From 21cb8ac18c64b35fc9f1487cd0a126667005f454 Mon Sep 17 00:00:00 2001
From: Zachary Charlop-Powers <zach.charlop.powers@gmail.com>
Date: Tue, 15 Oct 2024 17:33:49 -0400
Subject: [PATCH] refactor base plotting

---
 src/components/fasta_processing.js |  26 ++++++++
 src/fastx/fasta_simple.md          |   6 +-
 src/fastx/fastx_stats.md           | 100 +++--------------------------
 3 files changed, 37 insertions(+), 95 deletions(-)

diff --git a/src/components/fasta_processing.js b/src/components/fasta_processing.js
index 4f16613..8b76cd7 100644
--- a/src/components/fasta_processing.js
+++ b/src/components/fasta_processing.js
@@ -1,6 +1,7 @@
 import { open } from "@tauri-apps/plugin-dialog";
 import { invoke } from "npm:@tauri-apps/api/core";
 import { html } from "npm:htl";
+import * as Plot from "npm:@observablehq/plot";
 
 function choosefasta() {
   const selected = open({
@@ -37,3 +38,28 @@ export async function getFastaStats() {
     <p>Maximum Length: ${stats.maxlength}</p>
   </div>`;
 }
+
+export function stats_description(stats) {
+  return html`
+    <p>AVG Len: ${stats.avg_len}</p>
+    <p>Filename: ${stats.filename}</p>
+    <p>Format: ${stats.format}</p>
+    <p>MAX Len: ${stats.max_len}</p>
+    <p>MIN Len: ${stats.min_len}</p>
+    <p>Number of Records Len: ${stats.num_seqs}</p>
+    <p>Sum Len: ${stats.sum_len}</p>
+  `;
+}
+
+export function plot_stats(stats) {
+  return Plot.rectY(
+    { length: 10000 },
+    Plot.binX({ y: "count" }, { x: stats.contig_lengths }),
+  ).plot();
+}
+
+export async function getFastaStatsSeqkit() {
+  const fasta = await choosefasta();
+  const stats = await invoke("get_seqstats", { filename: fasta });
+  return stats;
+}
diff --git a/src/fastx/fasta_simple.md b/src/fastx/fasta_simple.md
index 7de9cde..9cdccb8 100644
--- a/src/fastx/fasta_simple.md
+++ b/src/fastx/fasta_simple.md
@@ -4,21 +4,19 @@ title: "Simple Fasta"
 
 Simplest example. uses Noodles to loop throught a fasta file and return the record count and maximul length in the file
 
-
 ```js
 import {getFastaStats} from "../components/fasta_processing.js";
 
 const fasta_stats = view(
-Inputs.button("Get Fasta Stats: Part 2 ", {
+Inputs.button("Get Fasta Stats", {
   value: null,
   reduce: () => getFastaStats()
 }));
-
 ```
 
 ```js
+// if null there is a spinning arrow.
 if (fasta_stats != null) {
   display(fasta_stats)
 }
-
 ```
diff --git a/src/fastx/fastx_stats.md b/src/fastx/fastx_stats.md
index 5dbfbbb..c147ec4 100644
--- a/src/fastx/fastx_stats.md
+++ b/src/fastx/fastx_stats.md
@@ -2,74 +2,10 @@
 title: "Fastx stats"
 ---
 
-
-```js
-import { open } from "@tauri-apps/plugin-dialog";
-import { invoke } from "npm:@tauri-apps/api/core";
-
-
-// use the tauri open to get absolute file paths
-async function choosefasta(){
-    const selected = open({
-        multiple: false,
-        filters: [{
-            name: 'Fasta',
-            extensions: ['fa', 'fasta', 'fna']}]
-    });
-    return selected
-};
-
-async function choosefastq(){
-    const selected = open({
-        multiple: false,
-        filters: [{
-            name: 'Fastq',
-            extensions: ['fq', 'fastq']}]
-    });
-    return selected
-};
-
-```
-
-
-```js
-
-// const fasta_stats_seqkit = view(Inputs.button(
-//    "Get Fasta Stats",
-//    {
-//        value: null,
-//        reduce: () => choosefasta().then((fname) => invoke("get_seqstats", {filename: fname.path}))
-//    }));
-
-const fasta_stats_seqkit = view(Inputs.button(
-    "Get Fasta Stats",
-    {
-        value: null,
-        reduce: () => choosefasta().then((selected) => {
-            if (selected) {
-                console.log("selected!");
-                return invoke("get_seqstats", { filename: selected }).then(result => {
-                                        console.log("Stats received:", result);
-                                        return result; // This will update the button's value
-                                    });
-            } else {
-                return Promise.reject("No file selected");
-            }
-        })
-    }
-));
-
-let fasta_stats_seqkit_realized = (fasta_stats_seqkit == null)  ? "Click Above to Get Fasta Statistics" : fasta_stats_seqkit
-
-```
-
-
 ```txt
-
 https://downloads.pacbcloud.com/public/dataset/Sequel-IIe-202104/metagenomics/?utm_source=Website&utm_medium=webpage&utm_term=SQII-humanGut-microbiome-pooledStandards&utm_content=datasets&utm_campaign=0000-Website-Leads
 https://downloads.pacbcloud.com/public/dataset/AAV/2022-ssAAV-scAAV-mix/1-mapped-mixed/
 
-
 simple statistics of FASTA/Q files
 
 Columns:
@@ -94,40 +30,22 @@ Columns:
 
 ```
 
-
 ## Basic Stats
 
 ```js
+import {stats_description, plot_stats, getFastaStatsSeqkit} from "../components/fasta_processing.js";
 
-if (fasta_stats_seqkit_realized !== null) {
-    html`AVG Len: ${fasta_stats_seqkit_realized.avg_len}`
-    html`Filename: ${fasta_stats_seqkit_realized.filename}`
-    html`Format: ${fasta_stats_seqkit_realized.format}`
-    html`MAX Len: ${fasta_stats_seqkit_realized.max_len}`
-    html`MIN Len: ${fasta_stats_seqkit_realized.min_len}`
-    html`Number of Records Len: ${fasta_stats_seqkit_realized.num_seqs}`
-    html`Sum Len: ${fasta_stats_seqkit_realized.sum_len}`
-}
-
-```
-
-
-## Plot Histogram
+const fasta_stats = view(
+Inputs.button("Get Fasta Stats", {
+  value: null,
+  reduce: () => getFastaStatsSeqkit()
+}));
 
-```js
-if (fasta_stats_seqkit_realized !== null) {
-    display(fasta_stats_seqkit_realized)
-}
 ```
 
-
 ```js
-if (fasta_stats_seqkit_realized !== null) {
-    display(
-        Plot.rectY(
-            {length: 10000},
-            Plot.binX(
-                {y: "count"},
-                {x: fasta_stats_seqkit_realized.contig_lengths})).plot());
+if (fasta_stats != null) {
+  display(stats_description(fasta_stats));
+  display(plot_stats(fasta_stats));
 }
 ```