Merge pull request #27 from bcgsc/methylation

Merge pull request #26 from bcgsc/main
bcgsc · Mar 5, 2024 · 1aeb4dc · 1aeb4dc
2 parents 4513ec9 + a0d7030
commit 1aeb4dc
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Showing 26 changed files with 225 additions and 20 deletions.
diff --git a/Figures/Cohort/Cohort_figures.html b/Figures/Cohort/Cohort_figures.html
diff --git a/Figures/Cohort/Cohort_figures.md b/Figures/Cohort/Cohort_figures.md
@@ -1,7 +1,7 @@
 Cohort figure generation (Figure 1a,b and Extended Data Figure 1a)
 ================
 Erin Pleasance
-2024-02-16
+2024-02-22
 
 This is an R markdown used to generate figures describing the overall
 cohort.

diff --git a/Figures/Cohort/Cohort_figures_files/figure-gfm/genomic-1.png b/Figures/Cohort/Cohort_figures_files/figure-gfm/genomic-1.png
diff --git a/Figures/Cohort/Cohort_figures_files/figure-gfm/genomic-2.png b/Figures/Cohort/Cohort_figures_files/figure-gfm/genomic-2.png
diff --git a/Figures/Cohort/Cohort_figures_files/figure-gfm/genomic-3.png b/Figures/Cohort/Cohort_figures_files/figure-gfm/genomic-3.png
diff --git a/Figures/Fig1_Sequencing_Stats/figures/mohccn-2024-02-22pog-1.pdf b/Figures/Fig1_Sequencing_Stats/figures/mohccn-2024-02-22pog-1.pdf
diff --git a/Figures/Fig1_Sequencing_Stats/figures/mohccn-2024-02-22pog-1.png b/Figures/Fig1_Sequencing_Stats/figures/mohccn-2024-02-22pog-1.png
diff --git a/Figures/Fig1_Sequencing_Stats/figures/mohccn-2024-02-22pog-2.pdf b/Figures/Fig1_Sequencing_Stats/figures/mohccn-2024-02-22pog-2.pdf
diff --git a/Figures/Fig1_Sequencing_Stats/figures/mohccn-2024-02-22pog-2.png b/Figures/Fig1_Sequencing_Stats/figures/mohccn-2024-02-22pog-2.png
diff --git a/Figures/Fig1_Sequencing_Stats/figures/mohccn-2024-02-22sparks_dotplots-1.pdf b/Figures/Fig1_Sequencing_Stats/figures/mohccn-2024-02-22sparks_dotplots-1.pdf
diff --git a/Figures/Fig1_Sequencing_Stats/figures/mohccn-2024-02-22sparks_dotplots-1.png b/Figures/Fig1_Sequencing_Stats/figures/mohccn-2024-02-22sparks_dotplots-1.png
diff --git a/Figures/Fig1_Sequencing_Stats/sequencing_stats.html b/Figures/Fig1_Sequencing_Stats/sequencing_stats.html
@@ -11,7 +11,7 @@
 
 <meta name="author" content="Kieran O’Neill" />
 
-<meta name="date" content="2024-02-16" />
+<meta name="date" content="2024-02-22" />
 
 <title>Long-read POG QC Stats</title>
 
@@ -352,7 +352,7 @@
 
 <h1 class="title toc-ignore">Long-read POG QC Stats</h1>
 <h4 class="author">Kieran O’Neill</h4>
-<h4 class="date">2024-02-16</h4>
+<h4 class="date">2024-02-22</h4>
 
 </div>
 

diff --git a/Figures/Methylation/Methylation_Fig4a.ipynb b/Figures/Methylation/Methylation_Fig4a.ipynb
@@ -2,20 +2,20 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
-    "# title: Codes to generate methylation plots\n",
-    "# author: Andrew Galbraith\n",
-    "# Modules to import\n",
+    "# Modules to import - get rid of any not used - add to dockfile in github\n",
     "import pandas as pd\n",
     "import scipy\n",
     "import datashader as ds\n",
     "from datashader.mpl_ext import dsshow\n",
     "import scipy.stats\n",
     "import matplotlib.pyplot as plt\n",
-    "from matplotlib.colors import LinearSegmentedColormap\n"
+    "from matplotlib.colors import LinearSegmentedColormap\n",
+    "import ssl\n",
+    "from urllib.request import urlopen\n"
    ]
   },
   {
@@ -24,8 +24,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# import data\n",
-    "POG044_BS_Nano_df = pd.read_csv('https://www.bcgsc.ca/downloads/nanopore_pog/Methylation/POG044_BS_Nanopolish_Meth.bed.gz', sep=\"\\t\",header=None, compression='gzip')\n"
+    "# import data - make sure to change to data from GSC website\n",
+    "\n",
+    "# use ssl to securely open csv before loading into pandas dataframe\n",
+    "data_loc = 'https://www.bcgsc.ca/downloads/nanopore_pog/Methylation/POG044_BS_Nanopolish_Meth.bed.gz'\n",
+    "\n",
+    "context=ssl.create_default_context()\n",
+    "context.set_ciphers(\"DEFAULT\")\n",
+    "result = urlopen(data_loc, context=context)\n",
+    "\n",
+    "POG044_BS_Nano_df = pd.read_csv(result, sep=\"\\t\",header=None, compression='gzip')\n"
    ]
   },
   {

diff --git a/Figures/Methylation/Methylation_Fig4a.nbconvert.ipynb b/Figures/Methylation/Methylation_Fig4a.nbconvert.ipynb
diff --git a/Figures/Methylation/Methylation_Fig4a.pdf b/Figures/Methylation/Methylation_Fig4a.pdf
diff --git a/...thylation/Methylation_Figures_GitHub_files/figure-gfm/Overall_Methylation-1.png b/...thylation/Methylation_Figures_GitHub_files/figure-gfm/Overall_Methylation-1.png
diff --git a/...ylation_Figures_GitHub_files/figure-gfm/TET_IDH_Mutation_Methylation_CGIs-1.png b/...ylation_Figures_GitHub_files/figure-gfm/TET_IDH_Mutation_Methylation_CGIs-1.png
diff --git a/Figures/Phasing/Phasing_figures.html b/Figures/Phasing/Phasing_figures.html
diff --git a/Figures/Phasing/Phasing_figures.md b/Figures/Phasing/Phasing_figures.md
@@ -1,7 +1,7 @@
 Phasing figures
 ================
 Katherine Dixon
-2024-02-16
+2024-02-22
 
 This is an R markdown used to generate figures describing phasing.
 

diff --git a/Figures/Phasing/Phasing_figures_files/figure-gfm/output-1.png b/Figures/Phasing/Phasing_figures_files/figure-gfm/output-1.png
diff --git a/Figures/Phasing/Phasing_figures_files/figure-gfm/output-2.png b/Figures/Phasing/Phasing_figures_files/figure-gfm/output-2.png
diff --git a/Figures/Phasing/Phasing_figures_files/figure-gfm/output-3.png b/Figures/Phasing/Phasing_figures_files/figure-gfm/output-3.png
diff --git a/Figures/Phasing/phasing-stats.pdf b/Figures/Phasing/phasing-stats.pdf
diff --git a/Figures/Phasing/phasing-stats.png b/Figures/Phasing/phasing-stats.png
diff --git a/Figures/ecDNA/Extended_data_ecDNA_D.html b/Figures/ecDNA/Extended_data_ecDNA_D.html
diff --git a/Figures/ecDNA/Extended_data_ecDNA_D_files/figure-gfm/unnamed-chunk-3-1.png b/Figures/ecDNA/Extended_data_ecDNA_D_files/figure-gfm/unnamed-chunk-3-1.png