mortazavilab
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diff --git a/‎README.md
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diff --git a/‎SUMMARY.md
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diff --git a/‎tutorials/getting_started.md
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@@ -34,8 +34,8 @@ After installation with pip, to enable visualizations using dashed edges, run th
 * [Input file format specifications](faqs/file_formats.md)
 
 ## Comprehensive Documentation
-For full documentaion, please visit [our website](https://freese.gitbook.io/swan/)
 
+For full documentaion, please visit [our website](https://freese.gitbook.io/swan/)
 
 Logo by the wonderful [Eamonn Casey](https://www.instagram.com/designsbyeamonn/)
 
@@ -14,4 +14,6 @@
 * [File format specifications](faqs/file_formats.md)
 
 ## Code documentation
-* [swan_vis.SwanGraph()](docs/swangraph.md)
+
+* [swan\_vis.SwanGraph\(\)](code-documentation/swangraph.md)
+
@@ -1,14 +1,14 @@
-## Classes
+# swan\_vis.SwanGraph\(\)
 
+## swan.Swangraph\(\)
 
-### swan.Swangraph()
 ```python
 SwanGraph(file=None)
-``` 
+```
 
 A graph class to represent a transcriptome and perform plotting and analysis from it
 
-```   
+```text
 Attributes:
 
         datasets (list of str):
@@ -43,16 +43,17 @@ Attributes:
                 transcript expression test
 ```
 
-### Methods
+## Methods
+
+### add\_abundance
 
-#### add_abundance
 ```python
 add_abundance(self, counts_file, count_cols, dataset_name, tid_col='annot_transcript_id')
 ```
 
 Adds abundance information to an existing dataset in the SwanGraph.
-        
-```               
+
+```text
 Parameters:
 
         counts_file (str): Path to tsv counts matrix
@@ -62,31 +63,30 @@ Parameters:
                 Default='annot_transcript_id'
 ```
 
+### add\_annotation
 
-#### add_annotation
 ```python
 add_annotation(self, fname)
 ```
 
 Adds an annotation from input fname to the SwanGraph.
- 
-```       
+
+```text
 Parameters:
         fname (str): Path to annotation GTF
 ```
 
+### add\_dataset
 
-
-#### add_dataset
 ```python
 add_dataset(self, col, fname, dataset_name=None, whitelist=None, annot=None, counts_file=None, count_cols=None, tid_col='annot_transcript_id', include_isms=False)
 ```
 
 Add transcripts from a dataset from either a GTF or a TALON database.
 
-```
+```text
 Parameters:
-        
+
     col (str): Name of column to add data to in the SwanGraph
     fname (str): Path to GTF or TALON db
 
@@ -111,16 +111,15 @@ Parameters:
             Default=False
 ```
 
+### de\_gene\_test
 
-
-#### de_gene_test
 ```python
 de_gene_test(self, dataset_groups)
 ```
 
 Runs a differential expression test on the gene level.
 
-```       
+```text
 Parameters:
 
         dataset_groups (list of list of str, len 2): Grouping of datasets 
@@ -133,19 +132,17 @@ Returns:
         test (pandas DataFrame): A summary table of the differential
                 expression test, including p and q-values, as well 
                 as log fold change.
-
 ```
 
+### de\_transcript\_test
 
-
-#### de_transcript_test
 ```python
 de_transcript_test(self, dataset_groups)
 ```
 
 Runs a differential expression test on the transcript level.
 
-```       
+```text
 Parameters:
 
         dataset_groups (list of list of str, len 2): Grouping of datasets 
@@ -160,48 +157,45 @@ Returns:
                 as log fold change.
 ```
 
+### find\_es\_genes
 
-#### find_es_genes
 ```python
 find_es_genes(self)
 ```
 
-Finds all unique genes containing novel exon skipping events.
-Requires that an annotation has been added to the SwanGraph.
-        
-```
+Finds all unique genes containing novel exon skipping events. Requires that an annotation has been added to the SwanGraph.
+
+```text
 Returns:
 
         es_genes (list of str): A list of gene ids from the SwanGraph with 
                 at least one novel exon skipping event
 ```
 
+### find\_ir\_genes
 
-#### find_ir_genes
 ```python
 find_ir_genes(self)
 ```
 
-Finds all unique genes containing novel intron retention events.
-Requires that an annotation has been added to the SwanGraph.
+Finds all unique genes containing novel intron retention events. Requires that an annotation has been added to the SwanGraph.
 
-```        
+```text
 Returns:
 
         ir_genes (list of str): A list of gene ids from the SwanGraph with 
                 at least one novel intron retention event
 ```
 
+### find\_isoform\_switching\_genes
 
-#### find_isoform_switching_genes
 ```python
 find_isoform_switching_genes(self, q=0.05, n_genes=None)
 ```
 
-Finds isoform switching genes; genes that are not differentially expressed but contain at least one transcript that is. 
-Requires that de_gene_test and de_transcript_test have been run.
-        
-```
+Finds isoform switching genes; genes that are not differentially expressed but contain at least one transcript that is. Requires that de\_gene\_test and de\_transcript\_test have been run.
+
+```text
 Parameters:
 
         q (float): q-value threshold to declare a gene/transcript 
@@ -218,15 +212,15 @@ Returns:
                 categorized as isoform switching
 ```
 
+### gen\_report
 
-#### gen_report
 ```python
 gen_report(self, gids, prefix, datasets='all', dataset_groups=False, dataset_group_names=False, novelty=False, heatmap=False, tpm=False, include_qvals=False, q=0.05, include_unexpressed=False, indicate_dataset=False, indicate_novel=False, browser=False, order='expression')
 ```
 
 Generates a PDF report for a given gene or list of genes according to the user's input.
-        
-```
+
+```text
 Parameters: 
 
         gids (str or list of str): Gene ids or names to generate
@@ -298,16 +292,15 @@ Parameters:
                                  'tid' if not
 ```
 
+### get\_de\_genes
 
-#### get_de_genes
 ```python
 get_de_genes(self, q=0.05, n_genes=None)
 ```
 
-Subsets the differential gene expression test summary table based on a q-value cutoff. 
-Requires that de_gene_test has already been run.
-        
-```
+Subsets the differential gene expression test summary table based on a q-value cutoff. Requires that de\_gene\_test has already been run.
+
+```text
 Parameters:
 
         q (float): q-value threshold to declare a gene as significant
@@ -323,15 +316,15 @@ Returns:
                 significance threshold
 ```
 
+### get\_de\_transcripts
 
-#### get_de_transcripts
 ```python
 get_de_transcripts(self, q=0.05, n_transcripts=None)
 ```
 
-Subsets the differential transcript expression test summary table based on a q-value cutoff. Requires that de_transcript_test has already been run.
-        
-```
+Subsets the differential transcript expression test summary table based on a q-value cutoff. Requires that de\_transcript\_test has already been run.
+
+```text
 Parameters:
 
         q (float): q-value threshold to declare a transcript as significant
@@ -344,19 +337,18 @@ Returns:
         tids (list of str): List of transcript ids that pass the 
                 significance threshold
         test (pandas DataFrame): Summary table of transcripts that pass
-                the significance threshold  
+                the significance threshold
 ```
 
+### plot\_each\_transcript
 
-
-#### plot_each_transcript
 ```python
 plot_each_transcript(self, tids, prefix, indicate_dataset=False, indicate_novel=False, browser=False)
 ```
 
 Plot each input transcript and automatically save figures.
-        
-```
+
+```text
 Parameters:
 
         tids (list of str): List of transcript ids to plot
@@ -375,15 +367,15 @@ Parameters:
                 indicate_novel
 ```
 
+### plot\_each\_transcript\_in\_gene
 
-#### plot_each_transcript_in_gene
 ```python
 plot_each_transcript_in_gene(self, gid, prefix, indicate_dataset=False, indicate_novel=False, browser=False)
 ```
 
 Plot each transcript in a given gene and automatically save figures.
-        
-```
+
+```text
 Parameters:
 
         gid (str): Gene id or gene name to plot transcripts from
@@ -402,16 +394,15 @@ Parameters:
                 indicate_novel
 ```
 
+### plot\_graph
 
-#### plot_graph
 ```python
 plot_graph(self, gid, indicate_dataset=False, indicate_novel=False, prefix=None)
 ```
 
-Plots a gene summary SwanGraph for an input gene.
-Does not automatically save the figure by default!
-        
-```
+Plots a gene summary SwanGraph for an input gene. Does not automatically save the figure by default!
+
+```text
 Parameters:
 
         gid (str): Gene ID to plot for (can also be gene name but 
@@ -429,15 +420,15 @@ Parameters:
                 Default: None, won't automatically save
 ```
 
+### plot\_transcript\_path
 
-#### plot_transcript_path
 ```python
 plot_transcript_path(self, tid, indicate_dataset=False, indicate_novel=False, browser=False, prefix=None)
 ```
 
 Plots a path of a single transcript isoform through a gene summary SwanGraph.
-        
-```
+
+```text
 Parameters:
 
         tid (str): Transcript id of transcript to plot
@@ -457,17 +448,18 @@ Parameters:
                 Default: None, won't automatically save
 ```
 
+### save\_graph
 
-#### save_graph
 ```python
 save_graph(self, prefix)
 ```
 
 Saves the current SwanGraph in pickle format with the .p extension.
- 
-```       
+
+```text
 Parameters: 
 
         prefix (str): Path and filename prefix. Resulting file will 
                 be saved as prefix.p
-```
+```
+
@@ -1,3 +1,5 @@
+# Understanding Swan visualizations
+
 Swan utilizes a representation of transcript structure and alternative splicing that most people aren't familiar with. The goal of this guide is to help the user understand and interpret the graphical output format from Swan, in a step-by-step manner.
 
 ## Table of contents
@@ -55,3 +57,4 @@ Exon skipping in a SwanGraph consists of an intronic \(pink\) edge that complete
 In a SwanGraph, intron retention is the opposite of exon skipping. It is seen when an exonic \(green\) edge completely spans an intronic \(pink\) edge. This means that an intronic region from one transcript model has been included in a different transcript model.
 
 ![](../.gitbook/assets/intron_retention.png)
+
@@ -3,6 +3,7 @@
 Swan has several analysis options to use.
 
 Table of contents
+
 * [Differential gene expression](analysis_tools.md#differential-gene-expression-tests)
 * [Differential transcript expression](analysis_tools.md#differential-transcript-expression-tests)
 * [Isoform switching](analysis_tools.md#isoform-switching)
 
@@ -5,6 +5,7 @@ First, if you haven't already, make sure to [install Swan](../#installation). Af
 Then, download the data and the reference transcriptome annotation from [here](https://hpc.oit.uci.edu/~freese/swan_files/). The bash commands to do so are given below.
 
 Table of contents
+
 * [Example data download](getting_started.md#download-example-data)
 * [Starting and initializing your SwanGraph](getting_started.md#starting-up-swan-and-initializing-your-swangraph)
 * [Add transcript models \(GTF\) and abundance info](getting_started.md#adding-transcript-models-gtf-and-abundance-information-at-the-same-time)