update website

.Rbuildignore

@@ -16,3 +16,27 @@ logo
 ^pkgdown$
 build_pkg_site.R
 ^\.github$
+vignettes/ATC.R
+vignettes/ATC_methods.Rmd
+vignettes/PAC.R
+vignettes/cola_general.Rmd
+vignettes/cola_quick.Rmd
+vignettes/compare_partitions.Rmd
+vignettes/consensus_partition_workflow.png
+vignettes/functional_enrichment.Rmd
+vignettes/hierarchical.Rmd
+vignettes/hierarchical_partitioning_workflow.png
+vignettes/large_k_problem_consensus_heatmap-min.png
+vignettes/large_k_problem_select_partition_number-min.png
+vignettes/lt_functional_enrichment_TCGA_GBM.rds
+vignettes/membership_heatmap.png
+vignettes/predict.Rmd
+vignettes/rand_jaccard.R
+vignettes/rand_jaccard.png
+vignettes/silhouette.R
+vignettes/skmeans.png
+vignettes/test_NMF.R
+vignettes/vignette_example.R
+vignettes/work_with_big_datasets.Rmd
+vignettes/AML.Rmd
+vignettes/examples.Rmd

LICENSE

@@ -1,3 +1,20 @@
-YEAR: 2021
+YEAR: 2024
 COPYRIGHT HOLDER: Zuguang Gu
 
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -6,21 +6,15 @@
 [ ![bioc](http://bioconductor.org//shields/lastcommit/devel/bioc/cola.svg) ](http://bioconductor.org/checkResults/devel/bioc-LATEST/cola/)
 
 
-## Features
-
-1. It modularizes the consensus clustering processes that various methods can
-   be easily integrated in different steps of the analysis.
-2. It provides rich visualizations for intepreting the results.
-3. It allows running multiple methods at the same time and provides
-   functionalities to compare results in a straightforward way.
-4. It provides a new method to extract features which are more efficient to
-   separate subgroups.
-5. It generates detailed HTML reports for the complete analysis.
 
 ## Citation
 
 Zuguang Gu, et al., cola: an R/Bioconductor package for consensus partitioning through a general framework, Nucleic Acids Research, 2021. https://doi.org/10.1093/nar/gkaa1146
 
+Zuguang Gu, et al., Improve consensus partitioning via a hierarchical procedure. Briefings in bioinformatics 2022. https://doi.org/10.1093/bib/bbac048 
+
+
+
 ## Install
 
 *cola* is available on [Bioconductor](http://bioconductor.org/packages/devel/bioc/html/cola.html), you can install it by:
@@ -38,30 +32,26 @@ library(devtools)
 install_github("jokergoo/cola")
 ```
 
-## Links
+## Methods
 
-Examples for *cola* analysis can be found at https://jokergoo.github.io/cola_examples/ and https://jokergoo.github.io/cola_collection/.
+The **cola** supports two types of consensus partitioning.
 
-Online documentation is at https://jokergoo.github.io/cola.
+### Standard consensus partitioning
 
-Supplementary for the *cola* manuscript is at https://github.com/jokergoo/cola_supplementary and the scripts are at https://github.com/jokergoo/cola_manuscript.
+#### Features
 
-## Vignettes
+1. It modularizes the consensus clustering processes that various methods can
+   be easily integrated in different steps of the analysis.
+2. It provides rich visualizations for intepreting the results.
+3. It allows running multiple methods at the same time and provides
+   functionalities to compare results in a straightforward way.
+4. It provides a new method to extract features which are more efficient to
+   separate subgroups.
+5. It generates detailed HTML reports for the complete analysis.
 
-There are the following vignettes:
 
-<ol style="list-style-type: decimal">
-<li><a href="https://jokergoo.github.io/cola_vignettes/cola_quick.html">A Quick Start of Using cola Package</a></li>
-<li><a href="https://jokergoo.github.io/cola_vignettes/cola.html">A Framework for Consensus Partitioning</a></li>
-<li><a href="https://jokergoo.github.io/cola_vignettes/functional_enrichment.html">Automatic Functional Enrichment on Signature genes</a></li>
-<li><a href="https://jokergoo.github.io/cola_vignettes/predict.html">Predict Classes for New Samples</a></li>
-<li><a href="https://jokergoo.github.io/cola_vignettes/work_with_big_datasets.html">Work with Big Datasets</a></li>
-<li><a href="https://jokergoo.github.io/cola_vignettes/compare_partitions.html">Compare Partitions</a></li>
-<li><a href="https://jokergoo.github.io/cola_vignettes/ATC_methods.html">ATC - More Forms</a></li>
-<li><a href="https://jokergoo.github.io/cola_vignettes/hierarchical.html">Hierarchical consensus partitioning</a></li>
-</ol>
 
-## Consensus Partitioning
+#### Workflow
 
 <img width="700" src="https://user-images.githubusercontent.com/449218/52628723-86af3400-2eb8-11e9-968d-b7f47a408818.png" />
 
@@ -89,7 +79,7 @@ The steps of consensus partitioning is:
 8. If rows in the matrix can be associated to genes, downstream analysis such
    as function enrichment analysis can be performed.
 
-### Usage
+#### Usage
 
 Three lines of code to perfrom *cola* analysis:
 
@@ -103,18 +93,53 @@ rl = run_all_consensus_partition_methods(
 cola_report(rl, output_dir = ...)
 ```
 
-### Plots
+#### Plots
 
 Following plots compare consensus heatmaps with k = 4 under all combinations of methods.
 
 <img src="https://user-images.githubusercontent.com/449218/52631118-3a66f280-2ebe-11e9-8dea-0172d9beab91.png" />
 
 
-## License
+### Hierarchical consensus partitioning
 
-MIT @ Zuguang Gu
 
-#### Acknowledgement
+#### Features
+
+1. It can detect subgroups which show major differences and also moderate differences.
+2. It can detect subgroups with large sizes as well as with tiny sizes.
+3. It generates detailed HTML reports for the complete analysis.
 
-The cola icon in logo is made by <a href="https://www.flaticon.com/authors/photo3idea-studio" title="photo3idea_studio">photo3idea_studio</a> from <a href="https://www.flaticon.com/" title="Flaticon">www.flaticon.com</a>.
+
+#### Hierarchical Consensus Partitioning
+
+
+<img src="https://user-images.githubusercontent.com/449218/126491482-31a9496f-cc4d-4c4f-80b7-7b752d8d8d06.png" width="400" />
+
+
+
+#### Usage
+
+Three lines of code to perfrom hierarchical consensus partitioning analysis:
+
+```r
+mat = adjust_matrix(mat) # optional
+rh = hierarchical_partition(mat, mc.cores = ...)
+cola_report(rh, output_dir = ...)
+```
+
+#### Plots
+
+Following figure shows the hierarchy of the subgroups.
+
+<img src="https://user-images.githubusercontent.com/449218/100014572-d7b2c280-2dd6-11eb-9265-a84d324122f2.png" width="300" />
+
+Following figure shows the signature genes.
+
+<img src="https://user-images.githubusercontent.com/449218/100014657-f913ae80-2dd6-11eb-9bf7-53f733e9f8f0.png" width="600" />
+
+
+
+## License
+
+MIT @ Zuguang Gu
 

_pkgdown.yml

@@ -1 +1,52 @@
 destination: docs
+
+navbar:
+  title: "cola"
+  left:
+    - text: "Articles"
+      menu:
+        - text: Standard consensus partitioning
+        - text: "A Quick Start of Using cola Package"
+          href: articles/cola_quick.html
+        - text: "A Framework for Consensus Partitioning"
+          href: articles/cola_general.html
+        - text: "Automatic Functional Enrichment on Signature genes"
+          href: articles/functional_enrichment.html
+        - text: "Predict Classes for New Samples"
+          href: articles/predict.html
+        - text: "Work with Big Datasets"
+          href: articles/work_with_big_datasets.html
+        - text: "Compare Partitions"
+          href: articles/compare_partitions.html
+        - text: "ATC - More Forms"
+          href: articles/ATC_methods.html
+
+        - text: -------
+        - text: Hierarchical partitioning
+        - text: "Hierarchical consensus partitioning"
+          href: articles/hierarchical.html
+
+        - text: -------
+        - text: Other examples
+        - text: "Re-analyze an AML proteomics dataset"
+          href: articles/AML.html
+
+        - text: -------
+        - text: On public datasets
+        - text: "Applications on public datasets"
+          href: articles/examples.html
+
+        - text: -------
+        - text: Supplementary files
+        - text: "Supplementary files for cola NAR paper"
+          href: https://jokergoo.github.io/cola_supplementary/
+        - text: "Supplementary files for cola BIB paper"
+          href: https://cola-rh.github.io/supplementary/
+
+    - text: "Reference"
+      href: reference/index.html
+
+
+template:
+  includes:
+    after_body: "<style>nav[data-toggle='toc'] .nav .nav {display: block;}</style>"

build_pkg_site.R

@@ -1,4 +1,3 @@
-writeLines("destination: docs", "_pkgdown.yml")
 if(file.exists(".Rbuildignore")) {
 	ln = readLines(".Rbuildignore")
 	if(!any(ln == "^_pkgdown\\.yml$")) {
@@ -21,4 +20,20 @@ if(file.exists(".Rbuildignore")) {
 ^pkgdown$", ".Rbuildignore")
 }
 
-pkgdown::build_site(run_dont_run = FALSE)
+pkgname = read.dcf("DESCRIPTION")[1, "Package"]
+
+vig_files = list.files(path = "vignettes", full.names = TRUE)
+vig_files = vig_files[basename(vig_files) != paste0(pkgname, ".Rmd")]
+
+ln = readLines(".Rbuildignore")
+
+for(v in vig_files) {
+	if(!any(ln == v)) {
+		ln = c(ln, v)
+	}
+}
+writeLines(ln, ".Rbuildignore")
+
+
+options(rmarkdown.html_vignette.check_title = FALSE)
+pkgdown::build_site(run_dont_run = TRUE)