Merge pull request #164 from TheJacksonLaboratory/develop

update docs

.gitignore

@@ -39,3 +39,6 @@ hs_err_pid*
 /isopret-interpro-overrep.txt
 /isopret-gui_1.0.0-1_amd64.deb
 /isopret-gui-1.0.0-M1.dmg
+.vscode/
+isopret-io/target/
+venv/

README.md

@@ -60,6 +60,7 @@ Enter the following code to install mkdocs and run a server locally. The GitHub
 ```
 python3 -m venv venv
 source venv/bin/activate
+pip install mkdocs
 pip install mkdocs-material
 pip install mkdocs-material[imaging]
 pip install mkdocs-material-extensions

docs/index.md

@@ -12,10 +12,6 @@ Isopret uses the analysis (output) file of
 
 TODO -- point to tutorial amd also mention EDGER
 
-HBA-DEALS
-analyzes RNA-Seq data to determine differentially expression and differential
-splicing simultaneous. Isopret then performs
-Gene Ontology analysis using a Java 17 implementation of code from
-the [Ontologizer](https://pubmed.ncbi.nlm.nih.gov/18511468/){:target="_blank"}.
+HBA-DEALS analyzes RNA-Seq data to determine differentially expression and differential splicing simultaneous. Isopret then performs Gene Ontology analysis using an updated implementation of code from the [Ontologizer](https://pubmed.ncbi.nlm.nih.gov/18511468/){:target="_blank"}.
 
 

docs/input.md

@@ -11,11 +11,15 @@ Hierarchical Bayesian Analysis of Differential Expression and ALternative Splici
 simultaneously characterizes differential expression and splicing in cohorts.
 
 
-.. figure:: /img/hbadeals.png
-   :width: 80%
-   :align: center
 
-   HBA-DEALS. The log-transformed expression of a gene with three isoforms (green, orange, and blue) is shown. The gene expression is the sum of the expression of the isoforms. Differential gene expression is modeled as two Normal distributions whose means differ by the parameter β. The proportions of the corresponding isoforms have a Dirichlet prior, and the difference in proportions between controls and cases is modeled by α (symbolized by the two triangles). An MCMC procedure is used to solve for the posterior distribution of the parameters of the model for all genes and isoforms at once.
+<figure markdown>
+![HBA-DEALS.](./img/hbadeals.png){ width="1000" }
+<figcaption>HBA-DEALS..</figcaption>
+</figure>
+
+
+
+The log-transformed expression of a gene with three isoforms (green, orange, and blue) is shown. The gene expression is the sum of the expression of the isoforms. Differential gene expression is modeled as two Normal distributions whose means differ by the parameter β. The proportions of the corresponding isoforms have a Dirichlet prior, and the difference in proportions between controls and cases is modeled by α (symbolized by the two triangles). An MCMC procedure is used to solve for the posterior distribution of the parameters of the model for all genes and isoforms at once.
 
 The HBA-DEALS algorithm is explained in [Karlebach et al, 2020, Genome Biology 21:171](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02072-6).
 Source code is available at the [HBA-DEALS GitHub repository](https://github.com/TheJacksonLaboratory/HBA-DEALS).
@@ -64,7 +68,7 @@ only [Ensembl](http://ensembl.org/) gene/transcript models.
 ## Running HBA-DEALS
 
 
-A Snakemake pipeline for running HBA-DEALS is described in the 
+A Snakemake pipeline for running HBA-DEALS is described in the
 [GitHub repository](https://github.com/TheJacksonLaboratory/covid19splicing)
 for the paper  [Betacoronavirus-specific alternate splicing](https://pubmed.ncbi.nlm.nih.gov/35074468/). The GitHub repository
 also contains 15 HBA-DEALS output files related to that publication that can be used as input for Isopret-Gui.

docs/output.md

@@ -15,7 +15,7 @@ false discovery rate (FDR) are highlighted in color.
 
 
 <figure markdown>
-![Overview tab](/img/isopret3.png){ width="1000" }
+![Overview tab](./img/isopret3.png){ width="1000" }
 <figcaption>IsopretGO overview tab.
 </figcaption>
 </figure>
@@ -33,7 +33,7 @@ and analysis results for that gene. The tab has three parts -- isoforms, protein
 The isoform section shows the structure of each isoform that has at least one read in the RNA-seq data.
 
 <figure markdown>
-![Gene tab](/img/isopret4.png){ width="1000" }
+![Gene tab](./img/isopret4.png){ width="1000" }
 <figcaption>IsopretGO gene tab, isoforms section.
 </figcaption>
 </figure>
@@ -57,7 +57,7 @@ at the top of the table and highlighted green.
 
 
 <figure markdown>
-![Gene Ontology section](/img/isopret6.png){ width="1000" }
+![Gene Ontology section](./img/isopret6.png){ width="1000" }
 <figcaption>IsopretGO gene tab, Gene Ontology section.
 </figcaption>
 </figure>
@@ -83,20 +83,24 @@ Clicking on the ``Compare DGE & DAS`` button will open a dialog that shows the n
 of GO terms to compare results for expression and splicing.
 
 <figure markdown>
-![Gene Ontology DAS tab](/img/isopret7.png){ width="1000" }
+![Gene Ontology DAS tab](./img/isopret7.png){ width="1000" }
 <figcaption>IsopretGO gene tab, Gene Ontology DAS tab.
 </figcaption>
 </figure>
-.. figure:: /img/isopret8.png
-   :width: 70%
-   :align: center
 
-   Isopret. Gene Ontology tab, compare differential expression and differential splicing
+
+<figure markdown>
+![Gene Ontology DAS tab](./img/isopret8.png){ width="1000" }
+<figcaption>Gene Ontology tab, compare differential expression and differential splicing
+</figcaption>
+</figure>
+
+
+
 
 
 
-Clicking on the ``Export`` button next to a GO term will show summaries for each gene that is annotated to the GO term
+Clicking on the **Export** button next to a GO term will show summaries for each gene that is annotated to the GO term
 and is also differentially expressed (for DGE) or spliced (for DAS). This generates an HTML page that can be
-used to explore the genes associated with the GO term together with their corresponding patterns of differential expression and splicing
-Note that the output is restricted to the first 100 genes to limit the size of the resulting HTML page.
+used to explore the genes associated with the GO term together with their corresponding patterns of differential expression and splicing. Note that the output is restricted to the first 100 genes to limit the size of the resulting HTML page.
 

docs/running-gui.md

@@ -18,7 +18,7 @@ java -jar Isopret.jar
 
 
 <figure markdown>
-![First run](/img/isopret1.png){ width="1000" }
+![First run](./img/isopret1.png){ width="1000" }
 <figcaption>Appearance of the app when started for the first time.</figcaption>
 </figure>
 
@@ -48,7 +48,7 @@ The drawback of the term-for-term approach is that it does not respect dependenc
 are caused by overlapping annotations. As a result of the true-path rule, each term in GO shares all the
 annotations of all of its descendants. Isopret also offers two algorithms for GO analysis that
 assess GO term overrepresentation that examines each term in the context of its parent terms,
-which we call the parent–child approach 
+which we call the parent–child approach
 ([Grossmann et al., 2007](https://academic.oup.com/bioinformatics/article/23/22/3024/208216?login=false)).
 In our experiments, the ``parent–child-intersection`` approach is generally more conservative than
 the ``parent–child-union`` approach.
@@ -57,13 +57,13 @@ the ``parent–child-union`` approach.
 
 
 Isopret offers the following multiple-testing correction options for the GO analysis: Bonferroni, Bonferroni-Holm,
-Sidak, Benjamini-Hochberg, Benjamini-Yukutieli, None. The book 
+Sidak, Benjamini-Hochberg, Benjamini-Yukutieli, None. The book
 [Introduction to Bio-Ontologies](https://www.routledge.com/Introduction-to-Bio-Ontologies/Robinson-Bauer/p/book/9780367659271)
 provides detailed explanations of the GO Overrepresentation analysis procedures and multiple testing correction approaches.
 
 <figure markdown>
 ![First run](/img/isopret2.png){ width="1000" }
-<figcaption>Appearance of the app after data download with an HBA-DEAL file chosen and the analysis set to 
+<figcaption>Appearance of the app after data download with an HBA-DEAL file chosen and the analysis set to
 Parent-Child Intersection with Benjamini-Hochberg MTC.</figcaption>
 </figure>
 

docs/running-inferrence.md

@@ -1,14 +1,16 @@
-.. _rstrunninginferrence:
+# Inference
+
+
 
-=====================================
-Running the isopret inferrence script
-=====================================
 
 Here, we explain how to set up and run the R scripts developed to perform expectation-maximization analysis to infer
 GO annotations for isoforms.
 
+## Running the isopret inferrence script
+
+
 The scripts are stored in the directory ``em-scripts`` in the project
-`GitHub repository <https://github.com/TheJacksonLaboratory/isopret>`_.
+[GitHub repository](https://github.com/TheJacksonLaboratory/isopret).
 
 The script ``translate_all_isoforms.R`` can be used for obtaining isoform amino-acid sequences.  It extracts isoform coordinates from a .gtf file and calls the tool gffread to translate the genomic sequence.  The variables containing the paths to the .fasta file containing the genome sequence and the .gtf file with isoform coordinates ('fasta.file' and 'gtf.file', respectively) should match the locations of the files in the system.
 

docs/setup.md

@@ -22,21 +22,24 @@ build isopret-gui from source, then the build process described below requires
 
 
 Go the GitHub page of [isopretGO](https://github.com/TheJacksonLaboratory/isopretGO), and clone the project.
-Build the executable from source with maven, and then test the build. ::
-
-    git clone https://github.com/TheJacksonLaboratory/isopret.git
-    cd isopret
-    mvn package
-    java -jar target/isopret.jar
-      Usage: isopret [-hV] [COMMAND]
-        Isoform interpretation tool.
-        -h, --help      Show this help message and exit.
-        -V, --version   Print version information and exit.
-      Commands:
-        download, D  Download files for prositometry
-        hbadeals, H  Analyze HBA-DEALS files
-        svg, V       Create SVG/PDF files for a specific gene
-        stats, S     Show descriptive statistics about data
+Build the executable from source with maven, and then test the build.
+
+```bash
+git clone https://github.com/TheJacksonLaboratory/isopret.git
+cd isopret
+mvn package
+java -jar target/isopret.jar
+  Usage: isopret [-hV] [COMMAND]
+    Isoform interpretation tool.
+    -h, --help      Show this help message and exit.
+    -V, --version   Print version information and exit.
+  Commands:
+    download, D  Download files for prositometry
+    hbadeals, H  Analyze HBA-DEALS files
+    svg, V       Create SVG/PDF files for a specific gene
+    stats, S     Show descriptive statistics about data
+```
+