Add option to embed JS in HTML report

nanoplot/NanoPlot.py

@@ -18,6 +18,7 @@
 import nanoplot.utils as utils
 from nanoplot.version import __version__
 from nanoplotter.plot import Plot
+from plotly.offline import get_plotlyjs
 
 
 def main():
@@ -401,9 +402,12 @@ def make_report(plots, settings):
         report.run_info(settings) if settings["info_in_report"] else "",
         "</main></body></html>",
     ]
+    if settings["include_js"] is False:
+        # embed plotly.js once, at the start of the body, rather than in every plot
+        html_content.insert(1, f'<script type="text/javascript">{get_plotlyjs()}</script>')
     with open(settings["path"] + "NanoPlot-report.html", "w") as html_file:
         html_file.write(report.html_head + "\n".join(html_content))
 
 
 if __name__ == "__main__":
-    main()
+    main()

nanoplot/utils.py

@@ -110,6 +110,12 @@ def get_args():
     general.add_argument(
         "--info_in_report", help="Add NanoPlot run info in the report.", action="store_true"
     )
+    general.add_argument(
+        "--include-js",
+        choices=["cdn", "embedded"],
+        help="Either cdn or embedded. If cdn (the default) is specified, the javascript for plotly images will be sourced from the web. If embedded is specified, then the javascript will be directly put into the html file, resulting in a larger but self-contained HTML file.",
+        default="cdn",
+    )
     filtering = parser.add_argument_group(
         title="Options for filtering or transforming input prior to plotting"
     )
@@ -298,6 +304,8 @@ def get_args():
         sys.exit("ARGUMENT ERROR: --barcoded only works with data provided as --summary!")
     settings = vars(args)
     settings["path"] = os.path.join(args.outdir, args.prefix)
+    if settings["include_js"] == "embedded":
+        settings["include_js"] = False
     return settings, args
 
 

nanoplotter/nanoplotter_main.py

@@ -146,7 +146,7 @@ def scatter(
             )
 
         dot_plot.fig = fig
-        dot_plot.html = dot_plot.fig.to_html(full_html=False, include_plotlyjs="cdn")
+        dot_plot.html = dot_plot.fig.to_html(full_html=False, include_plotlyjs=settings["include_js"])
         dot_plot.save(settings)
         plots_made.append(dot_plot)
 
@@ -177,7 +177,7 @@ def scatter(
             )
 
         kde_plot.fig = fig
-        kde_plot.html = kde_plot.fig.to_html(full_html=False, include_plotlyjs="cdn")
+        kde_plot.html = kde_plot.fig.to_html(full_html=False, include_plotlyjs=settings["include_js"])
         kde_plot.save(settings)
         plots_made.append(kde_plot)
 
@@ -433,7 +433,7 @@ def length_plots(array, name, path, settings, title=None, n50=None, color="#4CB3
         )
 
         histogram.fig = fig
-        histogram.html = histogram.fig.to_html(full_html=False, include_plotlyjs="cdn")
+        histogram.html = histogram.fig.to_html(full_html=False, include_plotlyjs=settings["include_js"])
         histogram.save(settings)
 
         log_histogram = Plot(
@@ -484,7 +484,7 @@ def length_plots(array, name, path, settings, title=None, n50=None, color="#4CB3
             fig.update_annotations(font_size=8)
 
         log_histogram.fig = fig
-        log_histogram.html = log_histogram.fig.to_html(full_html=False, include_plotlyjs="cdn")
+        log_histogram.html = log_histogram.fig.to_html(full_html=False, include_plotlyjs=settings["include_js"])
         log_histogram.save(settings)
 
         plots.extend([histogram, log_histogram])
@@ -560,7 +560,7 @@ def yield_by_minimal_length_plot(array, name, path, settings, title=None, color=
     )
 
     yield_by_length.fig = fig
-    yield_by_length.html = yield_by_length.fig.to_html(full_html=False, include_plotlyjs="cdn")
+    yield_by_length.html = yield_by_length.fig.to_html(full_html=False, include_plotlyjs=settings["include_js"])
     yield_by_length.save(settings)
 
     return yield_by_length

nanoplotter/plot.py

@@ -51,9 +51,15 @@ def save(self, settings):
             return
 
         if self.html:
-            # Save the interactive HTML
+            # Save the interactive HTML. With embedded javascript self.html contains no
+            # javascript at all (it is added once to the combined report), so write a
+            # self-contained copy here to keep individual plot files usable on their own.
+            if settings.get("include_js", "cdn") is False and self.fig is not None:
+                standalone = self.fig.to_html(full_html=False, include_plotlyjs=True)
+            else:
+                standalone = self.html
             with open(self.path, "w") as html_out:
-                html_out.write(self.html)
+                html_out.write(standalone)
 
             # Also save static images unless suppressed
             if not settings.get("no_static", False):

nanoplotter/spatial_heatmap.py

@@ -91,6 +91,6 @@ def spatial_heatmap(array, path, colormap, settings, title=None):
 
     activity_map.fig = fig
     activity_map.html = activity_map.fig.to_html(
-        full_html=False, include_plotlyjs='cdn')
+        full_html=False, include_plotlyjs=settings["include_js"])
     activity_map.save(settings)
     return [activity_map]

nanoplotter/timeplots.py

@@ -136,7 +136,7 @@ def length_over_time(dfs, path, title, settings, log_length=False, color="#4CB39
 
     time_length.fig = fig
     time_length.html = time_length.fig.to_html(
-        full_html=False, include_plotlyjs='cdn')
+        full_html=False, include_plotlyjs=settings["include_js"])
     time_length.save(settings)
 
     return time_length
@@ -163,7 +163,7 @@ def quality_over_time(dfs, path, settings, title=None, color="#4CB391", downsamp
 
     time_qual.fig = fig
     time_qual.html = time_qual.fig.to_html(
-        full_html=False, include_plotlyjs='cdn')
+        full_html=False, include_plotlyjs=settings["include_js"])
     time_qual.save(settings)
 
     return time_qual
@@ -193,7 +193,7 @@ def sequencing_speed_over_time(dfs, path, title, settings, color="#4CB391", down
 
     time_duration.fig = fig
     time_duration.html = time_duration.fig.to_html(
-        full_html=False, include_plotlyjs='cdn')
+        full_html=False, include_plotlyjs=settings["include_js"])
     time_duration.save(settings)
 
     return time_duration
@@ -226,7 +226,7 @@ def plot_over_time(dfs, path, title, settings, color="#4CB391"):
 
     num_reads.fig = fig
     num_reads.html = num_reads.fig.to_html(
-        full_html=False, include_plotlyjs='cdn')
+        full_html=False, include_plotlyjs=settings["include_js"])
     num_reads.save(settings)
 
     plots = [num_reads]
@@ -249,7 +249,7 @@ def plot_over_time(dfs, path, title, settings, color="#4CB391"):
 
         pores_over_time.fig = fig
         pores_over_time.html = pores_over_time.fig.to_html(
-            full_html=False, include_plotlyjs='cdn')
+            full_html=False, include_plotlyjs=settings["include_js"])
         pores_over_time.save(settings)
 
         plots.append(pores_over_time)
@@ -274,7 +274,7 @@ def cumulative_yield(dfs, path, title, color, settings):
 
     cum_yield_gb.fig = fig
     cum_yield_gb.html = cum_yield_gb.fig.to_html(
-        full_html=False, include_plotlyjs='cdn')
+        full_html=False, include_plotlyjs=settings["include_js"])
     cum_yield_gb.save(settings)
 
     cum_yield_reads = Plot(path=path + "CumulativeYieldPlot_NumberOfReads.html",
@@ -294,7 +294,7 @@ def cumulative_yield(dfs, path, title, color, settings):
 
     cum_yield_reads.fig = fig
     cum_yield_reads.html = cum_yield_reads.fig.to_html(
-        full_html=False, include_plotlyjs='cdn')
+        full_html=False, include_plotlyjs=settings["include_js"])
     cum_yield_reads.save(settings)
 
     return [cum_yield_gb, cum_yield_reads]