improving coloring of proteinAlphabet hydrophobicity scale

TeselaGen · Oct 20, 2021 · 411576a · 411576a
1 parent c28aad2
commit 411576a
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Showing 2 changed files with 35 additions and 41 deletions.
diff --git a/src/proteinAlphabet.js b/src/proteinAlphabet.js
@@ -5,203 +5,203 @@ module.exports = {
     threeLettersName: "Ala",
     hydrophobicity: 1.8,
     colorByFamily: "#00FFFF",
-    color: "#FF5C5C"
+    color: "hsl(327.3, 100%, 69%)"
   },
   R: {
     value: "R",
     name: "Arginine",
     threeLettersName: "Arg",
     hydrophobicity: -4.5,
     colorByFamily: "#FFC0CB",
-    color: "#190000"
+    color: "hsl(258.1, 100%, 69%)"
   },
   N: {
     value: "N",
     name: "Asparagine",
     threeLettersName: "Asn",
     hydrophobicity: -3.5,
     colorByFamily: "#D3D3D3",
-    color: "#4D0000"
+    color: "hsl(268.9, 100%, 69%)"
   },
   D: {
     value: "D",
     name: "Aspartic acid",
     threeLettersName: "Asp",
     hydrophobicity: -3.5,
     colorByFamily: "#EE82EE",
-    color: "#4D0000"
+    color: "hsl(268.9, 100%, 69%)"
   },
   C: {
     value: "C",
     name: "Cysteine",
     threeLettersName: "Cys",
     hydrophobicity: 2.5,
     colorByFamily: "#FFFF00",
-    color: "#FF8080"
+    color: "hsl(335.1, 100%, 69%)"
   },
   E: {
     value: "E",
     name: "Glutamic acid",
     threeLettersName: "Glu",
     hydrophobicity: -3.5,
     colorByFamily: "#EE82EE",
-    color: "#4D0000"
+    color: "hsl(268.9, 100%, 69%)"
   },
   Q: {
     value: "Q",
     name: "Glutamine",
     threeLettersName: "Gln",
     hydrophobicity: -3.5,
     colorByFamily: "#D3D3D3",
-    color: "#4D0000"
+    color: "hsl(268.9, 100%, 69%)"
   },
   G: {
     value: "G",
     name: "Glycine",
     threeLettersName: "Gly",
     hydrophobicity: -0.4,
     colorByFamily: "#00FFFF",
-    color: "#EB0000"
+    color: "hsl(303.1, 100%, 69%)"
   },
   H: {
     value: "H",
     name: "Histidine",
     threeLettersName: "His",
     hydrophobicity: -3.2,
     colorByFamily: "#FFC0CB",
-    color: "#5C0000"
+    color: "hsl(272.2, 100%, 69%)"
   },
   I: {
     value: "I",
     name: "Isoleucine ",
     threeLettersName: "Ile",
     hydrophobicity: 4.5,
     colorByFamily: "#00FFFF",
-    color: "#FFE6E6"
+    color: "hsl(356.9, 100%, 69%)"
   },
   L: {
     value: "L",
     name: "Leucine",
     threeLettersName: "Leu",
     hydrophobicity: 3.8,
     colorByFamily: "#00FFFF",
-    color: "#FFC2C2"
+    color: "hsl(349.4, 100%, 69%)"
   },
   K: {
     value: "K",
     name: "Lysine",
     threeLettersName: "Lys",
     hydrophobicity: -3.9,
     colorByFamily: "#FFC0CB",
-    color: "#380000"
+    color: "hsl(264.7, 100%, 69%)"
   },
   M: {
     value: "M",
     name: "Methionine",
     threeLettersName: "Met",
     hydrophobicity: 1.9,
     colorByFamily: "#FFFF00",
-    color: "#FF6161"
+    color: "hsl(328.5, 100%, 69%)"
   },
   F: {
     value: "F",
     name: "Phenylalanine",
     threeLettersName: "Phe",
     hydrophobicity: 2.8,
     colorByFamily: "#FFA500",
-    color: "#FF8F8F"
+    color: "hsl(338.4, 100%, 69%)"
   },
   P: {
     value: "P",
     name: "Proline",
     threeLettersName: "Pro",
     hydrophobicity: -1.6,
     colorByFamily: "#00FFFF",
-    color: "#AD0000"
+    color: "hsl(289.9, 100%, 69%)"
   },
   S: {
     value: "S",
     name: "Serine",
     threeLettersName: "Ser",
     hydrophobicity: -0.8,
     colorByFamily: "#90EE90",
-    color: "#D60000"
+    color: "hsl(298.6, 100%, 69%)"
   },
   T: {
     value: "T",
     name: "Threonine",
     threeLettersName: "Thr",
     hydrophobicity: -0.7,
     colorByFamily: "#90EE90",
-    color: "#DB0000"
+    color: "hsl(299.8, 100%, 69%)"
   },
   U: {
     value: "U",
     name: "Selenocysteine",
     threeLettersName: "Sec",
     colorByFamily: "#FF0000",
-    color: "#FF0000"
+    color: "hsl(0, 100%, 69%)"
   },
   W: {
     value: "W",
     name: "Tryptophan",
     threeLettersName: "Trp",
     hydrophobicity: -0.9,
     colorByFamily: "#FFA500",
-    color: "#D10000"
+    color: "hsl(297.6, 100%, 69%)"
   },
   Y: {
     value: "Y",
     name: "Tyrosine",
     threeLettersName: "Tyr",
     hydrophobicity: -1.3,
     colorByFamily: "#FFA500",
-    color: "#BD0000"
+    color: "hsl(293.2, 100%, 69%)"
   },
   V: {
     value: "V",
     name: "Valine",
     threeLettersName: "Val",
     hydrophobicity: 4.2,
     colorByFamily: "#00FFFF",
-    color: "#FFD6D6"
+    color: "hsl(353.6, 100%, 69%)"
   },
   "*": {
     value: "*",
     name: "Stop",
     threeLettersName: "Stop",
     colorByFamily: "#FF0000",
-    color: "#FF0000"
+    color: "hsl(0, 100%, 69%)"
   },
   ".": {
     //tnr: this is actually a deletion/gap character (previously we had this as a stop character which is incorrect) https://www.dnabaser.com/articles/IUPAC%20ambiguity%20codes.html
     value: ".",
     name: "Gap",
-    threeLettersName: "Stop",
+    threeLettersName: "Gap",
     colorByFamily: "#FF0000",
-    color: "#FF0000"
+    color: "hsl(0, 100%, 69%)"
   },
   "-": {
     value: "-",
     name: "Gap",
     threeLettersName: "Gap",
     colorByFamily: "#FF0000",
-    color: "#FF0000"
+    color: "hsl(0, 100%, 69%)"
   },
   B: {
     value: "B",
     threeLettersName: "ND",
-    colorByFamily: "lightpurple",
-    color: "lightpurple",
+    colorByFamily: "#D3D3D3",
+    color: "hsl(268.9, 100%, 69%)",
     isAmbiguous: true,
     name: "B",
     aliases: "ND"
   },
   J: {
     value: "J",
     threeLettersName: "IL",
-    colorByFamily: "lightpurple",
-    color: "lightpurple",
+    colorByFamily: "#00FFFF",
+    color: "hsl(352, 100%, 69%)",
     isAmbiguous: true,
     name: "J",
     aliases: "IL"
@@ -210,16 +210,16 @@ module.exports = {
     value: "X",
     threeLettersName: "ACDEFGHIKLMNPQRSTVWY",
     colorByFamily: "#FFFFFF",
-    color: "lightpurple",
+    color: "hsl(60, 100%, 69%)",
     isAmbiguous: true,
     name: "X",
     aliases: "ACDEFGHIKLMNPQRSTVWY"
   },
   Z: {
     value: "Z",
     threeLettersName: "QE",
-    colorByFamily: "lightpurple",
-    color: "lightpurple",
+    colorByFamily: "#D3D3D3",
+    color: "hsl(268.9, 100%, 69%)",
     isAmbiguous: true,
     name: "Z",
     aliases: "QE"

diff --git a/src/tidyUpSequenceData.test.js b/src/tidyUpSequenceData.test.js
@@ -80,9 +80,7 @@ describe("tidyUpSequenceData", function() {
           aminoAcid: {
             value: ".",
             name: "Gap",
-            threeLettersName: "Stop",
-            colorByFamily: "#FF0000",
-            color: "#FF0000"
+            threeLettersName: "Gap"
           },
           positionInCodon: 0,
           aminoAcidIndex: 17,
@@ -97,9 +95,7 @@ describe("tidyUpSequenceData", function() {
           aminoAcid: {
             value: ".",
             name: "Gap",
-            threeLettersName: "Stop",
-            colorByFamily: "#FF0000",
-            color: "#FF0000"
+            threeLettersName: "Gap"
           },
           positionInCodon: 1,
           aminoAcidIndex: 17,
@@ -114,9 +110,7 @@ describe("tidyUpSequenceData", function() {
           aminoAcid: {
             value: ".",
             name: "Gap",
-            threeLettersName: "Stop",
-            colorByFamily: "#FF0000",
-            color: "#FF0000"
+            threeLettersName: "Gap"
           },
           positionInCodon: 2,
           aminoAcidIndex: 17,