1. ggtree
  2. man
  3. gheatmap.Rd
Browse code

update man files and fixed R check

Guangchuang Yu authored on 23/03/2022 04:13:34
Showing 1 changed files
man/gheatmap.Rd
History View file @ fbeaa25d
... ... 
@@ -30,43 +30,50 @@ gheatmap(
30 30
31 31 
 \item{data}{matrix or data.frame}
32 32
33 
-\item{offset}{offset of heatmap to tree}
33 
+\item{offset}{set offset of the heatmap to tree}
34 34
35 
-\item{width}{total width of heatmap, compare to width of tree}
35 
+\item{width}{total width of heatmap, compare to width of tree, defaults to 1,
36 
+which means they are of the same length}
36 37
37 
-\item{low}{color of lowest value}
38 
+\item{low}{set color of the lowest value, defaults to "green"}
38 39
39 
-\item{high}{color of highest value}
40 
+\item{high}{set color of the highest value, defaults to "red"}
40 41
41 
-\item{color}{color of heatmap cell border}
42 
+\item{color}{set color of heatmap cell border, defaults to "white"}
42 43
43 
-\item{colnames}{logical, add matrix colnames or not}
44 
+\item{colnames}{logical, whether to add matrix colnames, defaults to "TRUE"}
44 45
45 
-\item{colnames_position}{one of 'bottom' or 'top'}
46 
+\item{colnames_position}{set the position of the colnames, one of 'bottom' (default) or 'top'}
46 47
47 
-\item{colnames_angle}{angle of column names}
48 
+\item{colnames_angle}{set the angle of colnames}
48 49
49 
-\item{colnames_level}{levels of colnames}
50 
+\item{colnames_level}{set levels of colnames}
50 51
51 
-\item{colnames_offset_x}{x offset for column names}
52 
+\item{colnames_offset_x}{set x offset for colnames}
52 53
53 
-\item{colnames_offset_y}{y offset for column names}
54 
+\item{colnames_offset_y}{set y offset for colnames}
54 55
55 
-\item{font.size}{font size of matrix colnames}
56 
+\item{font.size}{set font size of matrix colnames}
56 57
57 
-\item{family}{font of matrix colnames}
58 
+\item{family}{font of matrix colnames, can be any supported font}
58 59
59 
-\item{hjust}{hjust for column names (0: align left, 0.5: align center, 1: align righ)}
60 
+\item{hjust}{adjust horizonal position of column names (0: align left, 0.5: align center (default), 1: align righ)}
60 61
61 62 
 \item{legend_title}{title of fill legend}
62 63
63 
-\item{custom_column_labels}{instead of the column names from a matrix, input a custom vector of column labels}
64 
+\item{custom_column_labels}{instead of using the colnames from the input matrix/data.frame,
65 
+input a custom vector to be set as column labels}
64 66 
 }
65 67 
 \value{
66 68 
 tree view
67 69 
 }
68 70 
 \description{
69 
-append a heatmap of a matrix to right side of phylogenetic tree
71 
+append a heatmap of a matrix to the right side of a phylogenetic tree
72 
+}
73 
+\references{
74 
+For demonstration of this function, please refer to chapter 7.3 of
75 
+\emph{Data Integration, Manipulation and Visualization of Phylogenetic Trees}
76 
+\url{http://yulab-smu.top/treedata-book/index.html} by Guangchuang Yu.
70 77 
 }
71 78 
 \author{
72 79 
 Guangchuang Yu
Browse code

fixed R check

Guangchuang Yu authored on 15/09/2021 02:29:08
Showing 1 changed files
man/gheatmap.Rd
History View file @ 5d2d10d4
... ... 
@@ -21,7 +21,8 @@ gheatmap(
21 21 
   font.size = 4,
22 22 
   family = "",
23 23 
   hjust = 0.5,
24 
-  legend_title = "value"
24 
+  legend_title = "value",
25 
+  custom_column_labels = NULL
25 26 
 )
26 27 
 }
27 28 
 \arguments{
... ... 
@@ -58,6 +59,8 @@ gheatmap(
58 59 
 \item{hjust}{hjust for column names (0: align left, 0.5: align center, 1: align righ)}
59 60
60 61 
 \item{legend_title}{title of fill legend}
62 
+
63 
+\item{custom_column_labels}{instead of the column names from a matrix, input a custom vector of column labels}
61 64 
 }
62 65 
 \value{
63 66 
 tree view
Browse code

update docs

Guangchuang Yu authored on 19/03/2020 13:35:36
Showing 1 changed files
man/gheatmap.Rd
History View file @ cd229bf6
... ... 
@@ -19,6 +19,7 @@ gheatmap(
19 19 
   colnames_offset_x = 0,
20 20 
   colnames_offset_y = 0,
21 21 
   font.size = 4,
22 
+  family = "",
22 23 
   hjust = 0.5,
23 24 
   legend_title = "value"
24 25 
 )
... ... 
@@ -52,6 +53,8 @@ gheatmap(
52 53
53 54 
 \item{font.size}{font size of matrix colnames}
54 55
56 
+\item{family}{font of matrix colnames}
57 
+
55 58 
 \item{hjust}{hjust for column names (0: align left, 0.5: align center, 1: align righ)}
56 59
57 60 
 \item{legend_title}{title of fill legend}
Browse code

clip="off" and update docs

Guangchuang Yu authored on 06/12/2019 03:01:17
Showing 1 changed files
man/gheatmap.Rd
History View file @ fb0a330e
... ... 
@@ -4,12 +4,24 @@
4 4 
 \alias{gheatmap}
5 5 
 \title{gheatmap}
6 6 
 \usage{
7 
-gheatmap(p, data, offset = 0, width = 1, low = "green",
8 
-  high = "red", color = "white", colnames = TRUE,
9 
-  colnames_position = "bottom", colnames_angle = 0,
10 
-  colnames_level = NULL, colnames_offset_x = 0,
11 
-  colnames_offset_y = 0, font.size = 4, hjust = 0.5,
12 
-  legend_title = "value")
7 
+gheatmap(
8 
+  p,
9 
+  data,
10 
+  offset = 0,
11 
+  width = 1,
12 
+  low = "green",
13 
+  high = "red",
14 
+  color = "white",
15 
+  colnames = TRUE,
16 
+  colnames_position = "bottom",
17 
+  colnames_angle = 0,
18 
+  colnames_level = NULL,
19 
+  colnames_offset_x = 0,
20 
+  colnames_offset_y = 0,
21 
+  font.size = 4,
22 
+  hjust = 0.5,
23 
+  legend_title = "value"
24 
+)
13 25 
 }
14 26 
 \arguments{
15 27 
 \item{p}{tree view}
Browse code

legend_title parameter in gheatmap

Guangchuang Yu authored on 16/05/2019 07:07:03
Showing 1 changed files
man/gheatmap.Rd
History View file @ c00aac1c
... ... 
@@ -8,7 +8,8 @@ gheatmap(p, data, offset = 0, width = 1, low = "green",
8 8 
   high = "red", color = "white", colnames = TRUE,
9 9 
   colnames_position = "bottom", colnames_angle = 0,
10 10 
   colnames_level = NULL, colnames_offset_x = 0,
11 
-  colnames_offset_y = 0, font.size = 4, hjust = 0.5)
11 
+  colnames_offset_y = 0, font.size = 4, hjust = 0.5,
12 
+  legend_title = "value")
12 13 
 }
13 14 
 \arguments{
14 15 
 \item{p}{tree view}
... ... 
@@ -40,6 +41,8 @@ gheatmap(p, data, offset = 0, width = 1, low = "green",
40 41 
 \item{font.size}{font size of matrix colnames}
41 42
42 43 
 \item{hjust}{hjust for column names (0: align left, 0.5: align center, 1: align righ)}
44 
+
45 
+\item{legend_title}{title of fill legend}
43 46 
 }
44 47 
 \value{
45 48 
 tree view
Browse code

bug fixed of viewClade

Guangchuang Yu authored on 07/08/2018 12:07:15
Showing 1 changed files
man/gheatmap.Rd
History View file @ c3727414
... ... 
@@ -4,9 +4,10 @@
4 4 
 \alias{gheatmap}
5 5 
 \title{gheatmap}
6 6 
 \usage{
7 
-gheatmap(p, data, offset = 0, width = 1, low = "green", high = "red",
8 
-  color = "white", colnames = TRUE, colnames_position = "bottom",
9 
-  colnames_angle = 0, colnames_level = NULL, colnames_offset_x = 0,
7 
+gheatmap(p, data, offset = 0, width = 1, low = "green",
8 
+  high = "red", color = "white", colnames = TRUE,
9 
+  colnames_position = "bottom", colnames_angle = 0,
10 
+  colnames_level = NULL, colnames_offset_x = 0,
10 11 
   colnames_offset_y = 0, font.size = 4, hjust = 0.5)
11 12 
 }
12 13 
 \arguments{
Browse code

geom_motif #148

guangchuang yu authored on 22/08/2017 08:22:37
Showing 1 changed files
man/gheatmap.Rd
History View file @ 363c0555
... ... 
@@ -49,4 +49,3 @@ append a heatmap of a matrix to right side of phylogenetic tree
49 49 
 \author{
50 50 
 Guangchuang Yu
51 51 
 }
52 
-
Browse code

update docs

guangchuang yu authored on 16/08/2017 02:36:13
Showing 1 changed files
man/gheatmap.Rd
History View file @ f0e199ad
... ... 
@@ -49,3 +49,4 @@ append a heatmap of a matrix to right side of phylogenetic tree
49 49 
 \author{
50 50 
 Guangchuang Yu
51 51 
 }
52 
+
Browse code

add extend parameter in geom_cladelabel

guangchuang yu authored on 26/07/2017 02:13:53
Showing 1 changed files
man/gheatmap.Rd
History View file @ 353dfa09
... ... 
@@ -49,4 +49,3 @@ append a heatmap of a matrix to right side of phylogenetic tree
49 49 
 \author{
50 50 
 Guangchuang Yu
51 51 
 }
52 
-
Browse code

facet_plot

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@120776 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 07/09/2016 01:36:05
Showing 1 changed files
man/gheatmap.Rd
History View file @ 1652e9e8
... ... 
@@ -6,7 +6,8 @@
6 6 
 \usage{
7 7 
 gheatmap(p, data, offset = 0, width = 1, low = "green", high = "red",
8 8 
   color = "white", colnames = TRUE, colnames_position = "bottom",
9 
-  colnames_level = NULL, font.size = 4)
9 
+  colnames_angle = 0, colnames_level = NULL, colnames_offset_x = 0,
10 
+  colnames_offset_y = 0, font.size = 4, hjust = 0.5)
10 11 
 }
11 12 
 \arguments{
12 13 
 \item{p}{tree view}
... ... 
@@ -27,9 +28,17 @@ gheatmap(p, data, offset = 0, width = 1, low = "green", high = "red",
27 28
28 29 
 \item{colnames_position}{one of 'bottom' or 'top'}
29 30
31 
+\item{colnames_angle}{angle of column names}
32 
+
30 33 
 \item{colnames_level}{levels of colnames}
31 34
35 
+\item{colnames_offset_x}{x offset for column names}
36 
+
37 
+\item{colnames_offset_y}{y offset for column names}
38 
+
32 39 
 \item{font.size}{font size of matrix colnames}
40 
+
41 
+\item{hjust}{hjust for column names (0: align left, 0.5: align center, 1: align righ)}
33 42 
 }
34 43 
 \value{
35 44 
 tree view
Browse code

new features

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@113679 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 16/02/2016 04:04:44
Showing 1 changed files
man/gheatmap.Rd
History View file @ e4ea056a
... ... 
@@ -1,12 +1,12 @@
1 1 
 % Generated by roxygen2: do not edit by hand
2 
-% Please edit documentation in R/gplot.R
2 
+% Please edit documentation in R/gheatmap.R
3 3 
 \name{gheatmap}
4 4 
 \alias{gheatmap}
5 5 
 \title{gheatmap}
6 6 
 \usage{
7 7 
 gheatmap(p, data, offset = 0, width = 1, low = "green", high = "red",
8 8 
   color = "white", colnames = TRUE, colnames_position = "bottom",
9 
-  font.size = 4)
9 
+  colnames_level = NULL, font.size = 4)
10 10 
 }
11 11 
 \arguments{
12 12 
 \item{p}{tree view}
... ... 
@@ -27,6 +27,8 @@ gheatmap(p, data, offset = 0, width = 1, low = "green", high = "red",
27 27
28 28 
 \item{colnames_position}{one of 'bottom' or 'top'}
29 29
30 
+\item{colnames_level}{levels of colnames}
31 
+
30 32 
 \item{font.size}{font size of matrix colnames}
31 33 
 }
32 34 
 \value{
Browse code

lots updates

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@111813 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 22/12/2015 04:08:02
Showing 1 changed files
man/gheatmap.Rd
History View file @ 6c9cd355
... ... 
@@ -1,4 +1,4 @@
1 
-% Generated by roxygen2 (4.1.1): do not edit by hand
1 
+% Generated by roxygen2: do not edit by hand
2 2 
 % Please edit documentation in R/gplot.R
3 3 
 \name{gheatmap}
4 4 
 \alias{gheatmap}
Browse code

subview function

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107837 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 27/08/2015 04:23:07
Showing 1 changed files
man/gheatmap.Rd
History View file @ 2ab2876d
... ... 
@@ -5,7 +5,8 @@
5 5 
 \title{gheatmap}
6 6 
 \usage{
7 7 
 gheatmap(p, data, offset = 0, width = 1, low = "green", high = "red",
8 
-  color = "white", colnames = TRUE, font.size = 4)
8 
+  color = "white", colnames = TRUE, colnames_position = "bottom",
9 
+  font.size = 4)
9 10 
 }
10 11 
 \arguments{
11 12 
 \item{p}{tree view}
... ... 
@@ -24,6 +25,8 @@ gheatmap(p, data, offset = 0, width = 1, low = "green", high = "red",
24 25
25 26 
 \item{colnames}{logical, add matrix colnames or not}
26 27
28 
+\item{colnames_position}{one of 'bottom' or 'top'}
29 
+
27 30 
 \item{font.size}{font size of matrix colnames}
28 31 
 }
29 32 
 \value{
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 7c6eb6f90218928633147306f8bacd86a5cdd944

mask & scale_x_ggtree function



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@104466 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 02/06/2015 10:18:54
Showing 1 changed files
man/gheatmap.Rd
History View file @ 2dc67dc5
... ... 
@@ -4,7 +4,7 @@
4 4 
 \alias{gheatmap}
5 5 
 \title{gheatmap}
6 6 
 \usage{
7 
-gheatmap(p, data, offset = 0, width = NULL, low = "green", high = "red",
7 
+gheatmap(p, data, offset = 0, width = 1, low = "green", high = "red",
8 8 
   color = "white", colnames = TRUE, font.size = 4)
9 9 
 }
10 10 
 \arguments{
... ... 
@@ -14,7 +14,7 @@ gheatmap(p, data, offset = 0, width = NULL, low = "green", high = "red",
14 14
15 15 
 \item{offset}{offset of heatmap to tree}
16 16
17 
-\item{width}{width of each cell in heatmap}
17 
+\item{width}{total width of heatmap, compare to width of tree}
18 18
19 19 
 \item{low}{color of lowest value}
20 20
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 8450c8e87951a6eafa247c28535dd93b7d9aa9fa

o update add_colorbar <2015-05-21, Thu>



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@104028 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 21/05/2015 09:48:31
Showing 1 changed files
man/gheatmap.Rd
History View file @ 77d62986
... ... 
@@ -4,7 +4,7 @@
4 4 
 \alias{gheatmap}
5 5 
 \title{gheatmap}
6 6 
 \usage{
7 
-gheatmap(p, data, offset = 0, width, low = "green", high = "red",
7 
+gheatmap(p, data, offset = 0, width = NULL, low = "green", high = "red",
8 8 
   color = "white", colnames = TRUE, font.size = 4)
9 9 
 }
10 10 
 \arguments{
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: be8421a1e7f3fa220c129ffad6e504004c9c2a8d

update vignette


Commit id: c7eea4289c6eba9f4b8b9ebd94f43434f72a95c3

gheatmap


Commit id: 9ab91767cb73fcf158295ce393a6a3c10c2974bc

add_legend



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@103916 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 18/05/2015 11:18:46
Showing 1 changed files
man/gheatmap.Rd
History View file @ ad07ec89
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,38 @@
1 
+% Generated by roxygen2 (4.1.1): do not edit by hand
2 
+% Please edit documentation in R/gplot.R
3 
+\name{gheatmap}
4 
+\alias{gheatmap}
5 
+\title{gheatmap}
6 
+\usage{
7 
+gheatmap(p, data, offset = 0, width, low = "green", high = "red",
8 
+  color = "white", colnames = TRUE, font.size = 4)
9 
+}
10 
+\arguments{
11 
+\item{p}{tree view}
12 
+
13 
+\item{data}{matrix or data.frame}
14 
+
15 
+\item{offset}{offset of heatmap to tree}
16 
+
17 
+\item{width}{width of each cell in heatmap}
18 
+
19 
+\item{low}{color of lowest value}
20 
+
21 
+\item{high}{color of highest value}
22 
+
23 
+\item{color}{color of heatmap cell border}
24 
+
25 
+\item{colnames}{logical, add matrix colnames or not}
26 
+
27 
+\item{font.size}{font size of matrix colnames}
28 
+}
29 
+\value{
30 
+tree view
31 
+}
32 
+\description{
33 
+append a heatmap of a matrix to right side of phylogenetic tree
34 
+}
35 
+\author{
36 
+Guangchuang Yu
37 
+}
38 
+