overlap}{how to group numeric columns. If the overlapping rate between the ranges in the current column and previous numeric column is larger than this value, the two columns are treated as under same measurement and should be grouped.}
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-  \item{nlevel}{If the number of levels of a character column is larger than this value, the column will be excluded, because it doesn't make any sense to visualize a character vector or matrix that contains huge number of unique elements through a heatmap.}
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-  \item{show_row_names}{whether show row names after the last heatmap if there are row names.}
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-  \item{show_column_names}{whether show column names for all heatmaps.}
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-  \item{group}{a list of index that defines the groupping.}
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-  \item{group_names}{names for each group.}
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-  \item{main_heatmap}{which group is the main heatmap?}
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-  \item{km}{a value larger than 1 means applying k-means clustering on rows for the main heatmap.}
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-  \item{split}{one or multiple variables that split the rows.}
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-  \item{cluster_rows}{whether perform clustering on rows of the main heatmap.}
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-  \item{cluster_columns}{whether perform clustering on columns for all heatmaps.}
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-  \item{row_order}{order of rows, remember to turn off \code{cluster_rows}}
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-  \item{...}{pass to \code{\link{draw,HeatmapList-method}} or \code{\link{make_layout,HeatmapList-method}}}
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-
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-}
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-\details{
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-The data frame contains heterogeneous information. The \code{\link{plotDataFrame}} function provides a simple and quick way to
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-visualize information that are stored in a data frame.
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-
37
-There are only a few settings in this function, so the heamtap generated by this functioin
38
-may look ugly (in most of the time). However, users can customize the style of the heatmaps by manually
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-constructing a \code{\link{HeatmapList}} object.
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-}
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-\value{
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-A \code{\link{HeatmapList}} object.
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-}
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-\author{
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-Zuguang Gu <z.gu@dkfz.de>
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-}
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-\examples{
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-df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], letters[1:4])),
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-                large = runif(10)*100,
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-                t1 = sample(letters[1:3], 10, replace = TRUE),
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-                matrix(runif(60), nrow = 10, dimnames = list(LETTERS[1:10], LETTERS[1:6])),
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-                t2 = sample(LETTERS[1:3], 10, replace = TRUE))
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-plotDataFrame(df)
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-plotDataFrame(df, group = list(1:4, 5, 6, 7:12, 13), group_names = c("mat1", "large", "t1", "mat2", "t2"),
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-    main_heatmap = 4, km = 2, column_title = "column title", row_title = "row title")
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-
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-}
Browse code

Merge branch 'master' into devel

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@110567 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 12/11/2015 10:07:49
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@@ -10,13 +10,13 @@ Quickly visualize a data frame
10 10
 plotDataFrame(df, overlap = 0.25, nlevel = 30, show_row_names = TRUE,
11 11
     show_column_names = TRUE, group = NULL, group_names = names(group),
12 12
     main_heatmap = NULL, km = 1, split = NULL, cluster_rows = TRUE,
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-    cluster_columns = TRUE, ...)
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+    cluster_columns = TRUE, row_order = NULL, ...)
14 14
 }
15 15
 \arguments{
16 16
 
17 17
   \item{df}{a data frame.}
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-  \item{overlap}{how to group numeric columns. If the overlapping rate between the ranges in thecurrent column and previous numeric column is larger than this value, the two columnsare treated as under same measurement and should be grouped.}
19
-  \item{nlevel}{If the number of levels of a character column is larger than this value, the column willbe excluded, because it doesn't make any sense to visualize a character vector or matrixthat contains huge number of unique elements through a heatmap.}
18
+  \item{overlap}{how to group numeric columns. If the overlapping rate between the ranges in the current column and previous numeric column is larger than this value, the two columns are treated as under same measurement and should be grouped.}
19
+  \item{nlevel}{If the number of levels of a character column is larger than this value, the column will be excluded, because it doesn't make any sense to visualize a character vector or matrix that contains huge number of unique elements through a heatmap.}
20 20
   \item{show_row_names}{whether show row names after the last heatmap if there are row names.}
21 21
   \item{show_column_names}{whether show column names for all heatmaps.}
22 22
   \item{group}{a list of index that defines the groupping.}
... ...
@@ -26,6 +26,7 @@ plotDataFrame(df, overlap = 0.25, nlevel = 30, show_row_names = TRUE,
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   \item{split}{one or multiple variables that split the rows.}
27 27
   \item{cluster_rows}{whether perform clustering on rows of the main heatmap.}
28 28
   \item{cluster_columns}{whether perform clustering on columns for all heatmaps.}
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+  \item{row_order}{order of rows, remember to turn off \code{cluster_rows}}
29 30
   \item{...}{pass to \code{\link{draw,HeatmapList-method}} or \code{\link{make_layout,HeatmapList-method}}}
30 31
 
31 32
 }
Browse code

Merge branch 'master' into devel

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@108253 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 07/09/2015 20:39:32
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old mode 100644
2 2
new mode 100755
Browse code

resolve conflict from master branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@108131 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 03/09/2015 20:32:44
Showing1 changed files
... ...
@@ -33,12 +33,12 @@ plotDataFrame(df, overlap = 0.25, nlevel = 30, show_row_names = TRUE,
33 33
 The data frame contains heterogeneous information. The \code{\link{plotDataFrame}} function provides a simple and quick way to
34 34
 visualize information that are stored in a data frame.
35 35
 
36
-There are only a few advanced settings in this function, so the heamtap generated by this functioin
36
+There are only a few settings in this function, so the heamtap generated by this functioin
37 37
 may look ugly (in most of the time). However, users can customize the style of the heatmaps by manually
38 38
 constructing a \code{\link{HeatmapList}} object.
39 39
 }
40 40
 \value{
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-a \code{\link{HeatmapList}} object.
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+A \code{\link{HeatmapList}} object.
42 42
 }
43 43
 \author{
44 44
 Zuguang Gu <z.gu@dkfz.de>
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: db263179df8a28bd25eb5afcf64aa9c37b2fdd32

refresh docs



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107358 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 12/08/2015 22:49:59
Showing1 changed files
... ...
@@ -32,6 +32,7 @@ plotDataFrame(df, overlap = 0.25, nlevel = 30, show_row_names = TRUE,
32 32
 \details{
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 The data frame contains heterogeneous information. The \code{\link{plotDataFrame}} function provides a simple and quick way to
34 34
 visualize information that are stored in a data frame.
35
+
35 36
 There are only a few advanced settings in this function, so the heamtap generated by this functioin
36 37
 may look ugly (in most of the time). However, users can customize the style of the heatmaps by manually
37 38
 constructing a \code{\link{HeatmapList}} object.
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 1de356e1d1343725223e03ff696f931d80b2842b

Merge branch 'master' of https://github.com/jokergoo/mheatmap


Commit id: 478962957a34b7a5e87c8336989bae3df54f9559

change default colors



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107356 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 12/08/2015 22:03:22
Showing1 changed files
... ...
@@ -10,7 +10,8 @@ Quickly visualize a data frame
10 10
 plotDataFrame(df, overlap = 0.25, nlevel = 30, show_row_names = TRUE,
11 11
     show_column_names = TRUE, group = NULL, group_names = names(group),
12 12
     main_heatmap = NULL, km = 1, split = NULL, cluster_rows = TRUE,
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-    cluster_columns = TRUE, ...)}
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+    cluster_columns = TRUE, ...)
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+}
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 \arguments{
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   \item{df}{a data frame.}
... ...
@@ -26,6 +27,7 @@ plotDataFrame(df, overlap = 0.25, nlevel = 30, show_row_names = TRUE,
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   \item{cluster_rows}{whether perform clustering on rows of the main heatmap.}
27 28
   \item{cluster_columns}{whether perform clustering on columns for all heatmaps.}
28 29
   \item{...}{pass to \code{\link{draw,HeatmapList-method}} or \code{\link{make_layout,HeatmapList-method}}}
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+
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 }
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 \details{
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 The data frame contains heterogeneous information. The \code{\link{plotDataFrame}} function provides a simple and quick way to
... ...
@@ -49,4 +51,5 @@ df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], lett
49 51
 plotDataFrame(df)
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 plotDataFrame(df, group = list(1:4, 5, 6, 7:12, 13), group_names = c("mat1", "large", "t1", "mat2", "t2"),
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     main_heatmap = 4, km = 2, column_title = "column title", row_title = "row title")
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+
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 }
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: f1b195419490dad46029cf7b681508ed21ba8c60

refreshed documentations



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107316 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 11/08/2015 10:42:08
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@@ -2,11 +2,9 @@
2 2
 \alias{plotDataFrame}
3 3
 \title{
4 4
 Quickly visualize a data frame
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-
6 5
 }
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 \description{
8 7
 Quickly visualize a data frame
9
-
10 8
 }
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 \usage{
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 plotDataFrame(df, overlap = 0.25, nlevel = 30, show_row_names = TRUE,
... ...
@@ -32,33 +30,17 @@ plotDataFrame(df, overlap = 0.25, nlevel = 30, show_row_names = TRUE,
32 30
 \details{
33 31
 The data frame contains heterogeneous information. The \code{\link{plotDataFrame}} function provides a simple and quick way to
34 32
 visualize information that are stored in a data frame.
35
-
36 33
 There are only a few advanced settings in this function, so the heamtap generated by this functioin
37 34
 may look ugly (in most of the time). However, users can customize the style of the heatmaps by manually
38 35
 constructing a \code{\link{HeatmapList}} object.
39
-
40 36
 }
41 37
 \value{
42 38
 a \code{\link{HeatmapList}} object.
43
-
44 39
 }
45 40
 \author{
46 41
 Zuguang Gu <z.gu@dkfz.de>
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-
48 42
 }
49 43
 \examples{
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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 df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], letters[1:4])),
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                 large = runif(10)*100,
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                 t1 = sample(letters[1:3], 10, replace = TRUE),
... ...
@@ -66,4 +48,5 @@ df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], lett
66 48
                 t2 = sample(LETTERS[1:3], 10, replace = TRUE))
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 plotDataFrame(df)
68 50
 plotDataFrame(df, group = list(1:4, 5, 6, 7:12, 13), group_names = c("mat1", "large", "t1", "mat2", "t2"),
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-    main_heatmap = 4, km = 2, column_title = "column title", row_title = "row title")}
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+    main_heatmap = 4, km = 2, column_title = "column title", row_title = "row title")
52
+}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 262e3960558c1f61b986f5be7a2ffd4599f704fa

comprehensive modifications



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107311 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 10/08/2015 22:17:54
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@@ -54,6 +54,11 @@ Zuguang Gu <z.gu@dkfz.de>
54 54
 
55 55
 
56 56
 
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+
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+
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+
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+
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+
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 df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], letters[1:4])),
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                 large = runif(10)*100,
59 64
                 t1 = sample(letters[1:3], 10, replace = TRUE),
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 73171be89c157222e8e71e85daa8a37ce509a4e2

add border argument in anno_* family functions



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107201 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 06/08/2015 17:46:06
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@@ -53,6 +53,7 @@ Zuguang Gu <z.gu@dkfz.de>
53 53
 
54 54
 
55 55
 
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+
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 df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], letters[1:4])),
57 58
                 large = runif(10)*100,
58 59
                 t1 = sample(letters[1:3], 10, replace = TRUE),
Browse code

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Commit id: 3429d28233ef2cbeafcd05307042d7c7aa54a2a2

add decorate* family functions



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107197 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 06/08/2015 16:40:59
Showing1 changed files
... ...
@@ -49,6 +49,10 @@ Zuguang Gu <z.gu@dkfz.de>
49 49
 \examples{
50 50
 
51 51
 
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+
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+
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+
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+
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 df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], letters[1:4])),
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                 large = runif(10)*100,
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                 t1 = sample(letters[1:3], 10, replace = TRUE),
Browse code

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Commit id: d5adc92bdbf27b45a6a4b5c7e29d2e4fe8380194

allow reordering



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107130 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 04/08/2015 20:24:37
Showing1 changed files
... ...
@@ -47,6 +47,8 @@ Zuguang Gu <z.gu@dkfz.de>
47 47
 
48 48
 }
49 49
 \examples{
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+
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+
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 df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], letters[1:4])),
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                 large = runif(10)*100,
52 54
                 t1 = sample(letters[1:3], 10, replace = TRUE),
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 174dbdcbcad3be858d664784793f1b2424acc2c0

remove plot.HeatmapList and print.HeatmapList



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@106530 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 18/07/2015 18:14:29
Showing1 changed files
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@@ -1,44 +1,45 @@
1 1
 \name{plotDataFrame}
2 2
 \alias{plotDataFrame}
3 3
 \title{
4
-Visualize a data frame
4
+Quickly visualize a data frame
5 5
 
6 6
 }
7 7
 \description{
8
-Visualize a data frame
8
+Quickly visualize a data frame
9 9
 
10 10
 }
11 11
 \usage{
12
-plotDataFrame(df, overlap = 0.25, nlevel = 30, show_row_names = TRUE, show_column_names = TRUE,
13
-    group = NULL, group_names = names(group), main_heatmap = NULL, km = 1, split = NULL,
14
-    cluster_rows = TRUE, cluster_columns = TRUE, ...)}
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+plotDataFrame(df, overlap = 0.25, nlevel = 30, show_row_names = TRUE,
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+    show_column_names = TRUE, group = NULL, group_names = names(group),
14
+    main_heatmap = NULL, km = 1, split = NULL, cluster_rows = TRUE,
15
+    cluster_columns = TRUE, ...)}
15 16
 \arguments{
16 17
 
17
-  \item{df}{a data frame}
18
-  \item{overlap}{how to group numeric columns. If the overlapping rate between the ranges in thecurrent column and previous numeric column is larger than this value, the two columnsare thought under same measurement and should be grouped.}
19
-  \item{nlevel}{If the number of levels of a character column is larger than this value, the column willbe excluded.}
18
+  \item{df}{a data frame.}
19
+  \item{overlap}{how to group numeric columns. If the overlapping rate between the ranges in thecurrent column and previous numeric column is larger than this value, the two columnsare treated as under same measurement and should be grouped.}
20
+  \item{nlevel}{If the number of levels of a character column is larger than this value, the column willbe excluded, because it doesn't make any sense to visualize a character vector or matrixthat contains huge number of unique elements through a heatmap.}
20 21
   \item{show_row_names}{whether show row names after the last heatmap if there are row names.}
21
-  \item{show_column_names}{whether show column names for all heatmaps}
22
-  \item{group}{a list of index that defines the groupping}
23
-  \item{group_names}{names for each group}
24
-  \item{main_heatmap}{which group is the main heatmap}
25
-  \item{km}{apply k-means clustering on rows for the main heatmap}
26
-  \item{split}{set a splitting variable on rows for the main heatmap}
27
-  \item{cluster_rows}{whether perform clustering on rows of the first heatmap}
28
-  \item{cluster_columns}{whether perform clustering on columns for all heatmaps}
22
+  \item{show_column_names}{whether show column names for all heatmaps.}
23
+  \item{group}{a list of index that defines the groupping.}
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+  \item{group_names}{names for each group.}
25
+  \item{main_heatmap}{which group is the main heatmap?}
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+  \item{km}{a value larger than 1 means applying k-means clustering on rows for the main heatmap.}
27
+  \item{split}{one or multiple variables that split the rows.}
28
+  \item{cluster_rows}{whether perform clustering on rows of the main heatmap.}
29
+  \item{cluster_columns}{whether perform clustering on columns for all heatmaps.}
29 30
   \item{...}{pass to \code{\link{draw,HeatmapList-method}} or \code{\link{make_layout,HeatmapList-method}}}
30 31
 }
31 32
 \details{
32
-The data frame contains information from different aspects and different measurements are applied
33
-on the same element for each row. The \code{\link{plotDataFrame}} function provides a simple and quick way to
33
+The data frame contains heterogeneous information. The \code{\link{plotDataFrame}} function provides a simple and quick way to
34 34
 visualize information that are stored in a data frame.
35 35
 
36
-There are not many advanced settings in this function. Users can customize the style of the heatmaps
37
-by constructing a \code{\link{HeatmapList}} object.
36
+There are only a few advanced settings in this function, so the heamtap generated by this functioin
37
+may look ugly (in most of the time). However, users can customize the style of the heatmaps by manually
38
+constructing a \code{\link{HeatmapList}} object.
38 39
 
39 40
 }
40 41
 \value{
41
-a \code{\link{HeatmapList}} object
42
+a \code{\link{HeatmapList}} object.
42 43
 
43 44
 }
44 45
 \author{
... ...
@@ -46,7 +47,6 @@ Zuguang Gu <z.gu@dkfz.de>
46 47
 
47 48
 }
48 49
 \examples{
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-
50 50
 df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], letters[1:4])),
51 51
                 large = runif(10)*100,
52 52
                 t1 = sample(letters[1:3], 10, replace = TRUE),
Browse code

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Commit id: 4cbce102eabb1633fc8980b1374795bfb44507df

Merge branch 'master' of https://github.com/jokergoo/ComplexHeatmap


Commit id: a15bbec76c85c15bc27273ce15f5118ea087132f

refreshed documentatinos


Commit id: b1fe0a94aa09a4a47e5a02383ce662580f057bdc

ColorMapping object has default value for name slot



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@106487 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 16/07/2015 15:21:23
Showing1 changed files
... ...
@@ -46,6 +46,7 @@ Zuguang Gu <z.gu@dkfz.de>
46 46
 
47 47
 }
48 48
 \examples{
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+
49 50
 df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], letters[1:4])),
50 51
                 large = runif(10)*100,
51 52
                 t1 = sample(letters[1:3], 10, replace = TRUE),
Browse code

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Commit id: ff9ffa810ca9f16a253861d97301062962dbe38b

titles support expression now



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z.gu authored on 13/07/2015 21:26:16
Showing1 changed files
... ...
@@ -46,8 +46,6 @@ Zuguang Gu <z.gu@dkfz.de>
46 46
 
47 47
 }
48 48
 \examples{
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-
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-
51 49
 df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], letters[1:4])),
52 50
                 large = runif(10)*100,
53 51
                 t1 = sample(letters[1:3], 10, replace = TRUE),
Browse code

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Commit id: e811f8100ef035ff75c16312b3e5112cc82d4a49

continuous legend is supported



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z.gu authored on 13/07/2015 10:21:55
Showing1 changed files
... ...
@@ -46,6 +46,8 @@ Zuguang Gu <z.gu@dkfz.de>
46 46
 
47 47
 }
48 48
 \examples{
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+
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+
49 51
 df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], letters[1:4])),
50 52
                 large = runif(10)*100,
51 53
                 t1 = sample(letters[1:3], 10, replace = TRUE),
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 2786dac4ddaa97c69cc24e29e121ed1a1624cdf4

Merge branch 'master' of https://github.com/jokergoo/mheatmap


Commit id: a61c101325601aa0d4d3ba81e10c33d4a8b34c63

rows can be split if providing a clustering object



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105855 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 06/07/2015 22:31:19
Showing1 changed files
... ...
@@ -46,8 +46,6 @@ Zuguang Gu <z.gu@dkfz.de>
46 46
 
47 47
 }
48 48
 \examples{
49
-
50
-
51 49
 df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], letters[1:4])),
52 50
                 large = runif(10)*100,
53 51
                 t1 = sample(letters[1:3], 10, replace = TRUE),
... ...
@@ -55,6 +53,4 @@ df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], lett
55 53
                 t2 = sample(LETTERS[1:3], 10, replace = TRUE))
56 54
 plotDataFrame(df)
57 55
 plotDataFrame(df, group = list(1:4, 5, 6, 7:12, 13), group_names = c("mat1", "large", "t1", "mat2", "t2"),
58
-    main_heatmap = 4, km = 2, column_title = "column title", row_title = "row title")
59
-
60
-}
56
+    main_heatmap = 4, km = 2, column_title = "column title", row_title = "row title")}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 9d7fc297a370b44dd3bfb12696ed9eac33aed48a

refreshed documentations



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105365 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 23/06/2015 10:24:06
Showing1 changed files
... ...
@@ -47,6 +47,7 @@ Zuguang Gu <z.gu@dkfz.de>
47 47
 }
48 48
 \examples{
49 49
 
50
+
50 51
 df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], letters[1:4])),
51 52
                 large = runif(10)*100,
52 53
                 t1 = sample(letters[1:3], 10, replace = TRUE),
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 1d5cea822fed8ed91d7ead49f520f719b3fecfd9

refreshed documentations



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105355 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 23/06/2015 08:33:59
Showing1 changed files
... ...
@@ -46,6 +46,7 @@ Zuguang Gu <z.gu@dkfz.de>
46 46
 
47 47
 }
48 48
 \examples{
49
+
49 50
 df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], letters[1:4])),
50 51
                 large = runif(10)*100,
51 52
                 t1 = sample(letters[1:3], 10, replace = TRUE),
... ...
@@ -53,4 +54,6 @@ df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], lett
53 54
                 t2 = sample(LETTERS[1:3], 10, replace = TRUE))
54 55
 plotDataFrame(df)
55 56
 plotDataFrame(df, group = list(1:4, 5, 6, 7:12, 13), group_names = c("mat1", "large", "t1", "mat2", "t2"),
56
-    main_heatmap = 4, km = 2, column_title = "column title", row_title = "row title")}
57
+    main_heatmap = 4, km = 2, column_title = "column title", row_title = "row title")
58
+
59
+}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 1682e4aed696b8fa901530ebc6b9d67ad2a013ad

refresh documentations and NAMESPACE



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105345 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 22/06/2015 21:57:04
Showing1 changed files
... ...
@@ -1,25 +1,22 @@
1 1
 \name{plotDataFrame}
2 2
 \alias{plotDataFrame}
3 3
 \title{
4
-Visualize a data frame  
5
-
4
+Visualize a data frame
6 5
 
7 6
 }
8 7
 \description{
9
-Visualize a data frame  
10
-
8
+Visualize a data frame
11 9
 
12 10
 }
13 11
 \usage{
14 12
 plotDataFrame(df, overlap = 0.25, nlevel = 30, show_row_names = TRUE, show_column_names = TRUE,
15 13
     group = NULL, group_names = names(group), main_heatmap = NULL, km = 1, split = NULL,
16
-    cluster_rows = TRUE, cluster_columns = TRUE, ...)
17
-}
14
+    cluster_rows = TRUE, cluster_columns = TRUE, ...)}
18 15
 \arguments{
19 16
 
20 17
   \item{df}{a data frame}
21
-  \item{overlap}{how to group numeric columns. If the overlapping rate between the ranges in the current column and previous numeric column is larger than this value, the two columns are thought under same measurement and should be grouped.}
22
-  \item{nlevel}{If the number of levels of a character column is larger than this value, the column will be excluded.}
18
+  \item{overlap}{how to group numeric columns. If the overlapping rate between the ranges in thecurrent column and previous numeric column is larger than this value, the two columnsare thought under same measurement and should be grouped.}
19
+  \item{nlevel}{If the number of levels of a character column is larger than this value, the column willbe excluded.}
23 20
   \item{show_row_names}{whether show row names after the last heatmap if there are row names.}
24 21
   \item{show_column_names}{whether show column names for all heatmaps}
25 22
   \item{group}{a list of index that defines the groupping}
... ...
@@ -30,23 +27,22 @@ plotDataFrame(df, overlap = 0.25, nlevel = 30, show_row_names = TRUE, show_colum
30 27
   \item{cluster_rows}{whether perform clustering on rows of the first heatmap}
31 28
   \item{cluster_columns}{whether perform clustering on columns for all heatmaps}
32 29
   \item{...}{pass to \code{\link{draw,HeatmapList-method}} or \code{\link{make_layout,HeatmapList-method}}}
33
-
34 30
 }
35 31
 \details{
36
-The data frame contains information from different aspects and different measurements are applied on the same element for each row. The \code{\link{plotDataFrame}} function provides a simple and quick way to visualize information that are stored in a data frame.  
37
-
38
-There are not many advanced settings in this function. Users can customize the style of the heatmaps by constructing a \code{\link{HeatmapList}} object.  
32
+The data frame contains information from different aspects and different measurements are applied
33
+on the same element for each row. The \code{\link{plotDataFrame}} function provides a simple and quick way to
34
+visualize information that are stored in a data frame.
39 35
 
36
+There are not many advanced settings in this function. Users can customize the style of the heatmaps
37
+by constructing a \code{\link{HeatmapList}} object.
40 38
 
41 39
 }
42 40
 \value{
43
-a \code{\link{HeatmapList}} object  
44
-
41
+a \code{\link{HeatmapList}} object
45 42
 
46 43
 }
47 44
 \author{
48
-Zuguang Gu <z.gu@dkfz.de>  
49
-
45
+Zuguang Gu <z.gu@dkfz.de>
50 46
 
51 47
 }
52 48
 \examples{
... ...
@@ -57,5 +53,4 @@ df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], lett
57 53
                 t2 = sample(LETTERS[1:3], 10, replace = TRUE))
58 54
 plotDataFrame(df)
59 55
 plotDataFrame(df, group = list(1:4, 5, 6, 7:12, 13), group_names = c("mat1", "large", "t1", "mat2", "t2"),
60
-    main_heatmap = 4, km = 2, column_title = "column title", row_title = "row title")
61
-}
56
+    main_heatmap = 4, km = 2, column_title = "column title", row_title = "row title")}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: ff6ad79beeef75c709dc08588bb942ad86de9761

rotation for heatmap title supported



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105315 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 22/06/2015 15:09:06
Showing1 changed files
... ...
@@ -1,22 +1,25 @@
1 1
 \name{plotDataFrame}
2 2
 \alias{plotDataFrame}
3 3
 \title{
4
-Visualize a data frame
4
+Visualize a data frame  
5
+
5 6
 
6 7
 }
7 8
 \description{
8
-Visualize a data frame
9
+Visualize a data frame  
10
+
9 11
 
10 12
 }
11 13
 \usage{
12 14
 plotDataFrame(df, overlap = 0.25, nlevel = 30, show_row_names = TRUE, show_column_names = TRUE,
13 15
     group = NULL, group_names = names(group), main_heatmap = NULL, km = 1, split = NULL,
14
-    cluster_rows = TRUE, cluster_columns = TRUE, ...)}
16
+    cluster_rows = TRUE, cluster_columns = TRUE, ...)
17
+}
15 18
 \arguments{
16 19
 
17 20
   \item{df}{a data frame}
18
-  \item{overlap}{how to group numeric columns. If the overlapping rate between the ranges in thecurrent column and previous numeric column is larger than this value, the two columnsare thought under same measurement and should be grouped.}
19
-  \item{nlevel}{If the number of levels of a character column is larger than this value, the column willbe excluded.}
21
+  \item{overlap}{how to group numeric columns. If the overlapping rate between the ranges in the current column and previous numeric column is larger than this value, the two columns are thought under same measurement and should be grouped.}
22
+  \item{nlevel}{If the number of levels of a character column is larger than this value, the column will be excluded.}
20 23
   \item{show_row_names}{whether show row names after the last heatmap if there are row names.}
21 24
   \item{show_column_names}{whether show column names for all heatmaps}
22 25
   \item{group}{a list of index that defines the groupping}
... ...
@@ -27,22 +30,23 @@ plotDataFrame(df, overlap = 0.25, nlevel = 30, show_row_names = TRUE, show_colum
27 30
   \item{cluster_rows}{whether perform clustering on rows of the first heatmap}
28 31
   \item{cluster_columns}{whether perform clustering on columns for all heatmaps}
29 32
   \item{...}{pass to \code{\link{draw,HeatmapList-method}} or \code{\link{make_layout,HeatmapList-method}}}
33
+
30 34
 }
31 35
 \details{
32
-The data frame contains information from different aspects and different measurements are applied
33
-on the same element for each row. The \code{\link{plotDataFrame}} function provides a simple and quick way to
34
-visualize information that are stored in a data frame.
36
+The data frame contains information from different aspects and different measurements are applied on the same element for each row. The \code{\link{plotDataFrame}} function provides a simple and quick way to visualize information that are stored in a data frame.  
37
+
38
+There are not many advanced settings in this function. Users can customize the style of the heatmaps by constructing a \code{\link{HeatmapList}} object.  
35 39
 
36
-There are not many advanced settings in this function. Users can customize the style of the heatmaps
37
-by constructing a \code{\link{HeatmapList}} object.
38 40
 
39 41
 }
40 42
 \value{
41
-a \code{\link{HeatmapList}} object
43
+a \code{\link{HeatmapList}} object  
44
+
42 45
 
43 46
 }
44 47
 \author{
45
-Zuguang Gu <z.gu@dkfz.de>
48
+Zuguang Gu <z.gu@dkfz.de>  
49
+
46 50
 
47 51
 }
48 52
 \examples{
... ...
@@ -53,4 +57,5 @@ df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], lett
53 57
                 t2 = sample(LETTERS[1:3], 10, replace = TRUE))
54 58
 plotDataFrame(df)
55 59
 plotDataFrame(df, group = list(1:4, 5, 6, 7:12, 13), group_names = c("mat1", "large", "t1", "mat2", "t2"),
56
-    main_heatmap = 4, km = 2, column_title = "column title", row_title = "row title")}
60
+    main_heatmap = 4, km = 2, column_title = "column title", row_title = "row title")
61
+}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 6cf15a1b2514d9c86295206a55c9d5efadc00f70

check row orders



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@105276 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 21/06/2015 17:44:09
Showing1 changed files
... ...
@@ -1,25 +1,22 @@
1 1
 \name{plotDataFrame}
2 2
 \alias{plotDataFrame}
3 3
 \title{
4
-Visualize a data frame  
5
-
4
+Visualize a data frame
6 5
 
7 6
 }
8 7
 \description{
9
-Visualize a data frame  
10
-
8
+Visualize a data frame
11 9
 
12 10
 }
13 11
 \usage{
14 12
 plotDataFrame(df, overlap = 0.25, nlevel = 30, show_row_names = TRUE, show_column_names = TRUE,
15 13
     group = NULL, group_names = names(group), main_heatmap = NULL, km = 1, split = NULL,
16
-    cluster_rows = TRUE, cluster_columns = TRUE, ...)
17
-}
14
+    cluster_rows = TRUE, cluster_columns = TRUE, ...)}
18 15
 \arguments{
19 16
 
20 17
   \item{df}{a data frame}
21
-  \item{overlap}{how to group numeric columns. If the overlapping rate between the ranges in the current column and previous numeric column is larger than this value, the two columns are thought under same measurement and should be grouped.}
22
-  \item{nlevel}{If the number of levels of a character column is larger than this value, the column will be excluded.}
18
+  \item{overlap}{how to group numeric columns. If the overlapping rate between the ranges in thecurrent column and previous numeric column is larger than this value, the two columnsare thought under same measurement and should be grouped.}
19
+  \item{nlevel}{If the number of levels of a character column is larger than this value, the column willbe excluded.}
23 20
   \item{show_row_names}{whether show row names after the last heatmap if there are row names.}
24 21
   \item{show_column_names}{whether show column names for all heatmaps}
25 22
   \item{group}{a list of index that defines the groupping}
... ...
@@ -30,23 +27,22 @@ plotDataFrame(df, overlap = 0.25, nlevel = 30, show_row_names = TRUE, show_colum
30 27
   \item{cluster_rows}{whether perform clustering on rows of the first heatmap}
31 28
   \item{cluster_columns}{whether perform clustering on columns for all heatmaps}
32 29
   \item{...}{pass to \code{\link{draw,HeatmapList-method}} or \code{\link{make_layout,HeatmapList-method}}}
33
-
34 30
 }
35 31
 \details{
36
-The data frame contains information from different aspects and different measurements are applied on the same element for each row. The \code{\link{plotDataFrame}} function provides a simple and quick way to visualize information that are stored in a data frame.  
37
-
38
-There are not many advanced settings in this function. Users can customize the style of the heatmaps by constructing a \code{\link{HeatmapList}} object.  
32
+The data frame contains information from different aspects and different measurements are applied
33
+on the same element for each row. The \code{\link{plotDataFrame}} function provides a simple and quick way to
34
+visualize information that are stored in a data frame.
39 35
 
36
+There are not many advanced settings in this function. Users can customize the style of the heatmaps
37
+by constructing a \code{\link{HeatmapList}} object.
40 38
 
41 39
 }
42 40
 \value{
43
-a \code{\link{HeatmapList}} object  
44
-
41
+a \code{\link{HeatmapList}} object
45 42
 
46 43
 }
47 44
 \author{
48
-Zuguang Gu <z.gu@dkfz.de>  
49
-
45
+Zuguang Gu <z.gu@dkfz.de>
50 46
 
51 47
 }
52 48
 \examples{
... ...
@@ -57,5 +53,4 @@ df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], lett
57 53
                 t2 = sample(LETTERS[1:3], 10, replace = TRUE))
58 54
 plotDataFrame(df)
59 55
 plotDataFrame(df, group = list(1:4, 5, 6, 7:12, 13), group_names = c("mat1", "large", "t1", "mat2", "t2"),
60
-    main_heatmap = 4, km = 2, column_title = "column title", row_title = "row title")
61
-}
56
+    main_heatmap = 4, km = 2, column_title = "column title", row_title = "row title")}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 7ce8bf6b9a307c61c0f6297e94039cb5e8386bd2

support main heatmap in plotDataFrame()



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@104978 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 15/06/2015 18:58:19
Showing1 changed files
... ...
@@ -11,9 +11,9 @@ Visualize a data frame
11 11
 
12 12
 }
13 13
 \usage{
14
-plotDataFrame(df, overlap = 0.5, nlevel = 30, show_row_names = TRUE,
15
-    group = NULL, group_name = names(group), cluster_rows = TRUE,
16
-    cluster_columns = TRUE)
14
+plotDataFrame(df, overlap = 0.25, nlevel = 30, show_row_names = TRUE, show_column_names = TRUE,
15
+    group = NULL, group_names = names(group), main_heatmap = NULL, km = 1, split = NULL,
16
+    cluster_rows = TRUE, cluster_columns = TRUE, ...)
17 17
 }
18 18
 \arguments{
19 19
 
... ...
@@ -21,10 +21,15 @@ plotDataFrame(df, overlap = 0.5, nlevel = 30, show_row_names = TRUE,
21 21
   \item{overlap}{how to group numeric columns. If the overlapping rate between the ranges in the current column and previous numeric column is larger than this value, the two columns are thought under same measurement and should be grouped.}
22 22
   \item{nlevel}{If the number of levels of a character column is larger than this value, the column will be excluded.}
23 23
   \item{show_row_names}{whether show row names after the last heatmap if there are row names.}
24
+  \item{show_column_names}{whether show column names for all heatmaps}
24 25
   \item{group}{a list of index that defines the groupping}
25
-  \item{group_name}{names for each group}
26
+  \item{group_names}{names for each group}
27
+  \item{main_heatmap}{which group is the main heatmap}
28
+  \item{km}{apply k-means clustering on rows for the main heatmap}
29
+  \item{split}{set a splitting variable on rows for the main heatmap}
26 30
   \item{cluster_rows}{whether perform clustering on rows of the first heatmap}
27 31
   \item{cluster_columns}{whether perform clustering on columns for all heatmaps}
32
+  \item{...}{pass to \code{\link{draw,HeatmapList-method}} or \code{\link{make_layout,HeatmapList-method}}}
28 33
 
29 34
 }
30 35
 \details{
... ...
@@ -45,8 +50,12 @@ Zuguang Gu <z.gu@dkfz.de>
45 50
 
46 51
 }
47 52
 \examples{
48
-df = data.frame(x = rnorm(10), y = rnorm(10), z = rnorm(10, 10), 
49
-    l1 = letters[1:10], l2 = LETTERS[1:10])
53
+df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], letters[1:4])),
54
+                large = runif(10)*100,
55
+                t1 = sample(letters[1:3], 10, replace = TRUE),
56
+                matrix(runif(60), nrow = 10, dimnames = list(LETTERS[1:10], LETTERS[1:6])),
57
+                t2 = sample(LETTERS[1:3], 10, replace = TRUE))
50 58
 plotDataFrame(df)
51
-plotDataFrame(df, group = list(number = 1:3, letters = 4:5))
59
+plotDataFrame(df, group = list(1:4, 5, 6, 7:12, 13), group_names = c("mat1", "large", "t1", "mat2", "t2"),
60
+    main_heatmap = 4, km = 2, column_title = "column title", row_title = "row title")
52 61
 }
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: c2a58ed184d534d16fc4ec5cb5df64fa199fe5b0

change the way to overlap two intervals


Commit id: 7a90e91451128103fee12f7eeb03176aba3d724d

add plotDataFrame() which visualize a data frame



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@104970 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 15/06/2015 15:06:47
Showing1 changed files
1 1
new file mode 100644
... ...
@@ -0,0 +1,52 @@
1
+\name{plotDataFrame}
2
+\alias{plotDataFrame}
3
+\title{
4
+Visualize a data frame  
5
+
6
+
7
+}
8
+\description{
9
+Visualize a data frame  
10
+
11
+
12
+}
13
+\usage{
14
+plotDataFrame(df, overlap = 0.5, nlevel = 30, show_row_names = TRUE,
15
+    group = NULL, group_name = names(group), cluster_rows = TRUE,
16
+    cluster_columns = TRUE)
17
+}
18
+\arguments{
19
+
20
+  \item{df}{a data frame}
21
+  \item{overlap}{how to group numeric columns. If the overlapping rate between the ranges in the current column and previous numeric column is larger than this value, the two columns are thought under same measurement and should be grouped.}
22
+  \item{nlevel}{If the number of levels of a character column is larger than this value, the column will be excluded.}
23
+  \item{show_row_names}{whether show row names after the last heatmap if there are row names.}
24
+  \item{group}{a list of index that defines the groupping}
25
+  \item{group_name}{names for each group}
26
+  \item{cluster_rows}{whether perform clustering on rows of the first heatmap}
27
+  \item{cluster_columns}{whether perform clustering on columns for all heatmaps}
28
+
29
+}
30
+\details{
31
+The data frame contains information from different aspects and different measurements are applied on the same element for each row. The \code{\link{plotDataFrame}} function provides a simple and quick way to visualize information that are stored in a data frame.  
32
+
33
+There are not many advanced settings in this function. Users can customize the style of the heatmaps by constructing a \code{\link{HeatmapList}} object.  
34
+
35
+
36
+}
37
+\value{
38
+a \code{\link{HeatmapList}} object  
39
+
40
+
41
+}
42
+\author{
43
+Zuguang Gu <z.gu@dkfz.de>  
44
+
45
+
46
+}
47
+\examples{
48
+df = data.frame(x = rnorm(10), y = rnorm(10), z = rnorm(10, 10), 
49
+    l1 = letters[1:10], l2 = LETTERS[1:10])
50
+plotDataFrame(df)
51
+plotDataFrame(df, group = list(number = 1:3, letters = 4:5))
52
+}