1. ComplexHeatmap
  2. vignettes_old
  3. s1.introduction.Rmd
Browse code

remove old vignettes

jokergoo authored on 30/10/2018 12:52:23
Showing 1 changed files
vignettes_old/s1.introduction.Rmd
History View file @ b5d9976d
1 1 
deleted file mode 100755
... ... 
@@ -1,131 +0,0 @@
1 
-<!--
2 
-%\VignetteEngine{knitr}
3 
-%\VignetteIndexEntry{1. Introduction to ComplexHeatmap package}
4 
-
5 
-Introduction to ComplexHeatmap package
6 
-========================================
7 
-
8 
-**Author**: Zuguang Gu ( z.gu@dkfz.de )
9 
-
10 
-**Date**: `r Sys.Date()`
11 
-
12 
-
13 
-```{r global_settings, echo = FALSE, message = FALSE}
14 
-library(markdown)
15 
-options(markdown.HTML.options = c(options('markdown.HTML.options')[[1]], "toc"))
16 
-
17 
-library(knitr)
18 
-knitr::opts_chunk$set(
19 
-    error = FALSE,
20 
-    tidy  = FALSE,
21 
-    message = FALSE,
22 
-    fig.align = "center",
23 
-    fig.width = 5,
24 
-    fig.height = 5)
25 
-options(markdown.HTML.stylesheet = "custom.css")
26 
-
27 
-options(width = 100)
28 
-```
29 
-
30 
-Complex heatmaps are efficient to visualize associations
31 
-between different sources of data sets and reveal potential structures.
32 
-Here the **ComplexHeatmap** package provides a highly flexible way to arrange
33 
-multiple heatmaps and supports self-defined annotation graphics.
34 
-
35 
-## General design
36 
-
37 
-Generally, a heatmap list contains several heatmaps and row annotations.
38 
-
39 
-```{r design, echo = FALSE, fig.width = 10, fig.height = 5}
40 
-source("design.R")
41 
-```
42 
-
43 
-Surrounding the heatmap list,
44 
-there are legends for heatmaps and annotations, also there are titles which are placed
45 
-on the four sides of the heatmap list. And for each heatmap, there are also different components
46 
-surrounding the heatmap body.
47 
-
48 
-The **ComplexHeatmap** package is implemented in an object-oriented way. To describe a heatmap list,
49 
-there are following classes:
50 
-
51 
-- `Heatmap` class: a single heatmap containing heatmap body, row/column names, titles, dendrograms and column annotations.
52 
-- `HeatmapList` class: a list of heatmaps and row annotations.
53 
-- `HeatmapAnnotation` class: defines a list of row annotations and column annotations.
54 
-
55 
-There are also several internal classes:
56 
-
57 
-- `SingleAnnotation` class: defines a single row annotation or column annotation.
58 
-- `ColorMapping` class: mapping from values to colors.
59 
-
60 
-**ComplexHeatmap** is implemented under **grid** system, so users should know basic **grid** functionality
61 
-to get full use of the package.
62 
-
63 
-## Vignettes
64 
-
65 
-There are several vignettes in the package. Each vignette focuses on one specific topic. Following
66 
-lists the general topics discussed in these vignettes:
67 
-
68 
-  1. [**Making a Single Heatmap**](s2.single_heatmap.html)
69 
-
70 
-    This vignette introduces the basic configuration for making a single heatmap. Similar as other
71 
-    R functions/packages, the basic usage is quite similar, but there are several unique features
72 
-    for **ComplexHeamtap** package.
73 
-    - Works both for numeric matrix and character matrix.
74 
-    - For numeric matrix which contains continuous values, the package allows a color mapping function
75 
-      which can give more accurate colors and be robust to outliers.
76 
-    - Highly flexible for clustering. You can define the distance method for clustering by:
77 
-          * a pre-defined distance such as "euclidean" or "pearson",
78 
-          * a self-defined function which calculates distance from a matrix,
79 
-          * a self-defined function which calculates distance from two vectors.
80 
-
81 
-        You can define the clustering method by:
82 
-          * a clustering function such as `diana()` from **cluster** package
83 
-          * a `hclust` or `dendrogram` object.
84 
-    - `NA` is allowed for clustering and heatmap visualization.
85 
-    - Dendrogram and dimension names can be put on any side of the heatmap.
86 
-    - Rows on the heatmap can be split by `cutree`, by `kmeans` or by a data frame which contains
87 
-      different levels that split the heatmap.
88 
-    - The heatmap body itself can be completely self-defined.
89 
-
90 
-  2. [**Making a List of Heatmaps**](s3.a_list_of_heatmaps.html)
91 
-
92 
-    This vignette introduces how to concatenate a list of heatmaps and how adjustment is applied to keep
93 
-    the correspondence of the heatmaps.
94 
-
95 
-  3. [**Heatmap Annotations**](s4.heatmap_annotation.html)
96 
-
97 
-    This vignette introduces the concept of the heatmap annotation and demonstrates how to make simple annotations
98 
-    as well as complex annotations. Also, the vignette explains the difference between column annotations
99 
-    and row annotations.
100 
-
101 
-  4. [**Heatmap and Annotation Legends**](s5.legend.html)
102 
-
103 
-    This vignette introduces how to configurate the heatmap legend and annotation legend, also
104 
-    how to add self-defined legends.
105 
-
106 
-  5. [**Heatmap Decoration**](s6.heatmap_decoration.html)
107 
-
108 
-    This vignette introduces methods to add more self-defined graphics to the heatmaps after the heatmaps
109 
-    are generated.
110 
-
111 
-  6. [**Interactive with Heatmaps**](s7.interactive.html)
112 
-
113 
-    How to select a region in the heatmap to retrieve the sub-matrix.
114 
-
115 
-  7. [**OncoPrint**](s8.oncoprint.html)
116 
-
117 
-    How to make an oncoPrint.
118 
-
119 
-  8. [**Examples**](s9.examples.html)
120 
-
121 
-    More simulated and real-world examples are shown in this vignette.
122 
-
123 
-In the supplementaries of [the ComplexHeatmap paper](http://bioinformatics.oxfordjournals.org/content/early/2016/05/20/bioinformatics.btw313.abstract), there are four comprehensive examples which are applied
124 
-on real-world high-throughput datasets. [The examples can be found here.](http://jokergoo.github.io/supplementary/ComplexHeatmap-supplementary1-4/index.html)
125 
-
126 
-Also [my blog](http://jokergoo.github.io/blog.html) has some examples and tips for making better complex heatmaps.
127 
-
128 
-
129 
-
Browse code

a backup push

Zuguang Gu authored on 18/09/2018 10:40:29
Showing 1 changed files
vignettes_old/s1.introduction.Rmd
History View file @ 30d2c5b2
1 1 
new file mode 100755
... ... 
@@ -0,0 +1,131 @@
1 
+<!--
2 
+%\VignetteEngine{knitr}
3 
+%\VignetteIndexEntry{1. Introduction to ComplexHeatmap package}
4 
+-->
5 
+
6 
+Introduction to ComplexHeatmap package
7 
+========================================
8 
+
9 
+**Author**: Zuguang Gu ( z.gu@dkfz.de )
10 
+
11 
+**Date**: `r Sys.Date()`
12 
+
13 
+-------------------------------------------------------------
14 
+
15 
+```{r global_settings, echo = FALSE, message = FALSE}
16 
+library(markdown)
17 
+options(markdown.HTML.options = c(options('markdown.HTML.options')[[1]], "toc"))
18 
+
19 
+library(knitr)
20 
+knitr::opts_chunk$set(
21 
+    error = FALSE,
22 
+    tidy  = FALSE,
23 
+    message = FALSE,
24 
+    fig.align = "center",
25 
+    fig.width = 5,
26 
+    fig.height = 5)
27 
+options(markdown.HTML.stylesheet = "custom.css")
28 
+
29 
+options(width = 100)
30 
+```
31 
+
32 
+Complex heatmaps are efficient to visualize associations
33 
+between different sources of data sets and reveal potential structures.
34 
+Here the **ComplexHeatmap** package provides a highly flexible way to arrange
35 
+multiple heatmaps and supports self-defined annotation graphics.
36 
+
37 
+## General design
38 
+
39 
+Generally, a heatmap list contains several heatmaps and row annotations.
40 
+
41 
+```{r design, echo = FALSE, fig.width = 10, fig.height = 5}
42 
+source("design.R")
43 
+```
44 
+
45 
+Surrounding the heatmap list,
46 
+there are legends for heatmaps and annotations, also there are titles which are placed
47 
+on the four sides of the heatmap list. And for each heatmap, there are also different components
48 
+surrounding the heatmap body.
49 
+
50 
+The **ComplexHeatmap** package is implemented in an object-oriented way. To describe a heatmap list,
51 
+there are following classes:
52 
+
53 
+- `Heatmap` class: a single heatmap containing heatmap body, row/column names, titles, dendrograms and column annotations.
54 
+- `HeatmapList` class: a list of heatmaps and row annotations.
55 
+- `HeatmapAnnotation` class: defines a list of row annotations and column annotations.
56 
+
57 
+There are also several internal classes:
58 
+
59 
+- `SingleAnnotation` class: defines a single row annotation or column annotation.
60 
+- `ColorMapping` class: mapping from values to colors.
61 
+
62 
+**ComplexHeatmap** is implemented under **grid** system, so users should know basic **grid** functionality
63 
+to get full use of the package.
64 
+
65 
+## Vignettes
66 
+
67 
+There are several vignettes in the package. Each vignette focuses on one specific topic. Following
68 
+lists the general topics discussed in these vignettes:
69 
+
70 
+  1. [**Making a Single Heatmap**](s2.single_heatmap.html)
71 
+
72 
+    This vignette introduces the basic configuration for making a single heatmap. Similar as other
73 
+    R functions/packages, the basic usage is quite similar, but there are several unique features
74 
+    for **ComplexHeamtap** package.
75 
+    - Works both for numeric matrix and character matrix.
76 
+    - For numeric matrix which contains continuous values, the package allows a color mapping function
77 
+      which can give more accurate colors and be robust to outliers.
78 
+    - Highly flexible for clustering. You can define the distance method for clustering by:
79 
+          * a pre-defined distance such as "euclidean" or "pearson",
80 
+          * a self-defined function which calculates distance from a matrix,
81 
+          * a self-defined function which calculates distance from two vectors.
82 
+
83 
+        You can define the clustering method by:
84 
+          * a clustering function such as `diana()` from **cluster** package
85 
+          * a `hclust` or `dendrogram` object.
86 
+    - `NA` is allowed for clustering and heatmap visualization.
87 
+    - Dendrogram and dimension names can be put on any side of the heatmap.
88 
+    - Rows on the heatmap can be split by `cutree`, by `kmeans` or by a data frame which contains
89 
+      different levels that split the heatmap.
90 
+    - The heatmap body itself can be completely self-defined.
91 
+
92 
+  2. [**Making a List of Heatmaps**](s3.a_list_of_heatmaps.html)
93 
+
94 
+    This vignette introduces how to concatenate a list of heatmaps and how adjustment is applied to keep
95 
+    the correspondence of the heatmaps.
96 
+
97 
+  3. [**Heatmap Annotations**](s4.heatmap_annotation.html)
98 
+
99 
+    This vignette introduces the concept of the heatmap annotation and demonstrates how to make simple annotations
100 
+    as well as complex annotations. Also, the vignette explains the difference between column annotations
101 
+    and row annotations.
102 
+
103 
+  4. [**Heatmap and Annotation Legends**](s5.legend.html)
104 
+
105 
+    This vignette introduces how to configurate the heatmap legend and annotation legend, also
106 
+    how to add self-defined legends.
107 
+
108 
+  5. [**Heatmap Decoration**](s6.heatmap_decoration.html)
109 
+
110 
+    This vignette introduces methods to add more self-defined graphics to the heatmaps after the heatmaps
111 
+    are generated.
112 
+
113 
+  6. [**Interactive with Heatmaps**](s7.interactive.html)
114 
+
115 
+    How to select a region in the heatmap to retrieve the sub-matrix.
116 
+
117 
+  7. [**OncoPrint**](s8.oncoprint.html)
118 
+
119 
+    How to make an oncoPrint.
120 
+
121 
+  8. [**Examples**](s9.examples.html)
122 
+
123 
+    More simulated and real-world examples are shown in this vignette.
124 
+
125 
+In the supplementaries of [the ComplexHeatmap paper](http://bioinformatics.oxfordjournals.org/content/early/2016/05/20/bioinformatics.btw313.abstract), there are four comprehensive examples which are applied
126 
+on real-world high-throughput datasets. [The examples can be found here.](http://jokergoo.github.io/supplementary/ComplexHeatmap-supplementary1-4/index.html)
127 
+
128 
+Also [my blog](http://jokergoo.github.io/blog.html) has some examples and tips for making better complex heatmaps.
129 
+
130 
+
131 
+