fix(fixedColorcodingOfTraitLegendsInGroupedHeatmaps):

Author: gtollefson

README.md

@@ -25,7 +25,7 @@ macOS ( Sierra, High Sierra, and Mojave ), Windows (7 and 10), and Linux.
 
 ### Step 1: Install Julia
 
-1. Download [Julia v1.0.4]("https://julialang.org/downloads/") and install the language following the [platform specific instructions](https://julialang.org/downloads/platform.html).
+1. Download [Julia]("https://julialang.org/downloads/") and install the language following the [platform specific instructions](https://julialang.org/downloads/platform.html).
 
 2. Then, follow add Julia to the path variable to run VIVA.
 
@@ -35,7 +35,9 @@ Add the path to the Julia binaries (C:\Program Files\Julia\bin) to the PATH foll
 
 To add Julia to the PATH on Mac run the following line in the Terminal:
 
-> sudo ln -s /Applications/Julia-1.0.app/Contents/Resources/julia/bin/julia /usr/local/bin/julia
+> sudo ln -s /Applications/Julia-1.2.app/Contents/Resources/julia/bin/julia /usr/local/bin/julia
+
+Be sure to replace "/Applications/Julia-1.2.app/..." to reflect the version of Julia you've downloaded.
 
 
 *Linux Note*: To run on remote compute clusters, you may need to load the opengl and julia modules.

docs/src/installation.md

@@ -6,7 +6,7 @@ macOS ( Sierra, High Sierra, and Mojave ), Windows (7 and 10), and Linux.
 
 ### Step 1: Install Julia
 
-1. Download [Julia v1.0.4]("https://julialang.org/downloads/") and install the language following the [platform specific instructions](https://julialang.org/downloads/platform.html).
+1. Download [Julia]("https://julialang.org/downloads/") and install the language following the [platform specific instructions](https://julialang.org/downloads/platform.html).
 
 2. Then, follow add Julia to the path variable to run VIVA.
 
@@ -16,9 +16,9 @@ Add the path to the Julia binaries (C:\Program Files\Julia\bin) to the PATH foll
 
 To add Julia to the PATH on Mac run the following line in the Terminal:
 
-> sudo ln -s /Applications/Julia-1.0.app/Contents/Resources/julia/bin/julia /usr/local/bin/julia
+> sudo ln -s /Applications/Julia-1.2.app/Contents/Resources/julia/bin/julia /usr/local/bin/julia
 
-Be sure to replace "/Applications/Julia-1.1.app/..." to reflect the version of Julia you've downloaded.
+Be sure to replace "/Applications/Julia-1.2.app/..." to reflect the version of Julia you've downloaded.
 
 
 *Linux Note*: To run on remote compute clusters, you may need to load the opengl and julia modules.

src/plot_utils.jl

@@ -120,8 +120,8 @@ function genotype_heatmap_with_groups(input::Array{Int64,2},title::String,chrom_
                        transpose=true,
 
                                     colorscale = [
-                                                  [0, "rgb(151, 154, 154)"], #dark grey
-                                                  [0.2, "rgb(208, 211, 212)"], #light grey
+                                                  [0, "rgb(208, 211, 212)"], #light grey
+                                                  [0.2, "rgb(151, 154, 154)"], #dark grey
                                                   [0.4, "rgb(255,255,255)"], #white
                                                   #[0.4, "rgb(56,25,90)"], #dark blue
                                                   [0.6, "rgb(51,106,145)"], #blue
@@ -352,8 +352,8 @@ function dp_heatmap2_with_groups(input::Array{Int64,2},title::String,chrom_label
         transpose=true,
 
                      colorscale = [
-                                      [0, "rgb(151, 154, 154)"], #dark grey
-                                      [0.125, "rgb(208, 211, 212)"], #light grey
+                                      [0, "rgb(208, 211, 212)"], #light grey
+                                      [0.125, "rgb(151, 154, 154)"], #dark grey
                                       [0.25, "rgb(255, 255, 255)"],
                                       [0.4, "rgb(153,231,255)"],
                                       [0.5, "rgb(79,146,255)"],

viva

@@ -6,10 +6,14 @@ println()
 println("Loading dependency packages:")
 println()
 
-using VariantVisualization
+#using VariantVisualization
 println("...")
 
 using Pkg
+Pkg.activate(@__DIR__)
+using VariantVisualization
+
+
 try
     using GeneticVariation
 catch