1. KEGGlincs
  2. README.md
Browse code

replace BiocInstaller biocLite mentions with BiocManager

LiNk-NY authored on 30/08/2018 17:51:12
Showing 1 changed files
README.md
History View file @ e67a9df
... ... 
@@ -10,11 +10,12 @@ Installation:
10 10
11 11 
 ```{r}
12 12 
 #Make sure that the following bioconductor packages are installed
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-source("http://bioconductor.org/biocLite.R")
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-biocLite(c("hgu133a.db", "KEGGgraph", "KEGGREST", "KOdata"))
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+if (!requireNamespace("BiocManager", quietly=TRUE))
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+    install.packages("BiocManager")
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+BiocManager::install(c("hgu133a.db", "KEGGgraph", "KEGGREST", "KOdata"))
15 16
16 17 
 #Download package
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-biocLite("KEGGlincs")
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+BiocManager::install("KEGGlincs")
18 19
19 20 
 #Load/activate package for use
20 21 
 library(KEGGlincs)
Browse code

update and fix images/links in README

From: vandersm <vandersm@mail.uc.edu>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGlincs@127661 bc3139a8-67e5-0310-9ffc-ced21a209358

Shana White authored on 23/03/2017 16:05:34
Showing 1 changed files
README.md
History View file @ a23de20
... ... 
@@ -1,7 +1,7 @@
1 1 
 ---
2 2 
 title: "Introduction to KEGGlincs"
3 3 
 author: "Shana White"
4 
-date: "9/30/2016"
4 
+date: "03/23/2017"
5 5 
 ---
6 6
7 7 
 by [Shana White](https://github.com/shanawhite-UC)
... ... 
@@ -9,25 +9,18 @@ by [Shana White](https://github.com/shanawhite-UC)
9 9 
 Installation:
10 10
11 11 
 ```{r}
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-#In order to avoid unnecessary warnings, check for installation of devtools (>= 1.12.0):
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-packageVersion("devtools")
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-[1] ‘1.12.0’
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-
16 12 
 #Make sure that the following bioconductor packages are installed
17 13 
 source("http://bioconductor.org/biocLite.R")
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-biocLite(c("hgu133a.db", "KEGGgraph", "KEGGREST"))
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-
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-#Companion data package (L1000 Knock-out data and baseline expression data)
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-devtools::install_git("https://github.com/shanawhite-UC/KOdata")
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+biocLite(c("hgu133a.db", "KEGGgraph", "KEGGREST", "KOdata"))
22 15
23 
-#Main package
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-devtools::install_git("https://github.com/shanawhite-UC/KEGGlincs")
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+#Download package
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+biocLite("KEGGlincs")
25 18
26 19 
 #Load/activate package for use
27 20 
 library(KEGGlincs)
28 21 
 ```
29 22
30 
-#Overview of package
23 
+# Overview of package
31 24
32 25 
 ![](https://github.com/uc-bd2k/KEGGlincs/blob/master/vignettes/image_files/KEGGlincs_overview.jpeg)
33 26
... ... 
@@ -35,24 +28,24 @@ library(KEGGlincs)
35 28 
 KEGGlincs is an R package that provides a seamless interface for viewing detailed versions of KEGG pathways in Cytoscape such that the exact relationships (*edges*) that exist between pathway elements (*nodes*) are visualized in a meaningful manner.
36 29
37 30 
 This package is intended to be used as a tool to accurately regenerate KEGG pathways with *expanded* edges that are marked-up (in terms of color or color+width) to portray specific *edge attributes*.  Specifically,
38 
-- the edges are *expanded* to represent all relationships between genes encoded by the [KGML file] (http://www.kegg.jp/kegg/xml/) but not necessarily represented in the original [KEGG] pathway.  This 'expansion' occurs either because:
31 
+- the edges are *expanded* to represent all relationships between genes encoded by the [KGML file](http://www.kegg.jp/kegg/xml/) but not necessarily represented in the original [KEGG] pathway.  This 'expansion' occurs either because:
39 32 
   - one node may represent many [often paralogous] genes.
40 33 
   - a node is of type 'group' and represents two or more genes that are part of the same functional complex.
41 34 
 - the *edge attributes* represented can be specified by the user as either:
42 35 
   - Functional - the exact *type* and [in some cases] *subtype* of the relationship defined by the KGML file.
43 
-  - Data driven - based on quantitative experimental evidence for gene-gene relationships generated by experimental data.  As an added feature and motivating example, this package gives users an opportunity to use [LINCS L1000 knock-out data] (http://www.lincscloud.org/l1000/) in order to analyze/visualize the pathway edges as they pertain to specific [cell lines] (http://www.lincscloud.org/cell_types/).
36 
+  - Data driven - based on quantitative experimental evidence for gene-gene relationships generated by experimental data.  As an added feature and motivating example, this package gives users an opportunity to use [LINCS L1000 knock-out data](http://www.lincscloud.org/l1000/) in order to analyze/visualize the pathway edges as they pertain to specific [cell lines](http://www.lincscloud.org/cell_types/).
44 37
45 
-Aside from edge-specific annotation/mark-up, a unique feature of this package lies in the ability for users to generate graph objects in R and send them to [Cytoscape] (http://www.cytoscape.org/) for an interactive visualization experience via utilities developed by the [cyREST team] (https://github.com/idekerlab/cy-rest-R).
38 
+Aside from edge-specific annotation/mark-up, a unique feature of this package lies in the ability for users to generate graph objects in R and send them to [Cytoscape](http://www.cytoscape.org/) for an interactive visualization experience via utilities developed by the [cyREST team](https://github.com/idekerlab/cy-rest-R).
46 39
47 40 
 The following example showcases the ideas described above.
48 41
49 
-##Example: p53 pathway
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+## Example: p53 pathway
50 43
51 
-###Original KEGG pathway:
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-![p53 pathway from KEGG website] (http://www.genome.jp/kegg/pathway/hsa/hsa04115.png)
44 
+### Original KEGG pathway:
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+![p53 pathway from KEGG website](http://www.genome.jp/kegg/pathway/hsa/hsa04115.png)
53 46
54 
-###Using KEGGlincs without adding data:
55 
-####Detailed pathway visualized in Cytoscape
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+### Using KEGGlincs without adding data:
48 
+#### Detailed pathway visualized in Cytoscape
56 49 
  - Explicitly shows all documented edges
57 50 
  - Color-coded to easily interpret edge type (i.e. activation, inhibition, etc.)
58 51 
    - Edge color key: <a><img src="https://cdn.rawgit.com/uc-bd2k/KEGGlincs/master/vignettes/image_files/color_1.svg"/></a>
... ... 
@@ -61,12 +54,12 @@ The following example showcases the ideas described above.
61 54 
 ```{r}
62 55 
 KEGG_lincs("hsa04115")
63 56 
 ```
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-![] (https://github.com/uc-bd2k/KEGGlincs/blob/master/vignettes/image_files/p53_default.jpeg)
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+![](https://github.com/uc-bd2k/KEGGlincs/blob/master/vignettes/image_files/p53_default.jpeg)
65 58
66 59
67 60
68 
-###Overlay pathway edges with LINCS data:
69 
-####Pathway with edge attributes generated from LINCS L1000 knock-out data, *refined* by cell-line specific expression (default option, see below), and visualized in Cytoscape
61 
+### Overlay pathway edges with LINCS data:
62 
+#### Pathway with edge attributes generated from LINCS L1000 knock-out data, *refined* by cell-line specific expression (default option, see below), and visualized in Cytoscape
70 63 
  - Explicitly shows all documented edges; edges that do not exist in the data appear but are not marked-up for interpretation [of significance].
71 64 
    - If baseline expression data is available for the selected cell-line, the pathway will be *refined* to only include edges between genes that are expressed in a given cell line.  The nodes for unexpressed genes are colored gray.
72 65 
  - Widths: Magnitude of concordance for the edge in the selected cell-type
... ... 
@@ -75,14 +68,14 @@ KEGG_lincs("hsa04115")
75 68 
 <a><img src="https://cdn.rawgit.com/uc-bd2k/KEGGlincs/master/vignettes/image_files/color_2.svg"/></a>
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77 70
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-#####Pathway specific to PC3 cell-line (Prostate cancer)
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+#### Pathway specific to PC3 cell-line (Prostate cancer)
79 72 
 ```{r}
80 73 
 KEGG_lincs("hsa04115", "PC3")
81 74 
 ```
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-![] (https://github.com/uc-bd2k/KEGGlincs/blob/master/vignettes/image_files/p53_PC3.jpeg)
75 
+![](https://github.com/uc-bd2k/KEGGlincs/blob/master/vignettes/image_files/p53_PC3.jpeg)
83 76
84 
-#####Pathway specific to HA1E cell-line (Immortalized normal kidney epithelial)
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+#### Pathway specific to HA1E cell-line (Immortalized normal kidney epithelial)
85 78 
 ```{r}
86 79 
 KEGG_lincs("hsa04115", "HA1E")
87 80 
 ```
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-![] (https://github.com/uc-bd2k/KEGGlincs/blob/master/vignettes/image_files/p53_HA1E.jpeg)
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+![](https://github.com/uc-bd2k/KEGGlincs/blob/master/vignettes/image_files/p53_HA1E.jpeg)
89 82 
\ No newline at end of file
Browse code

change .png to .jpeg for overview pic

From: Shana White <vandersm@mail.uc.edu>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGlincs@124831 bc3139a8-67e5-0310-9ffc-ced21a209358

Shana White authored on 05/12/2016 19:12:03
Showing 1 changed files
README.md
History View file @ e72159d
... ... 
@@ -29,7 +29,7 @@ library(KEGGlincs)
29 29
30 30 
 #Overview of package
31 31
32 
-![](https://github.com/uc-bd2k/KEGGlincs/blob/master/vignettes/image_files/KEGGlincs_overview.png)
32 
+![](https://github.com/uc-bd2k/KEGGlincs/blob/master/vignettes/image_files/KEGGlincs_overview.jpeg)
33 33
34 34 
 ----
35 35 
 KEGGlincs is an R package that provides a seamless interface for viewing detailed versions of KEGG pathways in Cytoscape such that the exact relationships (*edges*) that exist between pathway elements (*nodes*) are visualized in a meaningful manner.
Browse code

Adding KEGGlincs, flowPloidy, MAST, PathoStat, matter, MoonlightR, psichomics, anamiR, MutationalPatterns, HelloRanges, crisprseekplus, annotatr, meshes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGlincs@122278 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 12/10/2016 17:44:52
Showing 1 changed files
README.md
History View file @ 4614338
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,88 @@
1 
+---
2 
+title: "Introduction to KEGGlincs"
3 
+author: "Shana White"
4 
+date: "9/30/2016"
5 
+---
6 
+
7 
+by [Shana White](https://github.com/shanawhite-UC)
8 
+
9 
+Installation:
10 
+
11 
+```{r}
12 
+#In order to avoid unnecessary warnings, check for installation of devtools (>= 1.12.0):
13 
+packageVersion("devtools")
14 
+[1] ‘1.12.0’
15 
+
16 
+#Make sure that the following bioconductor packages are installed
17 
+source("http://bioconductor.org/biocLite.R")
18 
+biocLite(c("hgu133a.db", "KEGGgraph", "KEGGREST"))
19 
+
20 
+#Companion data package (L1000 Knock-out data and baseline expression data)
21 
+devtools::install_git("https://github.com/shanawhite-UC/KOdata")
22 
+
23 
+#Main package
24 
+devtools::install_git("https://github.com/shanawhite-UC/KEGGlincs")
25 
+
26 
+#Load/activate package for use
27 
+library(KEGGlincs)
28 
+```
29 
+
30 
+#Overview of package
31 
+
32 
+![](https://github.com/uc-bd2k/KEGGlincs/blob/master/vignettes/image_files/KEGGlincs_overview.png)
33 
+
34 
+----
35 
+KEGGlincs is an R package that provides a seamless interface for viewing detailed versions of KEGG pathways in Cytoscape such that the exact relationships (*edges*) that exist between pathway elements (*nodes*) are visualized in a meaningful manner.
36 
+
37 
+This package is intended to be used as a tool to accurately regenerate KEGG pathways with *expanded* edges that are marked-up (in terms of color or color+width) to portray specific *edge attributes*.  Specifically,
38 
+- the edges are *expanded* to represent all relationships between genes encoded by the [KGML file] (http://www.kegg.jp/kegg/xml/) but not necessarily represented in the original [KEGG] pathway.  This 'expansion' occurs either because:
39 
+  - one node may represent many [often paralogous] genes.
40 
+  - a node is of type 'group' and represents two or more genes that are part of the same functional complex.
41 
+- the *edge attributes* represented can be specified by the user as either:
42 
+  - Functional - the exact *type* and [in some cases] *subtype* of the relationship defined by the KGML file.
43 
+  - Data driven - based on quantitative experimental evidence for gene-gene relationships generated by experimental data.  As an added feature and motivating example, this package gives users an opportunity to use [LINCS L1000 knock-out data] (http://www.lincscloud.org/l1000/) in order to analyze/visualize the pathway edges as they pertain to specific [cell lines] (http://www.lincscloud.org/cell_types/).
44 
+
45 
+Aside from edge-specific annotation/mark-up, a unique feature of this package lies in the ability for users to generate graph objects in R and send them to [Cytoscape] (http://www.cytoscape.org/) for an interactive visualization experience via utilities developed by the [cyREST team] (https://github.com/idekerlab/cy-rest-R).
46 
+
47 
+The following example showcases the ideas described above.
48 
+
49 
+##Example: p53 pathway
50 
+
51 
+###Original KEGG pathway:
52 
+![p53 pathway from KEGG website] (http://www.genome.jp/kegg/pathway/hsa/hsa04115.png)
53 
+
54 
+###Using KEGGlincs without adding data:
55 
+####Detailed pathway visualized in Cytoscape
56 
+ - Explicitly shows all documented edges
57 
+ - Color-coded to easily interpret edge type (i.e. activation, inhibition, etc.)
58 
+   - Edge color key: <a><img src="https://cdn.rawgit.com/uc-bd2k/KEGGlincs/master/vignettes/image_files/color_1.svg"/></a>
59 
+
60 
+*Note: An open Cytoscape session is required for pathway visualization; i.e. make sure that Cytoscape is open before running the following commands*
61 
+```{r}
62 
+KEGG_lincs("hsa04115")
63 
+```
64 
+![] (https://github.com/uc-bd2k/KEGGlincs/blob/master/vignettes/image_files/p53_default.jpeg)
65 
+
66 
+
67 
+
68 
+###Overlay pathway edges with LINCS data:
69 
+####Pathway with edge attributes generated from LINCS L1000 knock-out data, *refined* by cell-line specific expression (default option, see below), and visualized in Cytoscape
70 
+ - Explicitly shows all documented edges; edges that do not exist in the data appear but are not marked-up for interpretation [of significance].
71 
+   - If baseline expression data is available for the selected cell-line, the pathway will be *refined* to only include edges between genes that are expressed in a given cell line.  The nodes for unexpressed genes are colored gray.
72 
+ - Widths: Magnitude of concordance for the edge in the selected cell-type
73 
+ - Colors: Direction and significance for the edge in the selected cell-type (based on a modified odds-ratio score).
74 
+   - Edge color key (+/- refers to *direction* of score; scores are considered significant if adjusted p-value is >= 0.05):
75 
+<a><img src="https://cdn.rawgit.com/uc-bd2k/KEGGlincs/master/vignettes/image_files/color_2.svg"/></a>
76 
+
77 
+
78 
+#####Pathway specific to PC3 cell-line (Prostate cancer)
79 
+```{r}
80 
+KEGG_lincs("hsa04115", "PC3")
81 
+```
82 
+![] (https://github.com/uc-bd2k/KEGGlincs/blob/master/vignettes/image_files/p53_PC3.jpeg)
83 
+
84 
+#####Pathway specific to HA1E cell-line (Immortalized normal kidney epithelial)
85 
+```{r}
86 
+KEGG_lincs("hsa04115", "HA1E")
87 
+```
88 
+![] (https://github.com/uc-bd2k/KEGGlincs/blob/master/vignettes/image_files/p53_HA1E.jpeg)