diff --git a/AppImageBuilder.yml b/AppImageBuilder.yml index f21c054..04bc3c0 100644 --- a/AppImageBuilder.yml +++ b/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 diff --git a/Pipfile b/Pipfile index 56e6c3d..b2078f4 100644 --- a/Pipfile +++ b/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] diff --git a/example/density_list.tsv b/example/density_list.tsv index 678db65..8687318 100644 --- a/example/density_list.tsv +++ b/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 diff --git a/poetry.lock b/poetry.lock index 62481d6..47f6e76 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. 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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 "] license = "BSD-3" diff --git a/requirements.txt b/requirements.txt index 123e85b..2c32072 100644 --- a/requirements.txt +++ b/requirements.txt @@ -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 >= 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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" diff --git a/trackplot/plot.py b/trackplot/plot.py index 6fb6396..758eeef 100644 --- a/trackplot/plot.py +++ b/trackplot/plot.py @@ -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]) diff --git a/trackplot/plot_func.py b/trackplot/plot_func.py index b2dfda2..4ef75aa 100644 --- a/trackplot/plot_func.py +++ b/trackplot/plot_func.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 diff --git a/web/package.json b/web/package.json index b3731f9..182f243 100644 --- a/web/package.json +++ b/web/package.json @@ -1,7 +1,7 @@ { "name": "trackplot", "private": true, - "version": "0.3.7", + "version": "0.3.8", "type": "module", "scripts": { "dev": "vite",