Merge pull request #53 from compbiocore/develop

Fix sample labels when select columns, docs fixes

Author: Fernando Gelin

README.md

@@ -5,7 +5,7 @@
 
 | 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) |
+|[![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/master/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
 
@@ -23,17 +23,11 @@ Note: Once you have set up VIVA, you can quickly run the command line tool [EXAM
 
 ### Supported Operating Systems:
 
-#### macOS 
+macOS ( Sierra, High Sierra, and Mojave ), Windows, and Linux.
 
-Sierra, High Sierra, and Mojave.
+Expected Time for Installation: Installation time depends on your network bandwidth, but should take less than 10 minutes for VIVA installation to install all dependency packages. Installing and using Julia packages for the first time takes longer than when using them in subsequent sessions. 
 
-#### Windows
-
-Windows 10, Windows 7
-
-#### Linux
-
-*Note*: When installing VariantVisualization.jl and running VIVA on Linux systems on remote compute clusters, you may need to load the OpenGl module in addition to loading the Julia module.
+*Note*: When installing VariantVisualization.jl and running VIVA remote compute clusters, you may need to load the OpenGl module in addition to loading the Julia module.
 
 ### Command Line Tool
 

docs/src/assets/Genotype_Genomic_Range.png

@@ -1,8 +1,13 @@
 # Examples
 
-To run examples, download the five test files found [here](https://github.com/compbiocore/VariantVisualization.jl/tree/master/test/test_files) and put them into a working directory with the VIVA script. 
+To run examples:
 
-Once Julia and VariantVisualization.jl are installed, you can run the following examples and should see the same outputs.
+1. Install Julia and the VariantVisualization.jl package
+2. Download the five test files found [here](https://github.com/compbiocore/VariantVisualization.jl/tree/master/test/test_files) and put them into a working directory with the VIVA script. 
+3. Open the command line (Terminal or Powershell), copy the provided commands into the command line prompt, and press enter. 
+4. Your first VIVA run will take longer than usual (several minutes) because of the way Julia compiles packages. All subsequent runs will be much faster. Each example should take 30-50 seconds to run and you should see the same outputs as those below each demo. 
+
+We encourage you to also run these examples without the flag `-s png` to save and view interactive HTML graphics with cursor hovertext, zooming, panning, and screen capture features. View HTML graphics in your browser by opening the HTML file.
 
 ## Default Options
 
@@ -11,7 +16,6 @@ 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)
@@ -39,9 +43,9 @@ julia VIVA -f test_4X_191.vcf -t Grouped_by_Sequencing_Site -g sample_metadata_m
 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_4X_191.vcf -t Genomic_Range_Chr4:3076150-3076390 -r chr4:3076150-3076390 -y positions --select_samples select_samples_list.txt -s png
+julia VIVA -f test_4X_191.vcf -t Genomic_Range -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)
+docs/src/assets/Read_Depth_Genomic_Range.png
+![Genomic Range Genotype Heatmap](assets/Genotype_Genomic_Range.png)
+![Genomic Range Read Depth Heatmap](assets/Read_Depth_Genomic_Range.png)
 

docs/src/assets/Genotype_Genomic_Range_Chr4:3076150-3076390.png

@@ -7,10 +7,10 @@ function alias()
     end
 
     dir = split(@__DIR__, "/src")[1]
-    exe = joinpath(dir, "VIVA")
+    exe = joinpath(dir, "viva")
 
     open(joinpath(homedir(), rcfile), "a+") do io
-        write(io, "\n # VIVA Alias \nalias VIVA=\"$exe\"")
+        write(io, "\n # viva Alias \nalias viva=\"$exe\"")
     end
     chmod(exe, 333)
 end

docs/src/assets/Read_Depth_Genomic_Range.png

@@ -36,7 +36,7 @@ function genotype_heatmap2(input,title,chrom_label_info,sample_names,chr_pos_tup
                    layout = Layout(
                                    title = "$title_no_underscores",
                                    xaxis=attr(title="Sample ID", showgrid=false, zeroline=false, tickvals=sample_name_indices,
-                                   ticktext=sample_names, tickfont_size=5, tickangle=45,showticklabels=true),
+                                   ticktext=sample_names, tickangle=45,showticklabels=true),
                                    yaxis=attr(title="Genomic Location", zeroline=false, tickvals=chrom_label_indices,
                                    ticktext=chrom_labels,tickfont_size=font_size,hovermode=true,automargin=true)
                    )
@@ -49,7 +49,7 @@ function genotype_heatmap2(input,title,chrom_label_info,sample_names,chr_pos_tup
                    layout = Layout(
                                    title = "$title_no_underscores",
                                    xaxis=attr(title="Sample ID", showgrid=false, zeroline=false, tickvals=sample_name_indices,
-                                   ticktext=sample_names, tickfont_size=5, tickangle=45, showticklabels=x_axis_label_option),
+                                   ticktext=sample_names, tickangle=45, showticklabels=x_axis_label_option),
                                    yaxis=attr(title="Genomic Location", zeroline=false, tickvals=chr_pos_tuple_indices,
                                    ticktext=chr_pos_tuple_list,tickfont_size=font_size,hovermode=true,automargin=true)
                    )
@@ -62,7 +62,7 @@ function genotype_heatmap2(input,title,chrom_label_info,sample_names,chr_pos_tup
                    layout = Layout(
                                    title = "$title_no_underscores",
                                    xaxis=attr(title="Sample ID", showgrid=false, zeroline=false, tickvals=sample_name_indices,
-                                   ticktext=sample_names, tickfont_size=5, tickangle=45,showticklabels=x_axis_label_option),
+                                   ticktext=sample_names, tickangle=45,showticklabels=x_axis_label_option),
                                    yaxis=attr(title="Genomic Location", zeroline=false, tickvals=chr_pos_tuple_indices,
                                    ticktext=chr_pos_tuple_list,tickfont_size=font_size,hovermode=true,automargin=true,showticklabels=false)
                    )
@@ -192,7 +192,7 @@ h_line_index_list = generate_hline_indices(number_rows,input)
                           title = "$title_no_underscores",
 
                           xaxis=attr(title="Sample ID (Grouped by $(group1_label) | $(group2_label))", showgrid=false, zeroline=false, tickvals=sample_name_indices,
-                          ticktext=id_list, tickfont_size=5, tickangle=45,showticklabels=x_axis_label_option),
+                          ticktext=id_list, tickangle=45,showticklabels=x_axis_label_option),
 
                           yaxis=attr(title="Genomic Location", zeroline=false, tickvals=chrom_label_indices,
                           ticktext=chrom_labels,tickfont_size=font_size,hovermode=true,automargin=true),
@@ -208,7 +208,7 @@ h_line_index_list = generate_hline_indices(number_rows,input)
                           title = "$title_no_underscores",
 
                           xaxis=attr(title="Sample ID (Grouped by $(group1_label) | $(group2_label))", showgrid=false, zeroline=false, tickvals=sample_name_indices,
-                          ticktext=id_list, tickfont_size=5, tickangle=45,showticklabels=x_axis_label_option),
+                          ticktext=id_list, tickangle=45,showticklabels=x_axis_label_option),
 
                           yaxis=attr(title="Genomic Location", zeroline=false, tickvals=chr_pos_tuple_indices,
                           ticktext=chr_pos_tuple_list,tickfont_size=font_size,hovermode=true,automargin=true),
@@ -224,7 +224,7 @@ h_line_index_list = generate_hline_indices(number_rows,input)
         layout = Layout(
                         title = "$title_no_underscores",
                         xaxis=attr(title="Sample ID (Grouped by $(group1_label) | $(group2_label))", showgrid=false, zeroline=false, tickvals=sample_name_indices,
-                        ticktext=id_list, tickfont_size=5, tickangle=45,showticklabels=x_axis_label_option),
+                        ticktext=id_list, tickangle=45,showticklabels=x_axis_label_option),
 
                         yaxis=attr(title="Genomic Location", zeroline=false, tickvals=chr_pos_tuple_indices,
                         ticktext=chr_pos_tuple_list,tickfont_size=font_size,hovermode=true,automargin=true,showticklabels=false),
@@ -281,7 +281,7 @@ function dp_heatmap2(input, title, chrom_label_info, sample_names,chr_pos_tuple_
            layout = Layout(
                            title = "$title_no_underscores",
                            xaxis=attr(title="Sample ID", showgrid=false, zeroline=false, tickvals=sample_name_indices,
-                           ticktext=sample_names, tickfont_size=5, tickangle=45,showticklabels=x_axis_label_option),
+                           ticktext=sample_names, tickangle=45,showticklabels=x_axis_label_option),
                            yaxis=attr(title="Genomic Location", zeroline=false, tickvals=chrom_label_indices,
                            ticktext=chrom_labels,tickfont_size=font_size,hovermode=true,automargin=true)
            )
@@ -294,7 +294,7 @@ function dp_heatmap2(input, title, chrom_label_info, sample_names,chr_pos_tuple_
            layout = Layout(
                            title = "$title_no_underscores",
                            xaxis=attr(title="Sample ID", showgrid=false, zeroline=false, tickvals=sample_name_indices,
-                           ticktext=sample_names, tickfont_size=5, tickangle=45,showticklabels=x_axis_label_option),
+                           ticktext=sample_names, tickangle=45,showticklabels=x_axis_label_option),
                            yaxis=attr(title="Genomic Location", zeroline=false, tickvals=chr_pos_tuple_indices,
                            ticktext=chr_pos_tuple_list,tickfont_size=font_size,hovermode=true,automargin=true)
            )
@@ -307,7 +307,7 @@ function dp_heatmap2(input, title, chrom_label_info, sample_names,chr_pos_tuple_
            layout = Layout(
                            title = "$title_no_underscores",
                            xaxis=attr(title="Sample ID", showgrid=false, zeroline=false, tickvals=sample_name_indices,
-                           ticktext=sample_names, tickfont_size=5, tickangle=45,showticklabels=x_axis_label_option),
+                           ticktext=sample_names, tickangle=45,showticklabels=x_axis_label_option),
                            yaxis=attr(title="Genomic Location", zeroline=false, tickvals=chr_pos_tuple_indices,
                            ticktext=chr_pos_tuple_list,tickfont_size=font_size,hovermode=true,automargin=true,showticklabels=false)
            )
@@ -383,7 +383,7 @@ if y_axis_label_option == "chromosomes"
 
                     xaxis=attr(title="Sample ID (Grouped by $(group1_label) | $(group2_label))",
                     showgrid=false, zeroline=false, tickvals=sample_name_indices,
-                    ticktext=id_list, tickfont_size=5, tickangle=45,showticklabels=x_axis_label_option),
+                    ticktext=id_list, tickangle=45,showticklabels=x_axis_label_option),
 
                     yaxis=attr(title="Genomic Location", zeroline=false,
                     tickvals=chrom_label_indices,ticktext=chrom_labels,
@@ -402,7 +402,7 @@ elseif y_axis_label_option == "positions"
 
                     xaxis=attr(title="Sample ID (Grouped by $(group1_label) | $(group2_label))",
                     showgrid=false, zeroline=false, tickvals=sample_name_indices,
-                    ticktext=id_list, tickfont_size=5, tickangle=45,showticklabels=x_axis_label_option),
+                    ticktext=id_list, tickangle=45,showticklabels=x_axis_label_option),
 
                     yaxis=attr(title="Genomic Location", zeroline=false,
                     tickvals=chr_pos_tuple_indices,
@@ -421,7 +421,7 @@ elseif y_axis_label_option == "hover_positions"
   layout = Layout(
                   title = "$title_no_underscores",
                   xaxis=attr(title="Sample ID (Grouped by $(group1_label) | $(group2_label))", showgrid=false, zeroline=false, tickvals=sample_name_indices,
-                  ticktext=id_list, tickfont_size=5, tickangle=45,showticklabels=x_axis_label_option),
+                  ticktext=id_list, tickangle=45,showticklabels=x_axis_label_option),
 
                   yaxis=attr(title="Genomic Location", zeroline=false, tickvals=chr_pos_tuple_indices,
                   ticktext=chr_pos_tuple_list,tickfont_size=font_size,hovermode=true,automargin=true,showticklabels=false),

docs/src/assets/Read_Depth_Genomic_Range_Chr4:3076150-3076390.png

@@ -839,7 +839,9 @@ function select_columns(filename_sample_list::AbstractString, num_array::Array{I
 
     selected_samples_num_array = Matrix(df_selected_samples_num_array)
 
-    return selected_samples_num_array,col_selectedcolumns
+    sample_names=permutedims(col_selectedcolumns)
+
+    return selected_samples_num_array,sample_names
 end
 
 

docs/src/examples.md

@@ -248,7 +248,7 @@ dp_num_array,dp_chromosome_labels=combined_all_read_depth_array_functions(sub)
         dp_num_array=select_columns("test_files/select_samples_list.txt", dp_num_array, sample_names)
         #println("select_columns dp_num_array type is $(typeof(dp_num_array))")
         #println("select_columns dp_num_array size is $(size(dp_num_array,1))")
-        @test typeof(dp_num_array) == Tuple{Array{Int64,2},Array{Any,1}}
+        @test typeof(dp_num_array) == Tuple{Array{Int64,2},Array{Any,2}}
         @test size(dp_num_array,1) == 2
         end
 

src/init.jl

@@ -273,6 +273,8 @@ if parsed_args["heatmap"] == "genotype"
                                           sample_names)
             sample_names = col_selectedcolumns
 
+
+
         elseif parsed_args["select_samples"] != nothing && length(parsed_args["group_samples"]) == 2
             println("Can not select samples with phenotype matrix provided. Please include same sample ids in phenotype matrix as in list of sample names to select.")
 
@@ -342,6 +344,8 @@ if parsed_args["heatmap"] == "read_depth"
             println("Selecting samples listed in $(parsed_args["select_samples"])")
             dp_num_array,col_selectedcolumns = select_columns(parsed_args["select_samples"], dp_num_array, sample_names)
             sample_names=col_selectedcolumns
+
+
         elseif parsed_args["select_samples"] != nothing && length(parsed_args["group_samples"]) == 2
             println("Can not select samples with phenotype matrix provided. Please include same sample ids in phenotype matrix as in list of sample names to select.")
         end
@@ -369,6 +373,8 @@ if parsed_args["heatmap"] == "read_depth"
             println("Selecting samples listed in $(parsed_args["select_samples"])")
 
             dp_num_array,col_selectedcolumns = select_columns(parsed_args["select_samples"], dp_num_array, sample_names)
+            sample_names=col_selectedcolumns
+
 
         elseif parsed_args["select_samples"] != nothing && length(parsed_args["group_samples"]) == 2
             println("Can not select samples with phenotype matrix provided. Please include same sample ids in phenotype matrix as in list of sample names to select.")
@@ -444,8 +450,7 @@ if parsed_args["heatmap"] == "genotype,read_depth" || parsed_args["heatmap"] ==
             println("Can not select samples with phenotype matrix provided. Please include same sample ids in phenotype matrix as in list of sample names to select.")
 
         end
-
-        graphic = VariantVisualization.genotype_heatmap2(gt_num_array,title,chrom_label_info,sample_names,chr_pos_tuple_list,y_axis_label_option,x_axis_label_option)
+                graphic = VariantVisualization.genotype_heatmap2(gt_num_array,title,chrom_label_info,sample_names,chr_pos_tuple_list,y_axis_label_option,x_axis_label_option)
     end
 
     println("Saving genotype heatmap")