Update installation

nvelden · Jan 13, 2025 · 7c15367 · 7c15367
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Showing 11 changed files with 119 additions and 139 deletions.
diff --git a/docs/articles/geneviewer.html b/docs/articles/geneviewer.html
diff --git a/docs/articles/geneviewer_files/D3-7.8.5/geneviewer.yaml b/docs/articles/geneviewer_files/D3-7.8.5/geneviewer.yaml
@@ -1,16 +1,16 @@
 dependencies:
   - name: geneviewerwidget
-    version: 0.1.10
+    version: 0.1.8
     src: htmlwidgets
     script: geneviewerwidget.js
   - name: Themes
-    version: 0.1.10
+    version: 0.1.8
     src: htmlwidgets
-    script: ./lib/geneviewer-0.1.10/Themes.js
+    script: ./lib/geneviewer-0.1.8/Themes.js
   - name: geneviewer
-    version: 0.1.10
+    version: 0.1.8
     src: htmlwidgets
-    script: ./lib/geneviewer-0.1.10/geneviewer.js
+    script: ./lib/geneviewer-0.1.8/geneviewer.js
   - name: D3
     version: 7.8.5
     src: htmlwidgets

diff --git a/.../D3-7.8.5/lib/geneviewer-0.1.10/Themes.js → ...s/D3-7.8.5/lib/geneviewer-0.1.8/Themes.js b/.../D3-7.8.5/lib/geneviewer-0.1.10/Themes.js → ...s/D3-7.8.5/lib/geneviewer-0.1.8/Themes.js
diff --git a/...7.8.5/lib/geneviewer-0.1.10/geneviewer.js → ...-7.8.5/lib/geneviewer-0.1.8/geneviewer.js b/...7.8.5/lib/geneviewer-0.1.10/geneviewer.js → ...-7.8.5/lib/geneviewer-0.1.8/geneviewer.js
@@ -351,6 +351,8 @@ function mergeOptions(defaultOptions, themeOptionsKey, userOptions) {
 function getColorScale(colorScheme, customColors, uniqueGroups) {
   let colorScale;
 
+  //customColors = { ...(customColors || {}), null: "#FFF" };
+
   const schemeCategory30 = [
     "#1f77b4", "#ff7f0e", "#2ca02c", "#d62728", "#9467bd",
     "#8c564b", "#e377c2", "#7f7f7f", "#bcbd22", "#17becf",
@@ -360,18 +362,9 @@ function getColorScale(colorScheme, customColors, uniqueGroups) {
     "#8c6d31", "#e7cb94", "#e7969c", "#7b4173", "#a55194"
   ];
 
-  if (customColors && typeof customColors === "string") {
-    // Handle customColors as a single color
-    colorScale = d3.scaleOrdinal()
-      .domain(uniqueGroups)
-      .range(uniqueGroups.map(() => customColors));
-  } else if (customColors && Array.isArray(customColors)) {
-    // Handle customColors as an array
-    colorScale = d3.scaleOrdinal()
-      .domain(uniqueGroups)
-      .range(uniqueGroups.map((group, index) => customColors[index % customColors.length] || "#FFF"));
-  } else if (customColors && typeof customColors === 'object') {
-    // Handle customColors as an object
+  // Check if customColors is an object and not an array
+  if (customColors && typeof customColors === 'object' && !Array.isArray(customColors)) {
+    // Create a color scale based on the customColors object
     colorScale = d3.scaleOrdinal()
       .domain(uniqueGroups)
       .range(uniqueGroups.map(group => customColors[group] || "#FFF"));
@@ -388,18 +381,15 @@ function getColorScale(colorScheme, customColors, uniqueGroups) {
       }
     }
   } else {
-    // Default to schemeCategory30
     colorScale = d3.scaleOrdinal(schemeCategory30)
       .domain(uniqueGroups)
       .range(uniqueGroups.map(group =>
         group === "No Hit" || group === null ? "#FFF" : schemeCategory30[uniqueGroups.indexOf(group) % schemeCategory30.length]
       ));
   }
-
   return colorScale;
 }
 
-
 function isInAnyDiscontinuity(value, breaks) {
   for (let gap of breaks) {
     if (value >= gap.start && value <= gap.end) {

diff --git a/docs/articles/geneviewer_files/FileSaver-2.0.4-2.0.4/geneviewer.yaml b/docs/articles/geneviewer_files/FileSaver-2.0.4-2.0.4/geneviewer.yaml
@@ -1,16 +1,16 @@
 dependencies:
   - name: geneviewerwidget
-    version: 0.1.10
+    version: 0.1.8
     src: htmlwidgets
     script: geneviewerwidget.js
   - name: Themes
-    version: 0.1.10
+    version: 0.1.8
     src: htmlwidgets
-    script: ./lib/geneviewer-0.1.10/Themes.js
+    script: ./lib/geneviewer-0.1.8/Themes.js
   - name: geneviewer
-    version: 0.1.10
+    version: 0.1.8
     src: htmlwidgets
-    script: ./lib/geneviewer-0.1.10/geneviewer.js
+    script: ./lib/geneviewer-0.1.8/geneviewer.js
   - name: D3
     version: 7.8.5
     src: htmlwidgets

diff --git a/...0.4-2.0.4/lib/geneviewer-0.1.10/Themes.js → ....0.4-2.0.4/lib/geneviewer-0.1.8/Themes.js b/...0.4-2.0.4/lib/geneviewer-0.1.10/Themes.js → ....0.4-2.0.4/lib/geneviewer-0.1.8/Themes.js
diff --git a/...2.0.4/lib/geneviewer-0.1.10/geneviewer.js → ...-2.0.4/lib/geneviewer-0.1.8/geneviewer.js b/...2.0.4/lib/geneviewer-0.1.10/geneviewer.js → ...-2.0.4/lib/geneviewer-0.1.8/geneviewer.js
@@ -351,6 +351,8 @@ function mergeOptions(defaultOptions, themeOptionsKey, userOptions) {
 function getColorScale(colorScheme, customColors, uniqueGroups) {
   let colorScale;
 
+  //customColors = { ...(customColors || {}), null: "#FFF" };
+
   const schemeCategory30 = [
     "#1f77b4", "#ff7f0e", "#2ca02c", "#d62728", "#9467bd",
     "#8c564b", "#e377c2", "#7f7f7f", "#bcbd22", "#17becf",
@@ -360,18 +362,9 @@ function getColorScale(colorScheme, customColors, uniqueGroups) {
     "#8c6d31", "#e7cb94", "#e7969c", "#7b4173", "#a55194"
   ];
 
-  if (customColors && typeof customColors === "string") {
-    // Handle customColors as a single color
-    colorScale = d3.scaleOrdinal()
-      .domain(uniqueGroups)
-      .range(uniqueGroups.map(() => customColors));
-  } else if (customColors && Array.isArray(customColors)) {
-    // Handle customColors as an array
-    colorScale = d3.scaleOrdinal()
-      .domain(uniqueGroups)
-      .range(uniqueGroups.map((group, index) => customColors[index % customColors.length] || "#FFF"));
-  } else if (customColors && typeof customColors === 'object') {
-    // Handle customColors as an object
+  // Check if customColors is an object and not an array
+  if (customColors && typeof customColors === 'object' && !Array.isArray(customColors)) {
+    // Create a color scale based on the customColors object
     colorScale = d3.scaleOrdinal()
       .domain(uniqueGroups)
       .range(uniqueGroups.map(group => customColors[group] || "#FFF"));
@@ -388,18 +381,15 @@ function getColorScale(colorScheme, customColors, uniqueGroups) {
       }
     }
   } else {
-    // Default to schemeCategory30
     colorScale = d3.scaleOrdinal(schemeCategory30)
       .domain(uniqueGroups)
       .range(uniqueGroups.map(group =>
         group === "No Hit" || group === null ? "#FFF" : schemeCategory30[uniqueGroups.indexOf(group) % schemeCategory30.length]
       ));
   }
-
   return colorScale;
 }
 
-
 function isInAnyDiscontinuity(value, breaks) {
   for (let gap of breaks) {
     if (value >= gap.start && value <= gap.end) {

diff --git a/docs/articles/geneviewer_files/html2canvas-1.4.1/geneviewer.yaml b/docs/articles/geneviewer_files/html2canvas-1.4.1/geneviewer.yaml
@@ -1,16 +1,16 @@
 dependencies:
   - name: geneviewerwidget
-    version: 0.1.10
+    version: 0.1.8
     src: htmlwidgets
     script: geneviewerwidget.js
   - name: Themes
-    version: 0.1.10
+    version: 0.1.8
     src: htmlwidgets
-    script: ./lib/geneviewer-0.1.10/Themes.js
+    script: ./lib/geneviewer-0.1.8/Themes.js
   - name: geneviewer
-    version: 0.1.10
+    version: 0.1.8
     src: htmlwidgets
-    script: ./lib/geneviewer-0.1.10/geneviewer.js
+    script: ./lib/geneviewer-0.1.8/geneviewer.js
   - name: D3
     version: 7.8.5
     src: htmlwidgets

diff --git a/...vas-1.4.1/lib/geneviewer-0.1.10/Themes.js → ...nvas-1.4.1/lib/geneviewer-0.1.8/Themes.js b/...vas-1.4.1/lib/geneviewer-0.1.10/Themes.js → ...nvas-1.4.1/lib/geneviewer-0.1.8/Themes.js
diff --git a/...1.4.1/lib/geneviewer-0.1.10/geneviewer.js → ...-1.4.1/lib/geneviewer-0.1.8/geneviewer.js b/...1.4.1/lib/geneviewer-0.1.10/geneviewer.js → ...-1.4.1/lib/geneviewer-0.1.8/geneviewer.js
@@ -351,6 +351,8 @@ function mergeOptions(defaultOptions, themeOptionsKey, userOptions) {
 function getColorScale(colorScheme, customColors, uniqueGroups) {
   let colorScale;
 
+  //customColors = { ...(customColors || {}), null: "#FFF" };
+
   const schemeCategory30 = [
     "#1f77b4", "#ff7f0e", "#2ca02c", "#d62728", "#9467bd",
     "#8c564b", "#e377c2", "#7f7f7f", "#bcbd22", "#17becf",
@@ -360,18 +362,9 @@ function getColorScale(colorScheme, customColors, uniqueGroups) {
     "#8c6d31", "#e7cb94", "#e7969c", "#7b4173", "#a55194"
   ];
 
-  if (customColors && typeof customColors === "string") {
-    // Handle customColors as a single color
-    colorScale = d3.scaleOrdinal()
-      .domain(uniqueGroups)
-      .range(uniqueGroups.map(() => customColors));
-  } else if (customColors && Array.isArray(customColors)) {
-    // Handle customColors as an array
-    colorScale = d3.scaleOrdinal()
-      .domain(uniqueGroups)
-      .range(uniqueGroups.map((group, index) => customColors[index % customColors.length] || "#FFF"));
-  } else if (customColors && typeof customColors === 'object') {
-    // Handle customColors as an object
+  // Check if customColors is an object and not an array
+  if (customColors && typeof customColors === 'object' && !Array.isArray(customColors)) {
+    // Create a color scale based on the customColors object
     colorScale = d3.scaleOrdinal()
       .domain(uniqueGroups)
       .range(uniqueGroups.map(group => customColors[group] || "#FFF"));
@@ -388,18 +381,15 @@ function getColorScale(colorScheme, customColors, uniqueGroups) {
       }
     }
   } else {
-    // Default to schemeCategory30
     colorScale = d3.scaleOrdinal(schemeCategory30)
       .domain(uniqueGroups)
       .range(uniqueGroups.map(group =>
         group === "No Hit" || group === null ? "#FFF" : schemeCategory30[uniqueGroups.indexOf(group) % schemeCategory30.length]
       ));
   }
-
   return colorScale;
 }
 
-
 function isInAnyDiscontinuity(value, breaks) {
   for (let gap of breaks) {
     if (value >= gap.start && value <= gap.end) {

diff --git a/vignettes/geneviewer.Rmd b/vignettes/geneviewer.Rmd
@@ -17,7 +17,13 @@ knitr::opts_chunk$set(
 
 ## Installation
 
-**geneviewer** is available through GitHub
+You can install the released version of **geneviewer** from CRAN with:
+
+```r
+install.packages("geneviewer")
+```
+
+And the development version from GitHub with: 
 
 ``` r
 # install.packages("devtools")