Added save functions to API

Author: kcleal

.gitignore

@@ -38,3 +38,5 @@
 /gwplot/glfw_interface.cpp
 /gwplot/glfw_interface.cpython-310-darwin.so
 /examples/m21009_241011_231051.GRCh38.haplotagged.bam.bai
+/examples/output_online.png
+/examples/output_online.pdf

docs/docs/API.md

@@ -232,6 +232,36 @@ Save the current raster image to a PNG file.
 gw.draw().save_png("visualization.png")
 ```
 
+### `save_pdf(path)`
+
+Save the current raster image to a PDF file. Note draw() does not need to be called.
+
+**Parameters:**
+- `path` (str): Path to save the PDF file
+
+**Returns:**
+- `Gw`: Self for method chaining
+
+**Example:**
+```python
+gw.save_pdf("visualization.pdf")
+```
+
+### `save_svg(path)`
+
+Save the current raster image to a SVG file. Note draw() does not need to be called.
+
+**Parameters:**
+- `path` (str): Path to save the SVG file
+
+**Returns:**
+- `Gw`: Self for method chaining
+
+**Example:**
+```python
+gw.save_svg("visualization.svg")
+```
+
 ### `encode_as_png(compression_level=6)`
 
 Encode the current canvas as PNG and return the binary data.

docs/index.md

@@ -26,7 +26,7 @@ pip install gwplot
 - **Customizable themes and colors** for creating high-quality visualizations
 - **Multi-regions and data tracks** for comparative genomics
 - **Interactive mode** for dynamic exploration of genomic regions
-- **Flexible output formats** including PNG, JPEG, and NumPy arrays for further processing
+- **Flexible output formats** including PNG, PDF, SVG, JPEG, and NumPy arrays for further processing
 - **Built-in access** to common reference genomes
 
 ## Example Visualization
@@ -42,5 +42,5 @@ gw.add_bam("sample.bam")
 gw.add_region("chr1", 1000000, 1100000)
 
 # Draw and save an image
-gw.draw().save_png("region.png")
+gw.save_pdf("region.pdf")
 ```

examples/gwplot_matplotlib.py

@@ -0,0 +1,40 @@
+from gwplot import Gw
+import matplotlib.pyplot as plt
+import numpy as np
+plt.style.use('_mpl-gallery')
+
+# Initialize with reference genome
+gw = Gw("hg19", theme="igv", canvas_width=2048, canvas_height=600)
+
+# Add data sources
+gw.add_bam("https://github.com/kcleal/gw/releases/download/v1.0.0/demo1.bam")
+gw.add_region("chr8", 37047270, 37055161)
+gw.set_font_size(18)
+# Get the visualization as a NumPy array
+img_array = gw.draw().array()
+
+# Create the figure with 2 subplots vertically stacked
+fig, (ax1, ax2) = plt.subplots(2, 1, figsize=(12, 8))
+
+
+# Display the gwplot visualization in the top subplot
+ax1.imshow(img_array)
+ax1.set_title('gwplot chr8:37047270-37055161')
+ax1.axis('off')
+
+# Create the matplotlib plot in the bottom subplot
+x = np.linspace(0, 10, 100)
+y = 4 + 1 * np.sin(2 * x)
+x2 = np.linspace(0, 10, 25)
+y2 = 4 + 1 * np.sin(2 * x2)
+
+ax2.plot(x2, y2 + 2.5, 'x', markeredgewidth=2)
+ax2.plot(x, y, linewidth=2.0)
+ax2.plot(x2, y2 - 2.5, 'o-', linewidth=2)
+
+ax2.set(xlim=(0, 8), xticks=np.arange(1, 8),
+       ylim=(0, 8), yticks=np.arange(1, 8))
+
+# Adjust layout to prevent overlap
+plt.tight_layout()
+plt.show()

examples/save_png_local.py

@@ -1,13 +1,13 @@
 from gwplot import Gw
 import os
-root = os.path.abspath(os.path.dirname(__file__))
 
+root = os.path.abspath(os.path.dirname(__file__)).replace("/examples", "")
 
 # Initialize with reference genome
-gw = Gw(root + "../tests/ref.fa")
+gw = Gw(root + "/tests/ref.fa")
 
 # Add data sources
-gw.add_bam(root + "/../tests/small.bam")
+gw.add_bam(root + "/tests/small.bam")
 
 # Set region to view
 gw.add_region("chr1", 1, 20000)

examples/save_png_online.py

@@ -11,5 +11,4 @@
 gw.add_region("chr8", 37047270, 37055161)
 
 # Render and save
-gw.draw()
-gw.save_png("output_online.png")
+gw.save_pdf("output_online.pdf")

gw

@@ -129,12 +129,16 @@ cdef extern from "plot_manager.h" namespace "Manager" nogil:
 
         void runDraw()
 
-        void rasterToPng(const char * path)
+        void rasterToPng(const char* path)
 
         vector[uint8_t]* encodeToPngVector(int compression_level)
 
         vector[uint8_t]* encodeToJpegVector(int quality)
 
+        void saveToPdf(const char* path)
+
+        void saveToSvg(const char * path)
+
         void keyPress(int key, int scancode, int action, int mods)
 
         void windowResize(int x, int y)

gwplot/interface.pxd

@@ -1632,6 +1632,45 @@ cdef class Gw:
         self.thisptr.rasterToPng(c.c_str())
         return self
 
+    def save_pdf(self, path):
+        """
+        Saves a PDF file using the current configuration. Note calling draw() is
+        not needed beforehand.
+
+        Parameters
+        ----------
+        path : str
+            Path to save the PDF file
+
+        Returns
+        -------
+        Gw
+            Self for method chaining
+        """
+        cdef string c = path.encode("utf-8")
+        self.thisptr.saveToPdf(c.c_str())
+        return self
+
+    def save_svg(self, path):
+        """
+        Saves an SVG file using the current configuration. Note calling draw() is
+        not needed beforehand.
+
+        Parameters
+        ----------
+        path : str
+            Path to save the SVG file
+
+        Returns
+        -------
+        Gw
+            Self for method chaining
+        """
+        cdef string c = path.encode("utf-8")
+        self.thisptr.saveToSvg(c.c_str())
+        return self
+
+
     def draw_interactive(self, clear_buffer=False):
         """
         Draw the visualization to the raster surface. Caches state for using with interactive functions.
@@ -1658,7 +1697,7 @@ cdef class Gw:
 
     def draw(self):
         """
-        Draw the visualization to the raster surface without buffering.
+        Draw the visualization to the raster surface.
 
         Creates the raster surface if it doesn't exist yet.
 
@@ -1670,7 +1709,10 @@ cdef class Gw:
         if not self.raster_surface_created:
             self.make_raster_surface()
         self.thisptr.processed = False
-        self.thisptr.runDrawNoBuffer()
+        if self.thisptr.opts.link_op == 0:
+            self.thisptr.runDrawNoBuffer()
+        else:
+            self.thisptr.runDraw()
         return self
 
     def draw_image(self):
@@ -1685,7 +1727,10 @@ cdef class Gw:
         if not self.raster_surface_created:
             self.make_raster_surface()
         self.thisptr.processed = False
-        self.thisptr.runDrawNoBuffer()
+        if self.thisptr.opts.link_op == 0:
+            self.thisptr.runDrawNoBuffer()
+        else:
+            self.thisptr.runDraw()
         return Image.fromarray(self.array())
 
     def view_region(self, chrom, start, end):