docs(ReadmeAndExamples.MdInDocs/Scr): replaced html graphics in examp…

…les with png. need to correct syntax for html. just use <filepath syntax

README.md

@@ -4,7 +4,7 @@
 
 
 | MacOS / Linux | Windows | License | Test Coverage | Documentation | Lifecycle |
-| --- | ---- | ------ | ------ | ---- |
+| --- | ---- | ------ | ------ | ---- | ---- |
 |[![Travis](https://img.shields.io/travis/compbiocore/VariantVisualization.jl/master.svg?style=flat-square)](https://travis-ci.org/compbiocore/VariantVisualization.jl)|[![Build status](https://ci.appveyor.com/api/projects/status/67hyn6rckulwr2dj/branch/master?svg=true)](https://ci.appveyor.com/project/fernandogelin/variantvisualization-jl/branch/master)|[![License](https://img.shields.io/badge/license-MIT-orange.svg?style=flat-square)](https://github.com/compbiocore/VariantVisualization.jl/blob/clean-up/LICENSE.md)|[![Coverage Status](https://coveralls.io/repos/github/compbiocore/VariantVisualization.jl/badge.svg?branch=master)](https://coveralls.io/github/compbiocore/VariantVisualization.jl?branch=master)|[![Docs](https://img.shields.io/badge/docs-stable-blue.svg?style=flat-square)](https://compbiocore.github.io/VariantVisualization.jl/stable) [![Docs](https://img.shields.io/badge/docs-latest-blue.svg?style=flat-square)](https://compbiocore.github.io/VariantVisualization.jl/latest) | ![Lifecycle](https://img.shields.io/badge/lifecycle-active-green.svg?style=flat-square) |
 
 ## Overview

docs/src/examples.md

@@ -9,12 +9,12 @@ Once Julia and VariantVisualization.jl are installed, you can run the following
 Running VIVA with no options produces heatmaps of genotype and read depth values for all samples and variant positions in the VCF file with default options. You can read about VIVA's default settings [here](https://compbiocore.github.io/VariantVisualization.jl/stable/#default-options)
 
 ```
-julia VIVA -f test_4X_191.vcf -t Default_Options
+julia VIVA -f test_4X_191.vcf -t Default_Options -s png
 ```
 
-![Default Genotype Heatmap](assets/Genotype_Default_Options.html)
+![Default Genotype Heatmap](assets/Genotype_Default_Options.png)
 
-![Default Read Depth Heatmap](assets/Read_Depth_Default_Options.html)
+![Default Read Depth Heatmap](assets/Read_Depth_Default_Options.png)
 
 ## Grouping Samples by Metadata Traits and Generating all Four Plots
 
@@ -23,25 +23,25 @@ Group samples by sequencing facility and generate heatmaps of genotype and read
 You can find grouping options [here]([options](https://compbiocore.github.io/VariantVisualization.jl/stable/filtering_vcf/#selecting-and-grouping-samples) to group samples by common traits.)
 
 ```
-julia VIVA -f test_4X_191.vcf -t Grouped_by_Sequencing_Site -g sample_metadata_matrix.csv seq_site_1,seq_site_2 --avg_dp variant,sample
+julia VIVA -f test_4X_191.vcf -t Grouped_by_Sequencing_Site -g sample_metadata_matrix.csv seq_site_1,seq_site_2 --avg_dp variant,sample -s png
 ```
 
-![Grouped Genotype Heatmap](assets/Read_Depth_Grouped_by_Sequencing_Site.html)
+![Grouped Genotype Heatmap](assets/Read_Depth_Grouped_by_Sequencing_Site.png)
 
-![Grouped Read Depth Heatmap](assets/Genotype_Grouped_by_Sequencing_Site.html)
+![Grouped Read Depth Heatmap](assets/Genotype_Grouped_by_Sequencing_Site.png)
 
-![Grouped Variant Average Read Depth Scatter Plot](assets/Average_Variant_Read_Depthtest_4X_191.vcf.html)
+![Grouped Variant Average Read Depth Scatter Plot](assets/Average_Variant_Read_Depthtest_4X_191.vcf.png)
 
-![Grouped Sample Average Read Depth Scatter Plot](assets/Average_Sample_Read_Depth_test_4X_191.vcf.html)
+![Grouped Sample Average Read Depth Scatter Plot](assets/Average_Sample_Read_Depth_test_4X_191.vcf.png)
 
 ##Genomic Range and Samples Selection - Genotype and Read Depth Heatmaps with Variant Position Labels
 
 Generate heatmaps of genotype and read depth values of variants selected within a genomic range, in this case, chromosome 4, nucleotides 200000-500000, with y-axis variant position labels.
 
 ```
-julia VIVA -f test/test_files/test_4X_191.vcf -t Genomic_Range_Chr4:3076150-3076390 -r chr4:3076150-3076390 -y positions --select_samples select_samples_list.txt
+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.html)
-![Genomic Range Read Depth Heatmap](assets/Read_Depth_Genomic_Range_Chr4/3076150-3076390.html)
+![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)