sphinx problem fix

seqyuan · Jul 3, 2024 · 5c5d23d · 5c5d23d
1 parent e972920
commit 5c5d23d
Show file tree

Hide file tree

Showing 29 changed files with 636 additions and 512 deletions.
diff --git a/docs/analysis_guide/TAD_calling.ipynb b/docs/analysis_guide/TAD_calling.ipynb
@@ -35,9 +35,9 @@
    ],
    "source": [
     "resolution = 10000\n",
-    "coolfile=f'./HFF_MicroC.mcool::resolutions/{resolution}'\n",
-    "clr=cooler.Cooler(coolfile)\n",
-    "windows = [3*resolution, 5*resolution, 10*resolution, 25*resolution]\n",
+    "coolfile = f\"./HFF_MicroC.mcool::resolutions/{resolution}\"\n",
+    "clr = cooler.Cooler(coolfile)\n",
+    "windows = [3 * resolution, 5 * resolution, 10 * resolution, 25 * resolution]\n",
     "insulation_table = insulation(clr, windows, verbose=True)"
    ]
   },
@@ -296,11 +296,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "df = insulation_table[['chrom', 'start', 'end', \n",
-    "                       'log2_insulation_score_30000', \n",
-    "                       'log2_insulation_score_50000', \n",
-    "                       'log2_insulation_score_100000', \n",
-    "                       'log2_insulation_score_250000']]"
+    "df = insulation_table[\n",
+    "    [\n",
+    "        \"chrom\",\n",
+    "        \"start\",\n",
+    "        \"end\",\n",
+    "        \"log2_insulation_score_30000\",\n",
+    "        \"log2_insulation_score_50000\",\n",
+    "        \"log2_insulation_score_100000\",\n",
+    "        \"log2_insulation_score_250000\",\n",
+    "    ]\n",
+    "]"
    ]
   },
   {
@@ -355,18 +361,21 @@
     "ten.add(pos=\"bottom\", height=1.5, hspace=0.05)\n",
     "ten.add(pos=\"bottom\", height=1, hspace=0.07)\n",
     "\n",
-    "tc.pl.mapC(\n",
-    "    ax=ten.axs(0),\n",
-    "    mat=HFF,\n",
-    "    label=\"HFF\",\n",
-    "    map_type=\"rec\",\n",
-    "    height=150\n",
-    ")\n",
+    "tc.pl.mapC(ax=ten.axs(0), mat=HFF, label=\"HFF\", map_type=\"rec\", height=150)\n",
     "\n",
-    "tc.pl.bdgmat_track(ax=ten.axs(1), bed=df, regions=regions, style='line', label='insulation score')\n",
-    "tc.pl.scale_track(ax=ten.axs(1), region=regions, scale_adjust=\"Mb\", tick_pos=\"bottom\", ratio2ax=1, space=0)\n",
+    "tc.pl.bdgmat_track(\n",
+    "    ax=ten.axs(1), bed=df, regions=regions, style=\"line\", label=\"insulation score\"\n",
+    ")\n",
+    "tc.pl.scale_track(\n",
+    "    ax=ten.axs(1),\n",
+    "    region=regions,\n",
+    "    scale_adjust=\"Mb\",\n",
+    "    tick_pos=\"bottom\",\n",
+    "    ratio2ax=1,\n",
+    "    space=0,\n",
+    ")\n",
     "\n",
-    "#tc.savefig('outfile.pdf')"
+    "# tc.savefig('outfile.pdf')"
    ]
   }
  ],

diff --git a/docs/analysis_guide/compartment_calling.ipynb b/docs/analysis_guide/compartment_calling.ipynb
@@ -27,12 +27,12 @@
    ],
    "source": [
     "import cooler\n",
-    "import pandas as pd\n",
     "import cooltools\n",
+    "import pandas as pd\n",
     "\n",
     "resolution = 100000\n",
-    "coolfile=f'/Users/yuanzan/Downloads/HFF_MicroC.mcool::resolutions/{resolution}'\n",
-    "clr=cooler.Cooler(coolfile)"
+    "coolfile = f\"/Users/yuanzan/Downloads/HFF_MicroC.mcool::resolutions/{resolution}\"\n",
+    "clr = cooler.Cooler(coolfile)"
    ]
   },
   {
@@ -197,15 +197,16 @@
    "source": [
     "## fasta sequence is required for calculating binned profile of GC conent\n",
     "import bioframe\n",
+    "\n",
     "bins = clr.bins()[:]\n",
     "### Unified chromosome Naming\n",
-    "bins['chrom'] = bins['chrom'].str.lstrip('chr')\n",
+    "bins[\"chrom\"] = bins[\"chrom\"].str.lstrip(\"chr\")\n",
     "\n",
-    "hg38_genome = bioframe.load_fasta('/Users/yuanzan/Documents/ref/GRCh38.105.fa');\n",
+    "hg38_genome = bioframe.load_fasta(\"/Users/yuanzan/Documents/ref/GRCh38.105.fa\")\n",
     "## note the next command may require installing pysam\n",
-    "gc_cov = bioframe.frac_gc(bins[['chrom', 'start', 'end']], hg38_genome)\n",
-    "gc_cov['chrom'] = 'chr' + gc_cov['chrom'].astype(str)\n",
-    "gc_cov.to_csv('hg38_gc_cov_100kb.tsv',index=False,sep='\\t')\n",
+    "gc_cov = bioframe.frac_gc(bins[[\"chrom\", \"start\", \"end\"]], hg38_genome)\n",
+    "gc_cov[\"chrom\"] = \"chr\" + gc_cov[\"chrom\"].astype(str)\n",
+    "gc_cov.to_csv(\"hg38_gc_cov_100kb.tsv\", index=False, sep=\"\\t\")\n",
     "display(gc_cov)"
    ]
   },
@@ -271,11 +272,14 @@
     }
    ],
    "source": [
-    "view_df = pd.DataFrame({'chrom': clr.chromnames,\n",
-    "                        'start': 0,\n",
-    "                        'end': clr.chromsizes.values,\n",
-    "                        'name': clr.chromnames}\n",
-    "                      )\n",
+    "view_df = pd.DataFrame(\n",
+    "    {\n",
+    "        \"chrom\": clr.chromnames,\n",
+    "        \"start\": 0,\n",
+    "        \"end\": clr.chromsizes.values,\n",
+    "        \"name\": clr.chromnames,\n",
+    "    }\n",
+    ")\n",
     "display(view_df)"
    ]
   },
@@ -360,14 +364,14 @@
    "source": [
     "# obtain first 3 eigenvectors\n",
     "cis_eigs = cooltools.eigs_cis(\n",
-    "                        clr,\n",
-    "                        gc_cov,\n",
-    "                        view_df=view_df,\n",
-    "                        n_eigs=3,\n",
-    "                        )\n",
+    "    clr,\n",
+    "    gc_cov,\n",
+    "    view_df=view_df,\n",
+    "    n_eigs=3,\n",
+    ")\n",
     "# cis_eigs[0] returns eigenvalues, here we focus on eigenvectors\n",
     "display(cis_eigs[0])\n",
-    "eigenvector_track = cis_eigs[1][['chrom','start','end','E1']]"
+    "eigenvector_track = cis_eigs[1][[\"chrom\", \"start\", \"end\", \"E1\"]]"
    ]
   },
   {
@@ -376,7 +380,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "eigenvector_track.to_csv('eigenvector_track.bdg', sep=\"\\t\", index=False, header=False)"
+    "eigenvector_track.to_csv(\"eigenvector_track.bdg\", sep=\"\\t\", index=False, header=False)"
    ]
   },
   {
@@ -432,34 +436,26 @@
     "ten.add(pos=\"bottom\", height=0.4, hspace=0.09)\n",
     "\n",
     "\n",
-    "tc.pl.mapC(\n",
-    "    ax=ten.axs(0),\n",
-    "    mat=HFF,\n",
-    "    label=\"HFF\",\n",
-    "    map_type=\"tri\",\n",
-    "    ax_on=False\n",
-    ")\n",
+    "tc.pl.mapC(ax=ten.axs(0), mat=HFF, label=\"HFF\", map_type=\"tri\", ax_on=False)\n",
     "\n",
     "tc.pl.bed_track(\n",
-    "    ax=ten.axs(1),\n",
-    "    bed=eigenvector_track,\n",
-    "    regions=regions,\n",
-    "    style=\"bar\",\n",
-    "    label=\"Eign1\"\n",
+    "    ax=ten.axs(1), bed=eigenvector_track, regions=regions, style=\"bar\", label=\"Eign1\"\n",
     ")\n",
     "\n",
     "\n",
     "tc.pl.bed_track(\n",
-    "    ax=ten.axs(2),\n",
-    "    bed=gc_cov,\n",
-    "    regions=regions,\n",
-    "    style=\"rec\",\n",
-    "    label=\"GC\",\n",
-    "    cmap='Blues'\n",
+    "    ax=ten.axs(2), bed=gc_cov, regions=regions, style=\"rec\", label=\"GC\", cmap=\"Blues\"\n",
     ")\n",
     "\n",
     "\n",
-    "tc.pl.scale_track(ax=ten.axs(2), region=regions, scale_adjust=\"Mb\", tick_pos=\"bottom\", ratio2ax=2, space=0)\n"
+    "tc.pl.scale_track(\n",
+    "    ax=ten.axs(2),\n",
+    "    region=regions,\n",
+    "    scale_adjust=\"Mb\",\n",
+    "    tick_pos=\"bottom\",\n",
+    "    ratio2ax=2,\n",
+    "    space=0,\n",
+    ")"
    ]
   }
  ],

diff --git a/docs/cli/cli-4C.ipynb b/docs/cli/cli-4C.ipynb
@@ -94,8 +94,9 @@
    "outputs": [],
    "source": [
     "import pandas as pd\n",
-    "import trackc as tc\n",
-    "import pyBigWig"
+    "import pyBigWig\n",
+    "\n",
+    "import trackc as tc"
    ]
   },
   {
@@ -109,7 +110,9 @@
     "regions = [\"chr8:127000000-129200000\", \"chr14:96500000-99300000\"]\n",
     "MYC_TSS = \"chr8:127735434-127735435\"\n",
     "\n",
-    "AML_1360_H3K27ac = pyBigWig.open(\"../../../trackc_data/tutorials/4C/GSM4604189_H3K27ac.bw\")"
+    "AML_1360_H3K27ac = pyBigWig.open(\n",
+    "    \"../../../trackc_data/tutorials/4C/GSM4604189_H3K27ac.bw\"\n",
+    ")"
    ]
   },
   {
@@ -210,8 +213,7 @@
    ],
    "source": [
     "gene_bed12 = pd.read_table(\n",
-    "    \"../../../trackc_data/tutorials/4C/Homo_sapiens.GRCh38.105.chr.bed13\", \n",
-    "    header=None\n",
+    "    \"../../../trackc_data/tutorials/4C/Homo_sapiens.GRCh38.105.chr.bed13\", header=None\n",
     ")\n",
     "gene_bed12 = gene_bed12[gene_bed12[12] == \"protein_coding\"]\n",
     "gene_bed12[0] = \"chr\" + gene_bed12[0]\n",
@@ -258,7 +260,7 @@
     "fruitpunch3 = LinearSegmentedColormap.from_list(\n",
     "    \"fruitpunch3\", [(0, \"white\"), (0.02, \"w\"), (0.25, \"r\"), (1, \"#0E3858\")], N=100\n",
     ")\n",
-    "#CF3F35\n",
+    "# CF3F35\n",
     "\n",
     "aml = tc.tl.extractContactRegions(clr=AML_1360, row_regions=regions)\n",
     "tc.pl.mapC(\n",

diff --git a/docs/cli/heatmap-1.ipynb b/docs/cli/heatmap-1.ipynb
@@ -50,10 +50,10 @@
    "outputs": [],
    "source": [
     "import cooler\n",
-    "import trackc as tc\n",
-    "\n",
     "from matplotlib.colors import LinearSegmentedColormap, ListedColormap\n",
     "\n",
+    "import trackc as tc\n",
+    "\n",
     "fruitpunch3 = LinearSegmentedColormap.from_list(\n",
     "    \"fruitpunch3\", [(0, \"white\"), (0.2, \"r\"), (1, \"#0E3858\")], N=100\n",
     ")"
@@ -102,7 +102,9 @@
     }
    ],
    "source": [
-    "clr = cooler.Cooler(\"/Users/yuanzan/Documents/RD/GSM4417639_SK-N-DZ_C6BC81F2_b38d5.mcool::/resolutions/5120000\")\n",
+    "clr = cooler.Cooler(\n",
+    "    \"/Users/yuanzan/Documents/RD/GSM4417639_SK-N-DZ_C6BC81F2_b38d5.mcool::/resolutions/5120000\"\n",
+    ")\n",
     "clr.chromsizes"
    ]
   },
@@ -153,7 +155,7 @@
     "    tick_fontsize=10,\n",
     ")\n",
     "\n",
-    "#tc.savefig('inter-chrom.pdf')"
+    "# tc.savefig('inter-chrom.pdf')"
    ]
   }
  ],

diff --git a/docs/cli/heatmap-2.ipynb b/docs/cli/heatmap-2.ipynb
@@ -79,6 +79,7 @@
    ],
    "source": [
     "import cooler\n",
+    "\n",
     "import trackc as tc\n",
     "\n",
     "ten = tc.tenon(figsize=(4, 1))\n",
@@ -87,21 +88,18 @@
     "\n",
     "clr = \"./GSM4417639_SK-N-DZ_C6BC81F2_b38d5.mcool::/resolutions/5120000\"\n",
     "\n",
-    "mat = tc.tl.extractContactRegions(\n",
-    "    clr=clr,\n",
-    "    row_regions=['chr6'],\n",
-    "    col_regions=['chr8']\n",
-    ")\n",
+    "mat = tc.tl.extractContactRegions(clr=clr, row_regions=[\"chr6\"], col_regions=[\"chr8\"])\n",
     "\n",
-    "tc.pl.mapC(ax=ten.axs(0), \n",
-    "           mat=mat.cmat, \n",
-    "           map_type=\"squ\", \n",
-    "           cmap='Blues', \n",
-    "           symmetric=True,\n",
-    "           maxrange= 1000,\n",
-    "           aspect=1,\n",
-    "          )\n",
-    "#tc.savefig('chr6_chr8_trans.pdf')"
+    "tc.pl.mapC(\n",
+    "    ax=ten.axs(0),\n",
+    "    mat=mat.cmat,\n",
+    "    map_type=\"squ\",\n",
+    "    cmap=\"Blues\",\n",
+    "    symmetric=True,\n",
+    "    maxrange=1000,\n",
+    "    aspect=1,\n",
+    ")\n",
+    "# tc.savefig('chr6_chr8_trans.pdf')"
    ]
   }
  ],

diff --git a/docs/cli/heatmap-3.ipynb b/docs/cli/heatmap-3.ipynb
@@ -94,30 +94,23 @@
     "ten.add(pos=\"bottom\", height=2)\n",
     "ten.add(pos=\"bottom\", height=0.6)\n",
     "\n",
-    "regions = ['chr6:0-25600000', 'chr8:122880000-143360000']\n",
-    "clr = '/Users/yuanzan/Documents/RD/GSM4417639_SK-N-DZ_C6BC81F2_b38d5.mcool::/resolutions/5120000'\n",
+    "regions = [\"chr6:0-25600000\", \"chr8:122880000-143360000\"]\n",
+    "clr = \"/Users/yuanzan/Documents/RD/GSM4417639_SK-N-DZ_C6BC81F2_b38d5.mcool::/resolutions/5120000\"\n",
     "\n",
-    "mat = tc.tl.extractContactRegions(\n",
-    "    clr=clr,\n",
-    "    row_regions=regions\n",
-    ")\n",
-    "\n",
-    "tc.pl.mapC(ax=ten.axs(0), \n",
-    "           mat=mat.cmat,\n",
-    "           map_type=\"tri\",\n",
-    "           ax_on=False,\n",
-    "           cmap='PuBu',\n",
-    "           maxrange=10000,\n",
-    "          )\n",
+    "mat = tc.tl.extractContactRegions(clr=clr, row_regions=regions)\n",
     "\n",
-    "tc.pl.multi_scale_track(\n",
-    "    ax=ten.axs(1),\n",
-    "    regions=regions,\n",
-    "    scale_adjust= 'Mb',\n",
-    "    intervals=2\n",
+    "tc.pl.mapC(\n",
+    "    ax=ten.axs(0),\n",
+    "    mat=mat.cmat,\n",
+    "    map_type=\"tri\",\n",
+    "    ax_on=False,\n",
+    "    cmap=\"PuBu\",\n",
+    "    maxrange=10000,\n",
     ")\n",
     "\n",
-    "#tc.savefig('trans_interactions.pdf')"
+    "tc.pl.multi_scale_track(ax=ten.axs(1), regions=regions, scale_adjust=\"Mb\", intervals=2)\n",
+    "\n",
+    "# tc.savefig('trans_interactions.pdf')"
    ]
   }
  ],