Updated docs.

Author: kcleal

docs/docs/API.md

@@ -7,3 +7,4 @@ permalink: /api
 ---
 
 # API Reference
+---

docs/docs/Install.md

@@ -6,6 +6,7 @@ nav_order: 2
 ---
 
 # Installation
+---
 
 ### From PyPI
 

docs/docs/api/gw-init.md

@@ -6,7 +6,8 @@ parent: API Reference
 nav_order: 1
 ---
 
-## Gw Class
+# Gw class
+---
 
 `Gw(reference, **kwargs)`
 

docs/docs/api/gw-interactive.md

@@ -9,6 +9,7 @@ nav_order: 7
 
 # Interactive Controls
 {: .no_toc .text-delta }
+---
 
 ## Table of contents
 {: .no_toc .text-delta }
@@ -18,7 +19,7 @@ nav_order: 7
 
 ---
 
-### apply_command
+## apply_command
 `apply_command(command)`
 
 Apply a GW command string.
@@ -28,7 +29,7 @@ Apply a GW command string.
 
 ---
 
-### key_press
+## key_press
 `key_press(key, scancode, action, mods)`
 
 Process a key press event.
@@ -41,7 +42,7 @@ Process a key press event.
 
 ---
 
-### mouse_event
+## mouse_event
 `mouse_event(x_pos, y_pos, button, action)`
 
 Process a mouse event.

docs/docs/api/gw-loading-data.md

@@ -5,8 +5,9 @@ parent: API Reference
 nav_order: 2
 ---
 
-## Loading Data
+# Loading Data
 {: .no_toc .text-delta }
+---
 
 ## Table of contents
 {: .no_toc .text-delta }
@@ -16,7 +17,7 @@ nav_order: 2
 
 ---
 
-### add_bam
+## add_bam
 `add_bam(path)`
 
 Add a BAM file to the visualisation.
@@ -33,7 +34,7 @@ gw.add_bam("sample.bam")
 ```
 ---
 
-### remove_bam
+## remove_bam
 `remove_bam(index)`
 
 Remove a BAM file from the visualisation.
@@ -46,7 +47,7 @@ Remove a BAM file from the visualisation.
 
 ---
 
-### add_track
+## add_track
 `add_track(path, vcf_as_track=True, bed_as_track=True)`
 
 
@@ -70,7 +71,7 @@ gw.add_track("features.bed")
 ```
 ---
 
-### remove_track
+## remove_track
 `remove_track(index)`
 
 Remove a data track from the visualisation.

docs/docs/api/gw-managing-regions.md

@@ -5,8 +5,9 @@ parent: API Reference
 nav_order: 3
 ---
 
-## Managing Regions
+# Managing Regions
 {: .no_toc .text-delta }
+---
 
 ## Table of contents
 {: .no_toc .text-delta }
@@ -16,7 +17,7 @@ nav_order: 3
 
 ---
 
-### add_region
+## add_region
 `add_region(chrom, start, end, marker_start=-1, marker_end=-1)`
 
 Add a genomic region for visualisation. Setting the markers will result in a small triangle being drawn at
@@ -40,7 +41,7 @@ gw.add_region("chr1", 1000000, 1100000, 1050000, 1060000)
 
 ---
 
-### remove_region
+## remove_region
 `remove_region(index)`
 
 Remove a genomic region from the visualisation.
@@ -53,7 +54,7 @@ Remove a genomic region from the visualisation.
 
 ---
 
-### view_region
+## view_region
 `view_region(chrom, start, end)`
 
 Clear existing regions and view a specific genomic region.
@@ -74,7 +75,7 @@ gw.view_region("chr1", 1000000, 1100000)
 
 ---
 
-### set_active_region_index
+## set_active_region_index
 `set_active_region_index(index)`
 
 Set the currently active region for dynamic visualisation.
@@ -87,21 +88,21 @@ Set the currently active region for dynamic visualisation.
 
 ---
 
-### clear
+## clear
 `clear()`
 
 Remove all data.
 
 ---
 
-### clear_regions
+## clear_regions
 `clear_regions()`
 
 Remove all defined genomic regions.
 
 ---
 
-### clear_alignments
+## clear_alignments
 `clear_alignments()`
 
 Remove all loaded alignment data.

docs/docs/api/gw-palette.md

@@ -5,9 +5,9 @@ parent: API Reference
 nav_order: 8
 ---
 
-
 # GwPalette Class
 {: .no_toc .text-delta }
+---
 
 ## Table of contents
 {: .no_toc .text-delta }

docs/docs/api/gw-saving-images.md

@@ -5,8 +5,9 @@ parent: API Reference
 nav_order: 5
 ---
 
-## Saving images
+# Saving images
 {: .no_toc .text-delta }
+---
 
 ## Table of contents
 {: .no_toc .text-delta }
@@ -16,7 +17,7 @@ nav_order: 5
 
 ---
 
-### save_png
+## save_png
 `save_png(path)`
 
 Save the current raster image to a PNG file.
@@ -34,7 +35,7 @@ gw.save_png("visualisation.png")
 
 ---
 
-### save_pdf
+## save_pdf
 `save_pdf(path)`
 
 Save the plot to a PDF file.
@@ -52,7 +53,7 @@ gw.save_pdf("visualization.pdf")
 
 ---
 
-### save_svg
+## save_svg
 `save_svg(path)`
 
 Save the plot to a SVG file.
@@ -70,7 +71,7 @@ gw.save_svg("visualization.svg")
 
 ---
 
-### encode_as_png
+## encode_as_png
 `encode_as_png(compression_level=6)`
 
 Encode the current canvas as PNG and return the binary data.
@@ -81,7 +82,7 @@ Encode the current canvas as PNG and return the binary data.
 **Returns:**
 - `bytes`: PNG encoded image data
 
-### encode_as_jpeg
+## encode_as_jpeg
 `encode_as_jpeg(quality=80)`
 
 Encode the current canvas as JPEG and return the binary data.
@@ -94,7 +95,7 @@ Encode the current canvas as JPEG and return the binary data.
 
 ---
 
-### array
+## array
 `array()`
 
 Convert the raster image to a numpy array.

docs/docs/api/gw-settings.md

@@ -5,8 +5,9 @@ parent: API Reference
 nav_order: 6
 ---
 
-### Display Settings
+# Display Settings
 {: .no_toc .text-delta }
+---
 
 ## Table of contents
 {: .no_toc .text-delta }
@@ -29,7 +30,7 @@ Set the canvas width and recreate the raster surface.
 
 ---
 
-### set_canvas_height
+# set_canvas_height
 `set_canvas_height(height)`
 
 Set the canvas height and recreate the raster surface.
@@ -42,7 +43,7 @@ Set the canvas height and recreate the raster surface.
 
 ---
 
-### set_canvas_size
+# set_canvas_size
 `set_canvas_size(width, height)`
 
 Set both canvas width and height and recreate the raster surface.
@@ -56,7 +57,7 @@ Set both canvas width and height and recreate the raster surface.
 
 ---
 
-### set_theme
+# set_theme
 `set_theme(theme_name)`
 
 Set a predefined visualisation theme.
@@ -75,7 +76,7 @@ gw.set_theme("dark")
 
 ---
 
-### set_paint_ARBG
+# set_paint_ARBG
 `set_paint_ARBG(paint_enum, a, r, g, b)`
 
 Set the ARGB color for a specific paint type.
@@ -95,7 +96,7 @@ gw.set_paint_ARBG(GwPalette.NORMAL_READ, 255, 0, 0, 128)
 
 ---
 
-### apply_theme
+# apply_theme
 `apply_theme(theme_dict)`
 
 Apply a custom theme using a dictionary of paint types and colors.
@@ -118,7 +119,7 @@ gw.apply_theme(custom_theme)
 
 ---
 
-### load_theme_from_json
+# load_theme_from_json
 `load_theme_from_json(filepath)`
 
 Load and apply a theme from a JSON file.
@@ -136,7 +137,7 @@ gw.load_theme_from_json("custom_theme.json")
 
 ---
 
-### save_theme_to_json
+# save_theme_to_json
 `save_theme_to_json(filepath)`
 
 Save the current theme settings to a JSON file.
@@ -155,7 +156,7 @@ gw.save_theme_to_json("my_theme.json")
 
 ---
 
-### set_font_size
+# set_font_size
 `set_font_size(size)`
 
 Set the font size.

docs/docs/api/gw-visual.md

@@ -5,8 +5,9 @@ parent: API Reference
 nav_order: 4
 ---
 
-## Visualisation
+# Visualisation
 {: .no_toc .text-delta }
+---
 
 ## Table of contents
 {: .no_toc .text-delta }
@@ -16,7 +17,7 @@ nav_order: 4
 
 ---
 
-### draw
+## draw
 `draw()`
 
 Draw the visualisation to the raster surface. Suitable for non-interactive visualisations.
@@ -26,7 +27,7 @@ Draw the visualisation to the raster surface. Suitable for non-interactive visua
 
 ---
 
-### draw_interactive
+## draw_interactive
 `draw_interactive(clear_buffer=False)`
 
 Draw the visualisation to the raster surface. Caches state for using with interactive functions.
@@ -39,7 +40,7 @@ Draw the visualisation to the raster surface. Caches state for using with intera
 
 ---
 
-### draw_image
+## draw_image
 `draw_image()`
 
 Draw the visualisation and return it as a PIL Image.