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CaoTianze · Mar 8, 2024 · 0c3cfed · 0c3cfed
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diff --git a/.nojekyll b/.nojekyll
diff --git a/404.html b/404.html
@@ -73,7 +73,7 @@
       <div class="wy-nav-content">
         <div class="rst-content"><div role="navigation" aria-label="breadcrumbs navigation">
   <ul class="wy-breadcrumbs">
-    <li><a href="/." class="icon icon-home" aria-label="Docs"></a> &raquo;</li>
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diff --git a/accepted_input_formats.png b/accepted_input_formats.png
diff --git a/bar_accepted_input_formats.png b/bar_accepted_input_formats.png
diff --git a/bar_no_sequence_letter.png b/bar_no_sequence_letter.png
diff --git a/col_schemes/index.html b/col_schemes/index.html
@@ -104,7 +104,7 @@
       <div class="wy-nav-content">
         <div class="rst-content"><div role="navigation" aria-label="breadcrumbs navigation">
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       <li class="breadcrumb-item active">color schemes</li>
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diff --git a/combining_plots.png b/combining_plots.png
diff --git a/css/fonts/Roboto-Slab-Bold.woff b/css/fonts/Roboto-Slab-Bold.woff
diff --git a/css/fonts/Roboto-Slab-Bold.woff2 b/css/fonts/Roboto-Slab-Bold.woff2
diff --git a/css/fonts/Roboto-Slab-Regular.woff b/css/fonts/Roboto-Slab-Regular.woff
diff --git a/css/fonts/Roboto-Slab-Regular.woff2 b/css/fonts/Roboto-Slab-Regular.woff2
diff --git a/css/fonts/fontawesome-webfont.eot b/css/fonts/fontawesome-webfont.eot
diff --git a/css/fonts/fontawesome-webfont.svg b/css/fonts/fontawesome-webfont.svg
diff --git a/css/fonts/fontawesome-webfont.ttf b/css/fonts/fontawesome-webfont.ttf
diff --git a/css/fonts/fontawesome-webfont.woff b/css/fonts/fontawesome-webfont.woff
diff --git a/css/fonts/fontawesome-webfont.woff2 b/css/fonts/fontawesome-webfont.woff2
diff --git a/css/fonts/lato-bold-italic.woff b/css/fonts/lato-bold-italic.woff
diff --git a/css/fonts/lato-bold-italic.woff2 b/css/fonts/lato-bold-italic.woff2
diff --git a/css/fonts/lato-bold.woff b/css/fonts/lato-bold.woff
diff --git a/css/fonts/lato-bold.woff2 b/css/fonts/lato-bold.woff2
diff --git a/css/fonts/lato-normal-italic.woff b/css/fonts/lato-normal-italic.woff
diff --git a/css/fonts/lato-normal-italic.woff2 b/css/fonts/lato-normal-italic.woff2
diff --git a/css/fonts/lato-normal.woff b/css/fonts/lato-normal.woff
diff --git a/css/fonts/lato-normal.woff2 b/css/fonts/lato-normal.woff2
diff --git a/css/theme.css b/css/theme.css
diff --git a/css/theme_extra.css b/css/theme_extra.css
diff --git a/custom_alphabet.png b/custom_alphabet.png
diff --git a/custom_alphabet_2.png b/custom_alphabet_2.png
diff --git a/custom_color_schemes1.png b/custom_color_schemes1.png
diff --git a/custom_color_schemes2.png b/custom_color_schemes2.png
diff --git a/custom_height_logos.png b/custom_height_logos.png
diff --git a/font/index.html b/font/index.html
@@ -90,7 +90,7 @@
       <div class="wy-nav-content">
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   <ul class="wy-breadcrumbs">
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       <li class="breadcrumb-item active">font</li>
     <li class="wy-breadcrumbs-aside">
     </li>

diff --git a/fonts.png b/fonts.png
diff --git a/gallery.png b/gallery.png
diff --git a/geom_alignedSeq/index.html b/geom_alignedSeq/index.html
@@ -88,7 +88,7 @@
       <div class="wy-nav-content">
         <div class="rst-content"><div role="navigation" aria-label="breadcrumbs navigation">
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       <li class="breadcrumb-item active">geom_alignedSeq</li>
     <li class="wy-breadcrumbs-aside">
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@@ -117,7 +117,7 @@ <h2 id="init-param"><em>Init param</em></h2>
              border_col: str = 'grey',
              scheme_applied: str = 'BACKGROUND',
              no_scheme_col: str = '#000000',
-             col_scheme: DataFrame | str = 'AUTO',
+             col_scheme: Dict | str = 'AUTO',
              low_col: str = 'black',
              high_col: str = 'yellow',
              na_col: str = '#333333',

diff --git a/geom_logo/index.html b/geom_logo/index.html
@@ -88,7 +88,7 @@
       <div class="wy-nav-content">
         <div class="rst-content"><div role="navigation" aria-label="breadcrumbs navigation">
   <ul class="wy-breadcrumbs">
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       <li class="breadcrumb-item active">geom_logo</li>
     <li class="wy-breadcrumbs-aside">
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@@ -115,7 +115,7 @@ <h2 id="init-param"><em>Init param</em></h2>
              font: str = 'roboto_medium',
              stack_width: float = 0.95,
              rev_stack_order: bool = False,
-             col_scheme: DataFrame | str = 'AUTO',
+             col_scheme: Dict | str = 'AUTO',
              low_col: str = 'black',
              high_col: str = 'yellow',
              na_col: str = '#333333',

diff --git a/geom_seqBar/index.html b/geom_seqBar/index.html
@@ -88,7 +88,7 @@
       <div class="wy-nav-content">
         <div class="rst-content"><div role="navigation" aria-label="breadcrumbs navigation">
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+    <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li>
       <li class="breadcrumb-item active">geom_seqBar</li>
     <li class="wy-breadcrumbs-aside">
     </li>
@@ -113,7 +113,7 @@ <h2 id="init-param"><em>Init param</em></h2>
              namespace: list[str] | None = None,
              font: str = 'roboto_medium',
              stack_width: float = 0.75,
-             bar_col_scheme: DataFrame | str = 'AUTO',
+             bar_col_scheme: Dict | str = 'AUTO',
              font_col: str = '#808080',
              low_col: str = 'black',
              high_col: str = 'yellow',

diff --git a/img/favicon.ico b/img/favicon.ico
diff --git a/index.html b/index.html
@@ -160,7 +160,7 @@
       <div class="wy-nav-content">
         <div class="rst-content"><div role="navigation" aria-label="breadcrumbs navigation">
   <ul class="wy-breadcrumbs">
-    <li><a href="." class="icon icon-home" aria-label="Docs"></a> &raquo;</li>
+    <li><a href="." class="icon icon-home" aria-label="Docs"></a></li>
       <li class="breadcrumb-item active">Getting Started</li>
     <li class="wy-breadcrumbs-aside">
     </li>
@@ -323,20 +323,12 @@ <h2 id="multiple-grouped-sequences">Multiple grouped sequences</h2>
 <h2 id="fonts">Fonts</h2>
 <p>You can adjust the font of letters by setting the font parameter. To list all the available color schemes use the font.list_fonts function. Take geom_logo for example.</p>
 <pre><code class="language-python">from plotnine import ggtitle
-import patchworklib as pw
 from plotnineseqsuite.font import list_fonts
-
 fonts = list_fonts()
-for i in range(0,12,3):
-    g1 = pw.load_ggplot(ggplot() + geom_logo(data=seqs_dna['MA0001.1'], font=fonts[i]) + theme_seq()+ggtitle(fonts[i]))
-    g2 = pw.load_ggplot(ggplot() + geom_logo(data=seqs_dna['MA0001.1'], font=fonts[i+1]) + theme_seq() + ggtitle(fonts[i+1]))
-    g3 = pw.load_ggplot(ggplot() + geom_logo(data=seqs_dna['MA0001.1'], font=fonts[i+2]) + theme_seq() + ggtitle(fonts[i+2]))
-    if i == 0:
-        allgg = g1|g2|g3
-    else:
-        temp = g1|g2|g3
-        allgg = temp/allgg
-allgg.savefig()
+for i in range(0, 15, 3):
+    print(ggplot() + geom_logo(data=seqs_dna['MA0001.1'], font=fonts[i]) + theme_seq() + ggtitle(fonts[i]))
+    print(ggplot() + geom_logo(data=seqs_dna['MA0001.1'], font=fonts[i + 1]) + theme_seq() + ggtitle(fonts[i + 1]))
+    print(ggplot() + geom_logo(data=seqs_dna['MA0001.1'], font=fonts[i + 2]) + theme_seq() + ggtitle(fonts[i + 2]))
 </code></pre>
 <p><img alt="" src="fonts.png" /></p>
 <h2 id="advanced-plotnineseqsuite">Advanced plotnineSeqSuite</h2>
@@ -418,6 +410,6 @@ <h3 id="used-concurrently-with-other-functions-of-plotnine">Used concurrently wi
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diff --git a/js/theme_extra.js b/js/theme_extra.js
diff --git a/modify_the_starting_position.png b/modify_the_starting_position.png
diff --git a/multiple_grouped_sequences.png b/multiple_grouped_sequences.png
diff --git a/no_background_color.png b/no_background_color.png
diff --git a/no_sequence_letter.png b/no_sequence_letter.png
diff --git a/plot_a_sequence_bar.png b/plot_a_sequence_bar.png
diff --git a/plot_a_sequence_logo.png b/plot_a_sequence_logo.png
diff --git a/plot_an_aligned_sequences.png b/plot_an_aligned_sequences.png
diff --git a/plotting_methods_1.png b/plotting_methods_1.png
diff --git a/plotting_methods_2.png b/plotting_methods_2.png
diff --git a/preset_alphabets.png b/preset_alphabets.png
diff --git a/preset_color_schemes.png b/preset_color_schemes.png
diff --git a/search.html b/search.html
@@ -73,7 +73,7 @@
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diff --git a/search/lunr.js b/search/lunr.js
diff --git a/search/main.js b/search/main.js
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diff --git a/sitemap.xml b/sitemap.xml
diff --git a/sitemap.xml.gz b/sitemap.xml.gz
diff --git a/switch_color_schme.png b/switch_color_schme.png
diff --git a/tagging_sequences.png b/tagging_sequences.png
diff --git a/test_annotate1.png b/test_annotate1.png
diff --git a/test_annotate2.png b/test_annotate2.png
diff --git a/theme/index.html b/theme/index.html
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