update to v0.3.8 to fix adjustText usage

Author: ygidtu

AppImageBuilder.yml

@@ -11,7 +11,7 @@ AppDir:
   app_info:
     id: org.appimage-crafters.trackplot
     name: trackplot
-    version: 0.3.7
+    version: 0.3.8
     # Set the python executable as entry point
     exec: "bin/python3"
     # Set the application main script path as argument. Use '$@' to forward CLI parameters

Pipfile

@@ -4,67 +4,67 @@ verify_ssl = false
 name = "pip_conf_index_global"
 
 [packages]
-adjusttext = "==0.7.3"
-asciitree = "==0.3.3"
-blinker = "==1.7.0"
-blosc2 = "==2.0.0"
-cairocffi = "==1.6.1"
-certifi = "==2023.11.17"
-cffi = "==1.16.0"
-charset-normalizer = "==3.3.2"
-click-option-group = "==0.5.6"
-click = "==8.1.7"
-colorama = "==0.4.6"
-contourpy = "==1.1.1"
-cooler = "==0.9.3"
-cycler = "==0.12.1"
-cython = "==3.0.5"
-cytoolz = "==0.12.2"
-dill = "==0.3.7"
-filetype = "==1.2.0"
-flask = "==2.3.3"
-fonttools = "==4.45.1"
-h5py = "==3.10.0"
-hicmatrix = "==15"
+adjusttext = ">=0.7.3"
+asciitree = ">=0.3.3"
+blinker = ">=1.7.0"
+blosc2 = ">=2.0.0"
+cairocffi = ">=1.6.1"
+certifi = ">=2023.11.17"
+cffi = ">=1.16.0"
+charset-normalizer = ">=3.3.2"
+click-option-group = ">=0.5.6"
+click = ">=8.1.7"
+colorama = ">=0.4.6"
+contourpy = ">=1.1.1"
+cooler = ">=0.9.3"
+cycler = ">=0.12.1"
+cython = ">=3.0.5"
+cytoolz = ">=0.12.2"
+dill = ">=0.3.7"
+filetype = ">=1.2.0"
+flask = ">=2.3.3"
+fonttools = ">=4.45.1"
+h5py = ">=3.10.0"
+hicmatrix = ">=15"
 idna = "*"
-importlib-metadata = "==6.8.0"
-importlib-resources = "==6.1.1"
-intervaltree = "==3.1.0"
-itsdangerous = "==2.1.2"
+importlib-metadata = ">=6.8.0"
+importlib-resources = ">=6.1.1"
+intervaltree = ">=3.1.0"
+itsdangerous = ">=2.1.2"
 jinja2 = "*"
-kiwisolver = "==1.4.5"
-loguru = "==0.6.0"
-markupsafe = "==2.1.3"
-matplotlib = "==3.7.4"
-msgpack = "==1.0.7"
-multiprocess = "==0.70.15"
-numexpr = "==2.8.6"
-numpy = "==1.24.4"
-packaging = "==23.2"
-pandas = "==1.5.3"
+kiwisolver = ">=1.4.5"
+loguru = ">=0.6.0"
+markupsafe = ">=2.1.3"
+matplotlib = ">=3.7.4"
+msgpack = ">=1.0.7"
+multiprocess = ">=0.70.15"
+numexpr = ">=2.8.6"
+numpy = ">=1.24.4"
+packaging = ">=23.2"
+pandas = ">=1.5.3"
 pillow = "*"
-py-cpuinfo = "==9.0.0"
-pybigwig = "==0.3.22"
-pycparser = "==2.21"
-pyfaidx = "==0.7.2.2"
-pyparsing = "==3.1.1"
-pysam = "==0.21.0"
-python-dateutil = "==2.8.2"
-pytz = "==2023.3.post1"
-pyyaml = "==6.0.1"
-requests = "==2.31.0"
-scipy = "==1.10.1"
-seaborn = "==0.12.2"
-simplejson = "==3.19.2"
-six = "==1.16.0"
-sortedcontainers = "==2.4.0"
-tables = "==3.8.0"
-toolz = "==0.12.0"
-urllib3 = "==2.1.0"
+py-cpuinfo = ">=9.0.0"
+pybigwig = ">=0.3.22"
+pycparser = ">=2.21"
+pyfaidx = ">=0.7.2.2"
+pyparsing = ">=3.1.1"
+pysam = ">=0.21.0"
+python-dateutil = ">=2.8.2"
+pytz = ">=2023.3.post1"
+pyyaml = ">=6.0.1"
+requests = ">=2.32.0"
+scipy = ">=1.10.1"
+seaborn = ">=0.12.2"
+simplejson = ">=3.19.2"
+six = ">=1.16.0"
+sortedcontainers = ">=2.4.0"
+tables = ">=3.8.0"
+toolz = ">=0.12.0"
+urllib3 = ">=2.1.0"
 werkzeug = "*"
-win32-setctime = "==1.1.0"
-xmltodict = "==0.13.0"
-zipp = "==3.17.0"
+win32-setctime = ">=1.1.0"
+xmltodict = ">=0.13.0"
+zipp = ">=3.17.0"
 
 [dev-packages]
 

example/density_list.tsv

@@ -6,4 +6,3 @@ example/bams/3.bam bam  3bam    blue
 example/bams/sc.bam bam sc	red	frf	1000000
 example/bams/sc.bam bam sc1	blue	frf	1000000
 example/depth.bgz   depth   depth
-example/bedgraph/ENCFF260QGF_lung_filter.bedgraph.gz bedgraph bedgraph

poetry.lock

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "trackplot"
-version = "0.3.7"
+version = "0.3.8"
 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"

pyproject.toml

@@ -1,6 +1,6 @@
 adjusttext==0.7.3 ; python_version >= "3.8" and python_version < "3.12"
 asciitree==0.3.3 ; python_version >= "3.8" and python_version < "3.12"
-blinker==1.8.1 ; python_version >= "3.8" and python_version < "3.12"
+blinker==1.8.2 ; python_version >= "3.8" and python_version < "3.12"
 blosc2==2.0.0 ; python_version >= "3.8" and python_version < "3.12"
 cairocffi==1.7.0 ; python_version >= "3.8" and python_version < "3.12"
 certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.12"
@@ -10,14 +10,14 @@ click-option-group==0.5.6 ; python_version >= "3.8" and python_version < "3.12"
 click==8.1.7 ; python_version >= "3.8" and python_version < "3.12"
 colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.12" and (platform_system == "Windows" or sys_platform == "win32")
 contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.12"
-cooler==0.9.3 ; python_version >= "3.8" and python_version < "3.12"
+cooler==0.10.0 ; python_version >= "3.8" and python_version < "3.12"
 cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.12"
 cython==3.0.10 ; python_version >= "3.8" and python_version < "3.12"
 cytoolz==0.12.3 ; python_version >= "3.8" and python_version < "3.12"
 dill==0.3.8 ; python_version >= "3.8" and python_version < "3.12"
 filetype==1.2.0 ; python_version >= "3.8" and python_version < "3.12"
 flask==2.3.3 ; python_version >= "3.8" and python_version < "3.12"
-fonttools==4.51.0 ; python_version >= "3.8" and python_version < "3.12"
+fonttools==4.52.4 ; python_version >= "3.8" and python_version < "3.12"
 h5py==3.11.0 ; python_version >= "3.8" and python_version < "3.12"
 hicmatrix==15 ; python_version >= "3.8" and python_version < "3.12"
 idna==3.7 ; python_version >= "3.8" and python_version < "3.12"
@@ -46,10 +46,10 @@ pysam==0.21.0 ; python_version >= "3.8" and python_version < "3.12"
 python-dateutil==2.9.0.post0 ; python_version >= "3.8" and python_version < "3.12"
 pytz==2024.1 ; python_version >= "3.8" and python_version < "3.12"
 pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.12"
-requests==2.31.0 ; python_version >= "3.8" and python_version < "3.12"
+requests==2.32.2 ; python_version >= "3.8" and python_version < "3.12"
 scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.12"
 seaborn==0.12.2 ; python_version >= "3.8" and python_version < "3.12"
-setuptools==69.5.1 ; python_version >= "3.8" and python_version < "3.12"
+setuptools==70.0.0 ; python_version >= "3.8" and python_version < "3.12"
 simplejson==3.19.2 ; python_version >= "3.8" and python_version < "3.12"
 six==1.16.0 ; python_version >= "3.8" and python_version < "3.12"
 sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.12"
@@ -59,4 +59,4 @@ urllib3==2.2.1 ; python_version >= "3.8" and python_version < "3.12"
 werkzeug==3.0.3 ; python_version >= "3.8" and python_version < "3.12"
 win32-setctime==1.1.0 ; python_version >= "3.8" and python_version < "3.12" and sys_platform == "win32"
 xmltodict==0.13.0 ; python_version >= "3.8" and python_version < "3.12"
-zipp==3.18.1 ; python_version >= "3.8" and python_version < "3.12"
+zipp==3.19.0 ; python_version >= "3.8" and python_version < "3.12"

requirements.txt

@@ -29,7 +29,7 @@
 faulthandler.enable()
 
 
-__version__ = "0.3.7"
+__version__ = "0.3.8"
 __author__ = "ygidtu & Ran Zhou"
 __email__ = "ygidtu@gmail.com"
 
@@ -1210,6 +1210,11 @@ def plot(self,
             if p.type == "density":
                 if isinstance(p.obj[0], Depth):
                     for key, readDepth in p.obj[0].data.items():
+                        temp_params = self.params.get(p, {})
+
+                        if "y_label" not in temp_params:
+                            temp_params["y_label"] = key
+
                         plot_density(
                             ax=ax_var,
                             data=readDepth,
@@ -1220,8 +1225,7 @@ def plot(self,
                             distance_between_label_axis=distance_between_label_axis,
                             raster=raster,
                             fill_step=fill_step,
-                            y_label=key,
-                            **self.params.get(p, {})
+                            **temp_params
                         )
                         curr_idx += 1
                         ax_var = plt.subplot(gs[curr_idx, 0])

trackplot/plot.py

@@ -807,8 +807,7 @@ def plot_density(
                 jxn_numbers.append(t)
 
         try:
-            adjust_text(jxn_numbers, force_text=0.2, arrowprops=dict(arrowstyle="-", color='black', lw=1),
-                        autoalign="y")
+            adjust_text(jxn_numbers, force_text=(0.2, 0.2), arrowprops=dict(arrowstyle="-", color='black', lw=1))
         except IndexError as err:
             logger.debug(err)
 
@@ -1366,6 +1365,9 @@ def plot_motif(ax: mpl.axes.Axes,
         graph_coords = init_graph_coords(region)
 
     # 在原始坐标轴上画motif
+    if not data:
+        logger.info("there is no any motif information to plot")
+        return
     ymin, ymax, xmin, xmax = 0, 0, \
                              graph_coords[min(data.keys()) - region.start], \
                              graph_coords[max(data.keys()) - region.start] + (1 + width) / 2

trackplot/plot_func.py

@@ -1,7 +1,7 @@
 {
   "name": "trackplot",
   "private": true,
-  "version": "0.3.7",
+  "version": "0.3.8",
   "type": "module",
   "scripts": {
     "dev": "vite",