fix bedgraph checks

Author: ygidtu

AppImageBuilder.yml

@@ -11,7 +11,7 @@ AppDir:
   app_info:
     id: org.appimage-crafters.trackplot
     name: trackplot
-    version: 0.3.2
+    version: 0.3.3
     # Set the python executable as entry point
     exec: "bin/python3"
     # Set the application main script path as argument. Use '$@' to forward CLI parameters

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "trackplot"
-version = "0.3.2"
+version = "0.3.3"
 description = "The trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets. https://sashimi.readthedocs.io/"
 authors = ["ygidtu <ygidtu@gmail.com>"]
 license = "BSD-3"

trackplot/cli.py

@@ -93,7 +93,7 @@ def process_file_list(infile: str, category: str = "density"):
             for idx, line in __read_iter__(infile):
                 path, category = line[0], line[1]
 
-                if category not in ["bam", "bigwig", "bw", "depth", "igv", "atac"]:
+                if category not in ["bam", "bigwig", "bw", "depth", "igv", "atac", "bedgraph", "bg"]:
                     raise ValueError(f"{category} is not supported in density plot.")
 
                 if len(line) < 3:
@@ -112,7 +112,7 @@ def process_file_list(infile: str, category: str = "density"):
             for idx, line in __read_iter__(infile):
                 path, category = line[0], line[1]
 
-                if category not in ["bam", "bigwig", "bw", "depth", "atac"]:
+                if category not in ["bam", "bigwig", "bw", "depth", "atac", "bedgraph", "bg"]:
                     raise ValueError(f"{category} is not supported in heatmap plot.")
 
                 if len(line) < 3:
@@ -134,7 +134,7 @@ def process_file_list(infile: str, category: str = "density"):
             for idx, line in __read_iter__(infile):
                 path, category = line[0], line[1]
 
-                if category not in ["bam", "bigwig", "bw", "depth"]:
+                if category not in ["bam", "bigwig", "bw", "depth", "bedgraph", "bg"]:
                     raise ValueError(f"{category} is not supported in density plot.")
 
                 if len(line) < 3:

trackplot/file/Depth.py

@@ -31,14 +31,30 @@ def __init__(self, path: str, label: List[str] = None, title: str = ""):
         self.region = None
 
     def __hash__(self):
-        return hash(tuple([hash(v) for v in self.data.items()]))
+        if self.data:
+            return hash(tuple([hash(v) for v in self.data.items()]))
+        return hash(tuple(self.label))
 
     def __eq__(self, other):
         return hash(self) == hash(other)
 
     def __len__(self) -> int:
         return len(self.data)
 
+    @property
+    def plus(self):
+        if self.data:
+            return np.array(self.data.values()).max(axis=0)
+        return np.array(0)
+
+    @property
+    def minus(self):
+        return None
+
+    @property
+    def wiggle(self):
+        return self.plus
+
     @classmethod
     def create(cls, path: str, label: List[str] = None, title: str = ""):
         u"""
@@ -94,4 +110,10 @@ def items(self):
 
 
 if __name__ == '__main__':
+    values = [
+        np.array([1, 2, 3, 4, 5]),
+        np.array([5, 4, 3, 2, 1])
+    ]
+
+    print(np.zeros())
     pass

trackplot/plot.py

@@ -30,7 +30,7 @@
 faulthandler.enable()
 
 
-__version__ = "0.3.2"
+__version__ = "0.3.3"
 __author__ = "ygidtu & Ran Zhou"
 __email__ = "ygidtu@gmail.com"
 
@@ -1215,7 +1215,7 @@ def plot(self,
             logger.info(f"plotting {p.type} at idx: {curr_idx} with height_ratio: {height_ratio[curr_idx]}")
             if p.type == "density":
                 if isinstance(p.obj[0], Depth):
-                    for _, readDepth in p.obj[0].data.items():
+                    for key, readDepth in p.obj[0].data.items():
                         plot_density(
                             ax=ax_var,
                             data=readDepth,
@@ -1226,6 +1226,7 @@ def plot(self,
                             distance_between_label_axis=distance_between_label_axis,
                             raster=raster,
                             fill_step=fill_step,
+                            y_label=key,
                             **self.params.get(p, {})
                         )
                         curr_idx += 1

web/package.json

@@ -1,7 +1,7 @@
 {
   "name": "trackplot",
   "private": true,
-  "version": "0.3.1",
+  "version": "0.3.3",
   "type": "module",
   "scripts": {
     "dev": "vite",