Merge pull request #47 from ygidtu/dev

update web to v0.0.5, fix several bugs, update docs

WebDockerfile

@@ -9,4 +9,4 @@ RUN cd $ROOT_DIR && \
     pip install -i $PYPI fastapi uvicorn pydantic jinja2 && \
     pip install -r requirements.txt && ls -l $ROOT_DIR
 
-ENTRYPOINT ["python", "/opt/sashimi/server.py"]
+ENTRYPOINT ["python", "/opt/sashimi/server.py", "--host", "0.0.0.0"]

docs/installation.md

@@ -69,9 +69,9 @@ docker run --rm -v $PWD:$PWD --user $(id -u):$(id -g) ygidtu/sashimi --help
 
 - `-v`, `--volumn`: mount the working directory to docker container
 - `--user`: prevent docker read and write file using root privileges
-- the rest usage please check [Command line usage](./command_line_usage.md)
+- the rest usage please check [Command line usage](./command.md)
 
-**Note: ** detailed command line usage please check [Command line Usage](./command_line_usage.md)
+**Note: ** detailed command line usage please check [Command line Usage](./command.md)
 
 
 ## Build Web interface from source
@@ -101,6 +101,8 @@ python server.py --help
 ```bash
 docker pull ygidtu/sashimiweb
 
-export PORT=8080  # the port your are trying to exposed
-docker run --rm -v $PWD:$PWD --user $(id -u):$(id -g) -p $PORT:5000 ygidtu/sashimiweb
+docker run --name sashimiweb \
+  --rm -v $PWD:$PWD \
+  -p 5000:5000 \
+  ygidtu/sashimiweb 
 ```

docs/web.md

@@ -6,7 +6,9 @@
 
 #### 1. requirements
 
-Except the sashimi, we still required `fastapi`, `uvicorn` and `pydantic`
+Except the sashimi, we required `fastapi`, `uvicorn` and `pydantic` and `nodejs`
+
+The deployment please check the [Build Web interface from source](./installation.md)
 
 ## Usage
 

sashimi/base/ReadDepth.py

@@ -55,10 +55,12 @@ def __init__(self,
 
     @property
     def wiggle(self) -> np.array:
-        if self.plus is None or np.sum(self.plus) == 0:
+        if (self.plus is None or np.sum(self.plus) == 0) and self.minus is not None:
             return self.minus
-        elif self.minus is None or np.sum(self.minus) == 0:
-            return self.plus
+
+        if self.plus is not None and self.minus is not None:
+            return self.plus + self.minus
+
         return self.plus
 
     def __add__(self, other):

sashimi/cli.py

@@ -564,7 +564,8 @@ def main(**kwargs):
                                       n_y_ticks=kwargs["n_y_ticks"],
                                       show_y_label=not kwargs["hide_y_label"],
                                       show_site_plot=kwargs["show_site"],
-                                      strand_choice=kwargs["site_strand"])
+                                      strand_choice=kwargs["site_strand"],
+                                      density_by_strand=kwargs["density_by_strand"],)
             elif key == "heatmap":
                 for f in process_file_list(kwargs[key], key):
                     if barcodes and f.label in barcodes.keys() and f.category in ["bam", "atac"]:

sashimi/file/Bam.py

@@ -53,7 +53,8 @@ def create(cls,
                barcodes: Optional[Set[str]] = None,
                barcode_tag: str = "CB",
                umi_tag: str = "UB",
-               library: str = "fru"
+               library: str = "fru",
+               density_by_strand: bool = False
                ):
         u"""
 
@@ -88,7 +89,8 @@ def create(cls,
             barcodes=barcode,
             barcode_tag=barcode_tag,
             umi_tag=umi_tag,
-            library=library
+            library=library,
+            density_by_strand=density_by_strand
         )
 
     def __hash__(self):
@@ -282,11 +284,11 @@ def load(self,
             spanned_junctions_plus, spanned_junctions_minus = {}, {}
 
         self.data = ReadDepth(
-            plus,
+            plus if self.density_by_strand else plus + minus,
             junctions_dict=filtered_junctions,
             site_plus=site_plus,
             site_minus=site_minus,
-            minus=minus,
+            minus=minus if self.density_by_strand else None,
             junction_dict_plus=spanned_junctions_plus,
             junction_dict_minus=spanned_junctions_minus,
             strand_aware=False if self.library == "fru" else True)

sashimi/plot.py

@@ -372,6 +372,7 @@ def __init_input_file__(path: str,
                             deletion_ignore: Optional[int] = True,
                             del_ratio_ignore: float = .5,
                             exon_focus: Optional[str] = None,
+                            density_by_strand: bool = False,
 
                             # for hic plot
                             trans: Optional[str] = None,
@@ -389,6 +390,7 @@ def __init_input_file__(path: str,
                 barcode_tag=barcode_tag,
                 umi_tag=umi_tag,
                 library=library,
+                density_by_strand=density_by_strand
             )
         elif category == "atac":
             obj = ATAC.create(
@@ -500,7 +502,8 @@ def add_density(self,
             barcode_tag=barcode_tag,
             umi_tag=umi_tag,
             library=library,
-            size_factor=size_factor
+            size_factor=size_factor,
+            density_by_strand=density_by_strand
         )
 
         type_ = "density"
@@ -515,7 +518,7 @@ def add_density(self,
         for p in self.plots:
             if p.category == info.category:
                 for obj_ in p.obj:
-                    if obj_.label == label and label:
+                    if obj_.label == label and label and not barcode:
                         param = self.params.pop(p)
                         p.obj.append(obj)
                         new_obj = False

sashimi/plot_func.py

@@ -607,7 +607,6 @@ def plot_density(
         y_label: str = "",
         theme: str = "ticks_blank",
         max_used_y_val: Optional[float] = None,
-        density_by_plot: bool = False,
         raster: bool = False,
         **kwargs
 ):
@@ -628,8 +627,7 @@ def plot_density(
     :param show_y_label: whether to show y-axis label
     :param y_label: the text of y-axis title
     :param theme: the theme name
-    :param max_used_y_val: used to set same max y axis
-    :param density_by_plot: whether to draw density plot in strand-specific manner.
+    :param max_used_y_val: used to set same max y-axis
     :param raster:
     :param kwargs:
     :return:

server.py

@@ -20,8 +20,10 @@
 from fastapi.templating import Jinja2Templates
 from pydantic import BaseModel
 
+from sashimi.cli import load_barcodes
 from sashimi.plot import *
 
+
 __DIR__ = os.path.abspath(os.path.dirname(__file__))
 __UI__ = os.path.join(__DIR__, "ui")
 
@@ -133,6 +135,12 @@ async def params(target: Optional[str] = None):
         if param.name == "return_image":
             continue
 
+        if param.name == "sc_height_ratio":
+            continue
+
+        if param.name == "barcode":
+            continue
+
         res.append(Param(
             key=param.name,
             annotation=clean(str(param.annotation)),
@@ -174,7 +182,23 @@ async def plot(pid: str, param: PlotParam, func: str):
         elif func == "set_region":
             p.set_region(**kwargs)
         else:
-            getattr(p, func)(param.path, **kwargs)
+            if "barcode_groups" in kwargs.keys() and kwargs["barcode_groups"]:
+                barcodes, sc_colors = load_barcodes(kwargs["barcode_groups"])
+                kwargs["barcode_groups"] = barcodes
+                for group in barcodes[kwargs["label"]].keys():
+                    kwargs["barcode"] = group
+                    kwargs["color"] = sc_colors[group]
+                    kwargs["y_label"] = group
+                    getattr(p, func)(param.path, **kwargs)
+            else:
+                for tag in ["vmin", "vmax"]:
+                    if tag in kwargs.keys():
+                        try:
+                            kwargs[tag] = float(kwargs[tag])
+                        except Exception:
+                            kwargs[tag] = None
+
+                getattr(p, func)(param.path, **kwargs)
     except (AssertionError, OSError, TypeError) as err:
         exc_type, exc_value, exc_traceback = sys.exc_info()
         raise HTTPException(status_code=404,

web/package.json

@@ -1,7 +1,7 @@
 {
   "name": "sashimi.py",
   "private": true,
-  "version": "0.0.0",
+  "version": "0.0.5",
   "type": "module",
   "scripts": {
     "dev": "vite",
@@ -13,6 +13,7 @@
     "element-plus": "^2.2.12",
     "file-saver": "^2.0.5",
     "vue": "^3.2.37",
+    "vue-axios": "^3.5.1",
     "vue-cookies": "^1.8.1",
     "vue-router": "4"
   },