From fed2b8fecbdde6f3bd64ef9b23513e6c6edab4e7 Mon Sep 17 00:00:00 2001
From: hiruna72 <hiruna72@gmail.com>
Date: Mon, 12 Feb 2024 23:41:21 +1100
Subject: [PATCH] introduce base index for x-axis when using fixed_width
 (molecule_scale)

---
 src/plot.py        | 13 ++++++++++++-
 src/plot_pileup.py | 13 ++++++++++++-
 src/plot_utils.py  |  5 ++++-
 3 files changed, 28 insertions(+), 3 deletions(-)

diff --git a/src/plot.py b/src/plot.py
index abaee38..d769463 100644
--- a/src/plot.py
+++ b/src/plot.py
@@ -5,7 +5,7 @@
 """
 import numpy as np
 from bokeh.plotting import figure, show, output_file, save
-from bokeh.models import BoxAnnotation, HoverTool, WheelZoomTool, ColumnDataSource, Label, LabelSet, Segment, Toggle, Range1d, FreehandDrawTool, CustomJS
+from bokeh.models import BoxAnnotation, HoverTool, WheelZoomTool, ColumnDataSource, Label, LabelSet, Segment, Toggle, Range1d, FreehandDrawTool, CustomJS, FixedTicker
 from bokeh.layouts import row
 from bokeh.colors import RGB
 from bokeh.io import export_svg, export_svgs
@@ -398,6 +398,17 @@ def plot_function_fixed_width(p, read_id, signal_tuple, sig_algn_data, fasta_seq
     p.add_layout(move_annotation_labels)
 
     p.line('x', 'y', name="sig_plot_line", line_width=2, source=source)
+
+    xticks = [i*draw_data["fixed_base_width"] for i in range(0, base_index+1, 5)]
+    mxticks = [i*draw_data["fixed_base_width"] for i in range(0, base_index, 1)]
+    xticks_dic = {}
+    j = 0
+    for i in xticks:
+        xticks_dic[i] = str(j)
+        j += 5
+    p.xaxis.major_label_overrides = xticks_dic
+    p.xaxis.ticker = FixedTicker(ticks=xticks, minor_ticks=mxticks)
+
     # add a circle renderer with a size, color, and alpha
     sample_labels = p.circle(fixed_width_x[:x_coordinate], y[:x_coordinate], radius=draw_data["point_size"], color=sample_label_colors, alpha=0.5, visible=draw_data['no_samples'])
     toggle_samples = Toggle(label="samples", button_type="danger", active=True, height=30, width=60)
diff --git a/src/plot_pileup.py b/src/plot_pileup.py
index b70a064..4602294 100644
--- a/src/plot_pileup.py
+++ b/src/plot_pileup.py
@@ -5,7 +5,7 @@
 """
 import numpy as np
 from bokeh.plotting import figure, show, output_file, save
-from bokeh.models import HoverTool, WheelZoomTool, ColumnDataSource, Label, LabelSet, Segment, Arrow, NormalHead, FreehandDrawTool, Range1d, CustomJS
+from bokeh.models import HoverTool, WheelZoomTool, ColumnDataSource, Label, LabelSet, Segment, Arrow, NormalHead, FreehandDrawTool, Range1d, CustomJS, FixedTicker
 from bokeh.layouts import column
 from bokeh.colors import RGB
 from bokeh.io import export_svg
@@ -217,6 +217,17 @@ def plot_function_fixed_width_pileup(read_id, signal_tuple, sig_algn_data, fasta
         if num_plots == 0:
             sample_label_colors_insert[0] = 'purple'
             sample_label_colors_match[0] = 'red'
+
+            xticks = [i*draw_data["fixed_base_width"] for i in range(0, base_index+1, 5)]
+            mxticks = [i*draw_data["fixed_base_width"] for i in range(0, base_index, 1)]
+            xticks_dic = {}
+            j = 0
+            for i in xticks:
+                xticks_dic[i] = str(j)
+                j += 5
+            p.xaxis.major_label_overrides = xticks_dic
+            p.xaxis.ticker = FixedTicker(ticks=xticks, minor_ticks=mxticks)
+
         sample_labels_match = p.circle(fixed_width_x[:x_coordinate], y[:x_coordinate]+y_shift, radius=draw_data["point_size"], color=sample_label_colors_match, alpha=0.5, legend_label='match', visible=False)
         sample_labels_insert = p.circle(fixed_width_x[:x_coordinate], y[:x_coordinate]+y_shift, radius=draw_data["point_size"], color=sample_label_colors_insert, alpha=0.5, legend_label='insertion', visible=False)
 
diff --git a/src/plot_utils.py b/src/plot_utils.py
index a5e6bab..d2a0a9b 100644
--- a/src/plot_utils.py
+++ b/src/plot_utils.py
@@ -85,10 +85,13 @@ def create_figure(args, plot_mode):
     p_defualt = None
     if plot_mode == 0:
         y_axis_label = "signal value (raw)"
+        x_axis_label = "signal value (raw)"
+        if args.fixed_width:
+            x_axis_label = "base index"
         if args.no_pa:
             y_axis_label = "signal value (pA)"
         tools_to_show = 'hover,box_zoom,pan,reset,save,wheel_zoom,zoom_in,zoom_out'
-        p_default = figure(x_axis_label='signal index',
+        p_default = figure(x_axis_label=x_axis_label,
                    y_axis_label=y_axis_label,
                    sizing_mode="stretch_width",
                    height=PLOT_HEIGHT,