Custom logo alignment and script change.

Author: Selcuk

public/custom_msa/GPR1_clade.fasta

@@ -213,89 +213,4 @@ VFKPG-------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------------------------------------
 ------------------------------
->tr|A1DHG4|A1DHG4_NEOFI|331117_A0A364MGU9_ASPFL/40-408
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
--------------------GSLR-----------------AGF----IA----IGAVALC
-S--ATFSLISFLTYRFIFW-Q---RY---KRP-AHNY----LIYNLLLVDI-QQATAFLL
-CL--HWVAR-------------------------GVNYPSAACVLQGWWIQTADPGSGLF
-VLAIAIHTCVVVLRG----------RQLPFTT-----------FVWCVVGLWA-FIILLG
-LI-------------AVGLYGSK--TF------------ISEA-----------------
-WCWLSPQ----AQDERLWGH--------YVWIFL-S------EFGTIV-LYGIMFFYLRR
-RMKQ----------------------------------------------AAA-------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------LR--QN
-------------------------------------------------------------
---------------------------------HQESLN----RLN--RVVVYMVIYPLVY
-VLLSL------P--LAA-GR-MS-TARH---------------------------VVPSK
-E-YFA-AAGALMAL-SGLVDVIVYT------------TRRHLLL---D--------TE--
-V---------S-TS--DR----------------------YYA----H------------
-----T-----------------------------S-N--LYNTH-----------STTVA
-G--ESKKS---KSRL-RR-QSINDTVLD------------------------RGDSTED-
---GPKGDMELSNMAHGVY------------------------------------------
-------------------------------------------------------------
----------------------------------------------------------QET
-T-----------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------
->tr|A0A1S9E0Y9|A0A1S9E0Y9_ASPOZ|5062_A0A364MGU9_ASPFL/33-416
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
--------------------GGDR-----------------AGF----IA----MGVVALC
-S--ASFCLLSFLTYRFIFW-K---RY---KRP-AANY----LIYNLLLIDI-QQATAFVL
-CL--YWVSR-------------------------HVDYPSAACVLQGWWIQIGDPGSGLF
-IMAIAMHTGAVVLRG----------RQLPHRT-----------FVCCVIGLWA-FIIVLG
-LI-------------PVGLFGSK--TF------------ISEAQGQR--------EYVLT
-QCWLGPE----HETERLWVH--------YLWIFL-A------EFGTVV-FYGMLFFHLRR
-RMKQ----------------------------------------------AAM-------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------LR--QG
-------------------------------------------------------------
---------------------------------HQESLK----RLN--RVVIYMVIYPIVY
-LVLSL------P--LAA-GR-MS-TARH---------------------------IVQSR
-G-YFA-VAGSLMAL-SGLVDVVVYT------------TRRHLLL---D--------TE--
-I---------S-TS--DK----------------------MYA----Y------------
-----S-----------------------------S-N--AYQTH-----------TTTTR
----ENKKP---GSRL-RR-QTINDTIND-------------------------GDSTED-
---RKDGDMEMADLGHGVY------------------------------------------
-------------------------------------------------------------
----------------------------------------------------------QET
-T-----------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------
+

public/custom_msa/GprD_clade.fasta

@@ -0,0 +1,86 @@
+>tr|A1DHG4|A1DHG4_NEOFI|331117_A0A364MGU9_ASPFL/40-408
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------GSLR-----------------AGF----IA----IGAVALC
+S--ATFSLISFLTYRFIFW-Q---RY---KRP-AHNY----LIYNLLLVDI-QQATAFLL
+CL--HWVAR-------------------------GVNYPSAACVLQGWWIQTADPGSGLF
+VLAIAIHTCVVVLRG----------RQLPFTT-----------FVWCVVGLWA-FIILLG
+LI-------------AVGLYGSK--TF------------ISEA-----------------
+WCWLSPQ----AQDERLWGH--------YVWIFL-S------EFGTIV-LYGIMFFYLRR
+RMKQ----------------------------------------------AAA-------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------LR--QN
+------------------------------------------------------------
+--------------------------------HQESLN----RLN--RVVVYMVIYPLVY
+VLLSL------P--LAA-GR-MS-TARH---------------------------VVPSK
+E-YFA-AAGALMAL-SGLVDVIVYT------------TRRHLLL---D--------TE--
+V---------S-TS--DR----------------------YYA----H------------
+----T-----------------------------S-N--LYNTH-----------STTVA
+G--ESKKS---KSRL-RR-QSINDTVLD------------------------RGDSTED-
+--GPKGDMELSNMAHGVY------------------------------------------
+------------------------------------------------------------
+---------------------------------------------------------QET
+T-----------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------
+>tr|A0A1S9E0Y9|A0A1S9E0Y9_ASPOZ|5062_A0A364MGU9_ASPFL/33-416
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------GGDR-----------------AGF----IA----MGVVALC
+S--ASFCLLSFLTYRFIFW-K---RY---KRP-AANY----LIYNLLLIDI-QQATAFVL
+CL--YWVSR-------------------------HVDYPSAACVLQGWWIQIGDPGSGLF
+IMAIAMHTGAVVLRG----------RQLPHRT-----------FVCCVIGLWA-FIIVLG
+LI-------------PVGLFGSK--TF------------ISEAQGQR--------EYVLT
+QCWLGPE----HETERLWVH--------YLWIFL-A------EFGTVV-FYGMLFFHLRR
+RMKQ----------------------------------------------AAM-------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------LR--QG
+------------------------------------------------------------
+--------------------------------HQESLK----RLN--RVVIYMVIYPIVY
+LVLSL------P--LAA-GR-MS-TARH---------------------------IVQSR
+G-YFA-VAGSLMAL-SGLVDVVVYT------------TRRHLLL---D--------TE--
+I---------S-TS--DK----------------------MYA----Y------------
+----S-----------------------------S-N--AYQTH-----------TTTTR
+---ENKKP---GSRL-RR-QTINDTIND-------------------------GDSTED-
+--RKDGDMEMADLGHGVY------------------------------------------
+------------------------------------------------------------
+---------------------------------------------------------QET
+T-----------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------

src/components/CustomSequenceLogo.tsx

@@ -2666,6 +2666,24 @@ const CustomSequenceLogo: React.FC<Props> = ({ fastaNames, folder }) => {
           .style('font-family', 'Helvetica')
           .text('Conservation %');
       }
+
+      // ─── Add column numbers on top ─────────────────────────────────────────
+      // Use the display positions (1-based) for labeling
+      chartSvg.selectAll('text.column-number')
+        .data(positionsWithData.map((pos, i) => ({ pos, display: i + 1 })))
+        .enter()
+        .append('text')
+        .attr('class', 'column-number')
+        // nudge the row slightly right by adding a small x-offset (e.g., 4px)
+        .attr('transform', d => {
+          const xPos = x.getX(d.pos.toString()) + x.bandwidth() / 2 + 4;
+          const yPos = margin.top / 2;
+          return `translate(${xPos},${yPos}) rotate(-90)`;
+        })
+        .attr('text-anchor', 'middle')
+        .style('font-weight', 'bold')
+        .text(d => d.display);
+      // ─────────────────────────────────────────────────────────────────────────
     }
 
     return () => {