diff --git a/README.md b/README.md index be6d4f5..6b5143e 100644 --- a/README.md +++ b/README.md @@ -17,7 +17,7 @@ To use VIVA, you must download the Julia programming language version >=1.0 and ## Getting Started: -Note: Once you have set up VIVA, you can quickly run the command line tool [examples](https://compbiocore.github.io/VariantVisualization.jl/stable/examples/) found in the documentation. +Note: Once you have set up VIVA, you can quickly run the command line tool [EXAMPLES](https://github.com/compbiocore/VariantVisualization.jl/blob/master/docs/src/examples.md) found in the documentation. ## *Installation* diff --git a/docs/src/examples.md b/docs/src/examples.md index d3937c4..853c4ed 100644 --- a/docs/src/examples.md +++ b/docs/src/examples.md @@ -11,7 +11,7 @@ Running VIVA with no options produces heatmaps of genotype and read depth values ``` julia VIVA -f test_4X_191.vcf -t Default_Options -s png ``` - +![VIVA Logo](assets/VIVA_logo.png) ![Default Genotype Heatmap](assets/Genotype_Default_Options.png) ![Default Read Depth Heatmap](assets/Read_Depth_Default_Options.png) @@ -42,6 +42,6 @@ Generate heatmaps of genotype and read depth values of variants selected within julia VIVA -f test_4X_191.vcf -t Genomic_Range_Chr4:3076150-3076390 -r chr4:3076150-3076390 -y positions --select_samples select_samples_list.txt -s png ``` -![Genomic Range Genotype Heatmap](assets/Genotype_Genomic_Range_Chr4/3076150-3076390.png) -![Genomic Range Read Depth Heatmap](assets/Read_Depth_Genomic_Range_Chr4/3076150-3076390.png) +![Genomic Range Genotype Heatmap](assets/Genotype_Genomic_Range_Chr4:3076150-3076390.png) +![Genomic Range Read Depth Heatmap](assets/Read_Depth_Genomic_Range_Chr4:3076150-3076390.png) diff --git a/examples/literate_src/1_viva.jl b/examples/literate_src/1_viva.jl deleted file mode 100644 index 8da68ba..0000000 --- a/examples/literate_src/1_viva.jl +++ /dev/null @@ -1,8 +0,0 @@ -# # Viva Example 1 - -#md # [![nbviewer](https://img.shields.io/badge/jupyter_notebook-nbviewer-orange.svg?style=flat-square)](http://nbviewer.jupyter.org/github/compbiocore/ViVa.jl/tree/master/docs/src/notebooks/1_viva.ipynb) - -# Example overview - -using GeneticVariation -using ViVa diff --git a/examples/runexamples.jl b/examples/runexamples.jl deleted file mode 100644 index 4ab6f97..0000000 --- a/examples/runexamples.jl +++ /dev/null @@ -1,16 +0,0 @@ -all_examples = [ - ("literate_src/1_viva.jl", " Running Example 1"), - ("literate_src/2_viva.jl", " Running Example 2") - ] - -println("Running examples:") - -for (example, str) in all_examples - println("-----------------------------------------") - println("-----------------------------------------") - println(str) - println("-----------------------------------------") - println("-----------------------------------------") - - include(example) -end diff --git a/googlefdc38aeb90acee4c.html b/googlefdc38aeb90acee4c.html deleted file mode 100644 index 3115cc6..0000000 --- a/googlefdc38aeb90acee4c.html +++ /dev/null @@ -1 +0,0 @@ -google-site-verification: googlefdc38aeb90acee4c.html \ No newline at end of file