Merge pull request #32 from a-slide/dev

Dev

deploy_anaconda.sh

@@ -12,13 +12,13 @@ conda config --set always_yes yes --set changeps1 no --set anaconda_upload no
 conda update -q conda
 
 echo "Install packages needed for package build and upload"
-conda install -q python=3.6 conda-build anaconda-client ripgrep conda-verify
+conda install -q python=3.7 conda-build anaconda-client ripgrep conda-verify
 
 echo "compile package from setup.py"
 python setup.py sdist
 
 echo "Build noarch package..."
-conda build meta.yaml --python 3.6 --numpy 1.1 --output-folder conda_build  -c bioconda -c conda-forge
+conda build meta.yaml --python 3.7 --numpy 1.1 --output-folder conda_build -c bioconda -c conda-forge -c plotly
 
 echo "Deploying to Anaconda.org..."
 anaconda -v -t $1 upload conda_build/**/*.tar.bz2

docs/Comp_Report/CLI_usage.ipynb

@@ -24,8 +24,8 @@
    "execution_count": 2,
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2020-07-09T13:26:07.327464Z",
-     "start_time": "2020-07-09T13:26:07.033194Z"
+     "end_time": "2020-07-13T10:25:45.753266Z",
+     "start_time": "2020-07-13T10:25:45.490831Z"
     },
     "init_cell": true
    },
@@ -61,8 +61,8 @@
    "execution_count": 3,
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2020-07-09T13:22:45.143253Z",
-     "start_time": "2020-07-09T13:22:43.827719Z"
+     "end_time": "2020-07-13T10:25:49.221115Z",
+     "start_time": "2020-07-13T10:25:47.958971Z"
     }
    },
    "outputs": [
@@ -165,8 +165,8 @@
    "execution_count": 4,
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2020-07-09T13:23:00.396019Z",
-     "start_time": "2020-07-09T13:22:57.799296Z"
+     "end_time": "2020-07-13T10:25:55.324118Z",
+     "start_time": "2020-07-13T10:25:52.892417Z"
     },
     "scrolled": false
    },
@@ -178,8 +178,8 @@
       "\u001b[01;34m## Checking options and input files ##\u001b[0m\n",
       "\u001b[37m\t[DEBUG]: Options summary\u001b[0m\n",
       "\u001b[37m\t[DEBUG]: \tPackage name: pycoMeth\u001b[0m\n",
-      "\u001b[37m\t[DEBUG]: \tPackage version: 0.4.7\u001b[0m\n",
-      "\u001b[37m\t[DEBUG]: \tTimestamp: 2020-07-09 14:22:59.200640\u001b[0m\n",
+      "\u001b[37m\t[DEBUG]: \tPackage version: 0.4.8\u001b[0m\n",
+      "\u001b[37m\t[DEBUG]: \tTimestamp: 2020-07-13 12:25:54.286588\u001b[0m\n",
       "\u001b[37m\t[DEBUG]: \tmethcomp_fn: ./data/Yeast_CGI_meth_comp.tsv.gz\u001b[0m\n",
       "\u001b[37m\t[DEBUG]: \tgff3_fn: ./data/yeast.gff3\u001b[0m\n",
       "\u001b[37m\t[DEBUG]: \tref_fasta_fn: ./data/yeast.fa\u001b[0m\n",
@@ -196,7 +196,7 @@
       "\u001b[37m\t[DEBUG]: \tprogress: False\u001b[0m\n",
       "\u001b[37m\t[DEBUG]: \tkwargs\u001b[0m\n",
       "\u001b[37m\t[DEBUG]: \t\tsubcommands: Comp_Report\u001b[0m\n",
-      "\u001b[37m\t[DEBUG]: \t\tfunc: <function Comp_Report at 0x7f26aebcf050>\u001b[0m\n",
+      "\u001b[37m\t[DEBUG]: \t\tfunc: <function Comp_Report at 0x7f67c71279e0>\u001b[0m\n",
       "\u001b[01;34m## Loading and preparing data ##\u001b[0m\n",
       "\u001b[32m\tLoading Methcomp data from TSV file\u001b[0m\n",
       "\u001b[32m\tLoading transcripts info from GFF file\u001b[0m\n",
@@ -240,11 +240,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 5,
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2020-07-09T13:26:40.196255Z",
-     "start_time": "2020-07-09T13:26:10.371755Z"
+     "end_time": "2020-07-13T10:26:40.115493Z",
+     "start_time": "2020-07-13T10:26:12.814818Z"
     },
     "scrolled": false
    },
@@ -264,7 +264,6 @@
       "\u001b[32m\tComputing source md5\u001b[0m\n",
       "\u001b[01;34m## Parsing methcomp data ##\u001b[0m\n",
       "\u001b[32m\tIterating over significant intervals\u001b[0m\n",
-      "[10219:0709/142616.540247:ERROR:buffer_manager.cc(488)] [.DisplayCompositor]GL ERROR :GL_INVALID_OPERATION : glBufferData: <- error from previous GL command\n",
       "\u001b[32m\tGenerating summary report\u001b[0m\n",
       "(pycoMeth) "
      ]

docs/installation.md

@@ -2,7 +2,7 @@
 
 ## Create a clean virtual environment (optional but recommended)
 
-Ideally, before installation, create a clean **python3.6+** virtual environment to deploy the package.
+Ideally, before installation, create a clean **python3.7+** virtual environment to deploy the package.
 Earlier version of Python3 should also work but **Python 2 is not supported**.
 For example one can use conda or virtualenvwrapper.
 
@@ -37,16 +37,9 @@ You might also want to install [Nanopolish](https://github.com/jts/nanopolish) i
 * `pyfaidx>=0.5.8`
 * `tqdm>=4.45.0`
 * `colorlog>=4.1.0`
+* `kaleido` *New library being developed by the plotly team for static image export*
 
-The correct versions of packages are installed together with the software when using pip
-
-in addition if you want to enable static images export you will also need the following dependencies:
-
-* `plotly-orca==1.2.1`
-* `psutil>=5.7.0`
-* `requests>=2.24.0`
-
-Those dependencies will only be installed with conda as `orca` is not a python package.
+The correct versions of packages are installed together with the software when using pip or conda
 
 ## Option 1: Installation with pip from pypi
 
@@ -64,7 +57,6 @@ pip install --index-url https://test.pypi.org/simple/ pycoMeth -U
 
 ## Option 2: Installation with conda from Anaconda cloud
 
-This option will also install `orca` which is required for static images export
 
 ```bash
 # First installation

meta.yaml

@@ -1,4 +1,4 @@
-{% set version = "0.4.8" %}
+{% set version = "0.4.13" %}
 {% set name = "pycoMeth" %}
 
 package:
@@ -31,9 +31,7 @@ requirements:
     - tqdm>=4.45.0
     - colorlog>=4.1.0
     - nbformat>=4.2.0
-    - plotly-orca=1.3.1
-    - psutil>=5.7.0
-    - requests>=2.24.0
+    - python-kaleido
 
 test:
   imports:

pycoMeth/Comp_Report.py

@@ -144,6 +144,7 @@ def Comp_Report (
         mkdir (os.path.join(outdir, reports_outdir), exist_ok=True)
         mkdir (os.path.join(outdir, tables_outdir), exist_ok=True)
         if export_static_plots:
+            kaleido = Kaleido()
             plot_outdir = "static_plots"
             mkdir (os.path.join(outdir, plot_outdir), exist_ok=True)
 
@@ -207,13 +208,16 @@ def Comp_Report (
                     table_out_path = os.path.join(outdir, tables_outdir, top_dict[idx]["bn"]+".tsv")
                     transcript_df.to_csv(table_out_path, sep="\t", index=False)
 
-                # Try to export static plots if orca is installed
+                # Try to export static plots if required
                 if export_static_plots:
-                    try:
-                        heatmap_fig.write_image(os.path.join(outdir, plot_outdir, top_dict[idx]["bn"]+"_heatmap.svg"), width=1400)
-                        ridgeplot_fig.write_image(os.path.join(outdir, plot_outdir, top_dict[idx]["bn"]+"_ridgeplot.svg"), width=1400)
-                    except Exception:
-                        pass
+                    kaleido.export_plotly_svg (
+                        fig = heatmap_fig,
+                        fn = os.path.join(outdir, plot_outdir, top_dict[idx]["bn"]+"_heatmap.svg"),
+                        width = 1400)
+                    kaleido.export_plotly_svg (
+                        fig = ridgeplot_fig,
+                        fn = os.path.join(outdir, plot_outdir, top_dict[idx]["bn"]+"_ridgeplot.svg"),
+                        width = 1400)
 
     # Convert to DataFrame
     all_cpg_df = pd.DataFrame.from_dict(all_cpg_d)
@@ -256,15 +260,24 @@ def Comp_Report (
             top_df = top_df.drop(columns=["detailled report"])
             top_df.to_csv(table_out_path, sep="\t", index=False)
 
-        # Try to export static plots if orca is installed
+        # Try to export static plots if required
         if export_static_plots:
-            try:
-                all_heatmap_fig.write_image(os.path.join(outdir, plot_outdir, "all_heatmap.svg"), width=1400)
-                all_ridgeplot_fig.write_image(os.path.join(outdir, plot_outdir, "all_ridgeplot.svg"), width=1400)
-                catplot_fig.write_image(os.path.join(outdir, plot_outdir, "all_catplot.svg"), width=1400)
-                ideogram_fig.write_image(os.path.join(outdir, plot_outdir, "all_ideogram.svg"), width=1400)
-            except Exception:
-                pass
+            kaleido.export_plotly_svg (
+                fig=all_heatmap_fig,
+                fn=os.path.join(outdir, plot_outdir, "all_heatmap.svg"),
+                width=1400)
+            kaleido.export_plotly_svg (
+                fig=all_ridgeplot_fig,
+                fn=os.path.join(outdir, plot_outdir, "all_ridgeplot.svg"),
+                width=1400)
+            kaleido.export_plotly_svg (
+                fig=catplot_fig,
+                fn=os.path.join(outdir, plot_outdir, "all_catplot.svg"),
+                width=1400)
+            kaleido.export_plotly_svg (
+                fig=ideogram_fig,
+                fn=os.path.join(outdir, plot_outdir, "all_ideogram.svg"),
+                width=1400)
 
 #~~~~~~~~~~~~~~~~~~~~~~~~HTML generating functions~~~~~~~~~~~~~~~~~~~~~~~~#
 
@@ -491,7 +504,8 @@ def cpg_heatmap (
     lim_llr:float = 10,
     min_diff_llr:float = 1,
     fig_width:int=None,
-    fig_height:int=None):
+    fig_height:int=None,
+    column_widths=[0.95, 0.05]):
     """
     Plot the values per CpG as a heatmap
     """
@@ -507,7 +521,7 @@ def cpg_heatmap (
         rows=1,
         cols=2,
         shared_yaxes=True,
-        column_widths=[0.95, 0.05],
+        column_widths=column_widths,
         specs=[[{"type": "heatmap"},{"type": "scatter"}]])
 
     # Plot dendogramm
@@ -525,7 +539,11 @@ def cpg_heatmap (
 
     # Define colorscale
     offset = min_diff_llr/lim_llr*0.5
-    colorscale = colorscale=[[0.0, unmethylated_color],[0.5-offset, ambiguous_color], [0.5+offset, ambiguous_color],[1.0, methylated_color]]
+    colorscale = [
+        [0.0, unmethylated_color],
+        [0.5-offset, ambiguous_color],
+        [0.5+offset, ambiguous_color],
+        [1.0, methylated_color]]
 
     # plot heatmap
     heatmap = go.Heatmap(name="heatmap", x=df.columns, y=df.index, z=df.values, zmin=-lim_llr, zmax=lim_llr, zmid=0, colorscale=colorscale, colorbar_title="Median LLR")
@@ -536,7 +554,7 @@ def cpg_heatmap (
         dict1 = {'showlegend':False, 'hovermode':'closest', "plot_bgcolor":'rgba(0,0,0,0)',"width":fig_width, "height":fig_height, "margin":{"t":50,"b":50}},
         xaxis2 = {"fixedrange":True, 'showgrid':False, 'showline':False, "showticklabels":False,'zeroline':False,'ticks':""},
         yaxis2 = {"fixedrange":True, 'showgrid':False, 'showline':False, "showticklabels":False,'zeroline':False,'ticks':"", "automargin":True},
-        xaxis = {"fixedrange":False, "domain":[0, 0.95], "showticklabels":False, "title":"CpG positions"},
+        xaxis = {"fixedrange":False, "domain":[0, column_widths[0]], "showticklabels":False, "title":"CpG positions"},
         yaxis = {"fixedrange":True, "domain":[0, 1], "ticks":"outside", "automargin":True})
 
     return fig

pycoMeth/__init__.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
 
 # Define self package variable
-__version__ = "0.4.8"
+__version__ = "0.4.13"
 __description__ = 'DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets'

pycoMeth/common.py

@@ -19,6 +19,16 @@
 # Third party imports
 import colorlog
 
+# Optional static export deps
+try:
+    from kaleido.scopes.plotly import PlotlyScope
+    from IPython.core.display import SVG, display
+    STATIC_EXPORT=True
+except (ModuleNotFoundError, ImportError) as E:
+    print("Cannot import dependencies required for static image export")
+    STATIC_EXPORT=False
+    pass
+
 #~~~~~~~~~~~~~~FUNCTIONS~~~~~~~~~~~~~~#
 def opt_summary (local_opt):
     """Simplifiy option dict creation"""
@@ -367,21 +377,30 @@ def log_list (l, logger, header="", indent="\t"):
     for i in l:
         logger("{}*{}".format(indent, i))
 
-def static_display (fig, width=None, height=None):
-    """
-    Function to render a plotly figure in SVG inside jupyter
-    Requires jupyter and Orca to be installed
-    """
-    # if not orca_running():
-    #     raise ImportError ("plotly-orca is required for static image export")
-
-    # function specific imports
-    from tempfile import NamedTemporaryFile
-    from IPython.core.display import display, SVG
 
-    with NamedTemporaryFile(suffix=".svg") as temp_svg:
-        fig.write_image(temp_svg.name, width=width, height=height)
-        display(SVG(temp_svg.name))
+class Kaleido:
+    def __init__ (self):
+        # Init scopes
+        if not STATIC_EXPORT:
+            raise ImportError ("Static export is not possible due to missing dependencies")
+        self.plotly_scope = PlotlyScope()
+
+    def render_plotly_svg (self, fig, width=None, height=None):
+        """
+        Function to render a plotly figure in SVG inside jupyter
+        """
+        if STATIC_EXPORT:
+            svg_fig = self.plotly_scope.transform(fig, format="svg", width=width, height=height)
+            return SVG(svg_fig)
+
+    def export_plotly_svg (self, fig, fn, width=None, height=None):
+        """
+        Function to export a plotly figure to SVG
+        """
+        if STATIC_EXPORT:
+            svg_fig = self.plotly_scope.transform(fig, format="svg", width=width, height=height)
+            with open (fn, mode="wb") as fp:
+                fp.write(svg_fig)
 
 #~~~~~~~~~~~~~~CUSTOM EXCEPTION AND WARN CLASSES~~~~~~~~~~~~~~#
 class pycoMethError (Exception):

setup.py

@@ -5,7 +5,7 @@
 
 # Define package info
 name = "pycoMeth"
-version = "0.4.8"
+version = "0.4.13"
 description = "DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets"
 with open("README.md", "r") as fh:
     long_description = fh.read()
@@ -38,7 +38,8 @@
         "pyfaidx>=0.5.8",
         "tqdm>=4.45.0",
         "colorlog>=4.1.0",
-        "nbformat>=4.2.0"],
+        "nbformat>=4.2.0",
+        "kaleido"],
     packages = [name],
     package_dir = {name: name},
     package_data = {name: ['templates/*']},