Merge pull request #1018 from deeptools/fix_1013

Fix #1013, #1003

.planemo.sh

@@ -28,5 +28,5 @@ else
 fi
 
 planemo lint ${wrappers}
-planemo test --no_dependency_resolution --galaxy_branch release_18.05 --install_galaxy ${wrappers} 2>&1 | grep -v -e "^galaxy" | grep -v -e "^requests"
+planemo test --no_dependency_resolution --galaxy_branch release_20.09 --install_galaxy ${wrappers} 2>&1 | grep -v -e "^galaxy" | grep -v -e "^requests"
 test ${PIPESTATUS[0]} -eq 0

deeptools/bamPEFragmentSize.py

@@ -341,7 +341,7 @@ def main(args=None):
 
         if args.plotFileFormat == 'plotly':
             fig = go.Figure()
-            fig['data'] = data
+            fig.add_traces(data)
             fig['layout']['yaxis1'].update(title='Frequency')
             fig['layout']['xaxis1'].update(title='Fragment Length')
             fig['layout'].update(title=args.plotTitle)

deeptools/computeGCBias.py

@@ -571,7 +571,7 @@ def plotlyGCbias(file_name, frequencies, reads_per_gc, region_size):
     x = np.linspace(0, 1, frequencies.shape[0])
     trace = go.Scatter(x=x, y=np.log2(frequencies[:, 2]), xaxis='x2', yaxis='y2', showlegend=False, line=dict(color='rgb(107,174,214)'))
     data.append(trace)
-    fig['data'] = data
+    fig.add_traces(data)
     fig['layout']['annotations'] = annos
     py.plot(fig, filename=file_name, auto_open=False)
 

deeptools/computeMatrixOperations.py

@@ -73,7 +73,7 @@ def parse_arguments():
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
         parents=[infoArgs(), relabelArgs()],
         help="Change sample and/or group label information",
-        usage='An example usage is:\n  computeMatrixOperations relabel -m input.mat.gz -o output.mat.gz --samples "sample 1" "sample 2"\n\n')
+        usage='An example usage is:\n  computeMatrixOperations relabel -m input.mat.gz -o output.mat.gz --sampleLabels "sample 1" "sample 2"\n\n')
 
     # subset
     subparsers.add_parser(
@@ -795,10 +795,9 @@ def main(args=None):
     hm = heatmapper.heatmapper()
     if not isinstance(args.matrixFile, list):
         hm.read_matrix_file(args.matrixFile)
-
     if args.command == 'info':
         printInfo(hm)
-    if args.command == 'dataRange':
+    elif args.command == 'dataRange':
         printDataRange(hm)
     elif args.command == 'subset':
         sIdx = getSampleBounds(args, hm)

deeptools/correlation.py

@@ -422,7 +422,7 @@ def plotly_scatter(self, plot_filename, corr_matrix, plot_title='', minXVal=None
         data[-1]['colorbar'].update(title="log10(instances per bin)", titleside="right")
         data[-1].update(showscale=True)
 
-        fig['data'] = data
+        fig.add_traces(data)
         fig['layout'].update(title=plot_title, showlegend=False, annotations=annos)
 
         offline.plot(fig, filename=plot_filename, auto_open=False)
@@ -589,7 +589,7 @@ def plotly_pca(self, plotFile, Wt, pvar, PCs, eigenvalues, cols, plotTitle):
         annos.append({'yanchor': 'bottom', 'xref': 'paper', 'xanchor': 'center', 'yref': 'paper', 'text': 'PCA', 'y': 1.0, 'x': 0.25, 'font': {'size': 16}, 'showarrow': False})
         annos.append({'yanchor': 'bottom', 'xref': 'paper', 'xanchor': 'center', 'yref': 'paper', 'text': 'Scree plot', 'y': 1.0, 'x': 0.75, 'font': {'size': 16}, 'showarrow': False})
 
-        fig['data'] = data
+        fig.add_traces(data)
         fig['layout']['annotations'] = annos
         offline.plot(fig, filename=plotFile, auto_open=False)
 

deeptools/plotCoverage.py

@@ -320,7 +320,7 @@ def main(args=None):
         # Don't clip plots
         y_max = max(y_max)
         if args.plotFileFormat == "plotly":
-            fig['data'] = data
+            fig.add_traces(data)
             fig['layout']['yaxis1'].update(range=[0.0, min(1, y_max + (y_max * 0.10))])
             fig['layout']['yaxis2'].update(range=[0.0, 1.0])
             py.plot(fig, filename=args.plotFile, auto_open=False)

deeptools/plotEnrichment.py

@@ -440,7 +440,7 @@ def plotEnrichment(args, featureCounts, totalCounts, features):
                 ax.set_ylim(0.0, 100.0)
 
     if args.plotFileFormat == 'plotly':
-        fig['data'] = data
+        fig.add_traces(data)
         py.plot(fig, filename=args.plotFile, auto_open=False)
         # colors
     else:

deeptools/plotFingerprint.py

@@ -430,7 +430,7 @@ def main(args=None):
 
         if args.plotFileFormat == 'plotly':
             fig = go.Figure()
-            fig['data'] = data
+            fig.add_traces(data)
             fig['layout'].update(title=args.plotTitle)
             fig['layout']['xaxis1'].update(title="rank")
             fig['layout']['yaxis1'].update(title="fraction w.r.t bin with highest coverage")

deeptools/plotHeatmap.py

@@ -371,7 +371,7 @@ def plotlyMatrix(hm,
         trace.update(zmin=zMinUse, zmax=zMaxUse, colorscale=convertCmap(cmap[0], vmin=zMinUse, vmax=zMaxUse))
 
     dataSummary.extend(dataHeatmap)
-    fig['data'] = dataSummary
+    fig.add_traces(dataSummary)
     fig['layout']['annotations'] = annos
     py.plot(fig, filename=outFilename, auto_open=False)
 

deeptools/plotProfile.py

@@ -454,7 +454,7 @@ def plotly_hexbin(self):
         for trace in data:
             trace.update(zmin=vmin, zmax=vmax)
 
-        fig['data'] = data
+        fig.add_traces(data)
         fig['layout']['annotations'] = annos
         py.plot(fig, filename=self.out_file_name, auto_open=False)
 
@@ -668,7 +668,7 @@ def plotly_heatmap(self):
                 zmaxUse = self.y_max[i % len(self.y_max)]
             trace.update(zmin=zminUse, zmax=zmaxUse)
 
-        fig['data'] = data
+        fig.add_traces(data)
         fig['layout']['annotations'] = annos
         py.plot(fig, filename=self.out_file_name, auto_open=False)
 
@@ -828,15 +828,16 @@ def plotly_profile(self):
         yMin = None
         yMax = None
         for i in range(self.numplots):
-            row = rows - i / self.plots_per_row - 1
+            row = np.floor(i / self.plots_per_row)
+            # row = rows - i / self.plots_per_row - 1
             col = i % self.plots_per_row
             xanchor = 'x{}'.format(i + 1)
             yanchor = 'y{}'.format(i + 1)
             base = row * (domainHeight + bufferHeight)
             domain = [base, base + domainHeight]
             titleY = base + domainHeight
-            base = col * (domainWidth + bufferWidth)
             fig['layout']['yaxis{}'.format(i + 1)] = {'domain': domain, 'title': self.y_axis_label, 'anchor': xanchor, 'autorange': False}
+            base = col * (domainWidth + bufferWidth)
             domain = [base, base + domainWidth]
             titleX = base + 0.5 * domainWidth
             fig['layout']['xaxis{}'.format(i + 1)] = {'domain': domain, 'anchor': yanchor}
@@ -900,7 +901,7 @@ def plotly_profile(self):
                 yRange[1] = self.y_max[i % len(self.y_max)]
             fig['layout'][yaxis].update(range=yRange)
 
-        fig['data'] = data
+        fig.add_traces(data)
         fig['layout']['annotations'] = annos
         py.plot(fig, filename=self.out_file_name, auto_open=False)
 

deeptools/utilities.py

@@ -41,7 +41,7 @@ def convertCmap(c, vmin=0, vmax=1):
     h = 1.0 / 254
     colorScale = []
     for k in range(255):
-        C = map(np.uint8, np.array(cmap(k * h)[:3]) * 255)
+        C = list(map(np.uint8, np.array(cmap(k * h)[:3]) * 255))
         colorScale.append([k * h, 'rgb' + str((C[0], C[1], C[2]))])
 
     return colorScale

galaxy/wrapper/computeMatrixOperations.xml

@@ -74,6 +74,7 @@
             #else if $submodule.command == "dataRange":
                 dataRange
                 -m $submodule.matrixFile
+                > $outFileTxt
             #end if
 ]]>
     </command>
@@ -159,7 +160,6 @@
             <when value="dataRange">
                 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
                        label="Matrix file from the computeMatrix tool" help=""/>
-                </param>
             </when>
         </conditional>
     </inputs>
@@ -218,6 +218,7 @@ What it does
 + dataRange      | Returns the min, max, median, 10th and 90th percentile of the matrix values per sample.                                  |
 +----------------+--------------------------------------------------------------------------------------------------------------------------+
 
+
 These operations are useful when you want to run computeMatrix on multiple files (thereby keeping all of the values together) and later exclude regions/samples or add new ones. Another common use would be if you require the output of computeMatrix to be sorted to match the order of regions in the input file.
 
 -----

requirements.txt

@@ -5,5 +5,5 @@ pysam>=0.14.0
 py2bit>=0.2.0
 numpydoc>=0.5
 pyBigWig>=0.2.1
-plotly>=2.0.0
+plotly>=4.9
 deeptoolsintervals>=0.1.8

setup.py

@@ -89,7 +89,7 @@ def openREADME():
         "numpydoc >= 0.5",
         "pyBigWig >= 0.2.1",
         "py2bit >= 0.2.0",
-        "plotly >= 2.0.0",
+        "plotly >= 4.9",
         "deeptoolsintervals >= 0.1.8"
     ],
     zip_safe=True,