add group autoscale

docs/content/describe_figure.rst

@@ -151,12 +151,18 @@ Parameters:
 * ``scale``: how the maximum value for the y-axis is chosen
 
   * ``auto`` (default): will select as maximum the maximum across all regions.
+
+  * ``group auto`` (default): will select as maximum the maximum across all regions, for all tracks in the same group (defined by the group parameter, see below).
 
   * ``auto per region``: will select as maximum the maximum of each region (so a different scale is used for each region)
+
+  * ``group auto per region``: will select as maximum the maximum of each region (so a different scale is used for each region), for all tracks in the same group (defined by the group parameter, see below).
 
   * ``custom``: manually specify the maximum value. Can either specify a single value, which will then be used for all regions, or a comma-separated list of values (one per region)
 
 * ``scale_max``: in case "scale" is "custom", indicate the maximum value for the y-axis.
+
+* ``group``: if "scale" is "group auto" or "group auto per region", all tracks with the same value for this parameter will be scaled together.
 
 * ``scale_pos``: where the scale (min and max value of the y-axis) will be displayed
 
@@ -218,12 +224,18 @@ Parameters:
 * ``scale``: how the maximum value for the y-axis is chosen
 
   * ``auto`` (default): will select as maximum the maximum across all regions.
+
+  * ``group auto`` (default): will select as maximum the maximum across all regions, for all tracks in the same group (defined by the group parameter, see below).
 
   * ``auto per region``: will select as maximum the maximum of each region (so a different scale is used for each region)
+
+  * ``group auto per region``: will select as maximum the maximum of each region (so a different scale is used for each region), for all tracks in the same group (defined by the group parameter, see below).
 
   * ``custom``: manually specify the maximum value. Can either specify a single value, which will then be used for all regions, or a comma-separated list of values (one per region)
-  
+
 * ``scale_max``: in case "scale" is "custom", indicate the maximum value for the y-axis.
+
+* ``group``: if "scale" is "group auto" or "group auto per region", all tracks with the same value for this parameter will be scaled together.
 
 * ``scale_pos``: where the scale (min and max value of the y-axis) will be displayed
 

figeno/cli/cli.py

@@ -2,7 +2,7 @@
 
 from figeno.cli import gui, init,make
 
-__version__ = "1.3.3"
+__version__ = "1.4.0"
 
 def main():
     parser = ArgumentParser("figeno",formatter_class=ArgumentDefaultsHelpFormatter)

figeno/figeno.py

@@ -316,6 +316,9 @@ def draw(self,output_config=None,warnings=[]):
         if max_size>100*min_size:
             warnings.append("You used regions with very different sizes, so the smaller regions may not be visible.")
 
+        # Check if group autoscale was used, in which case compute them.
+        self.compute_scales()
+
         if self.figure_layout=="horizontal": 
             self.draw_horizontal(**self.output,warnings=warnings)
         elif self.figure_layout=="stacked":
@@ -507,6 +510,55 @@ def draw_circular(self,file,width=183,dpi=150,transparent=False,warnings=[]):
         plt.clf() 
         plt.close('all')
 
+    def compute_scales(self):
+        self.compute_scales_instance(bigwig_track,"bigwig")
+        self.compute_scales_instance(coverage_track,"coverage")
+
+    def compute_scales_instance(self,instance=bigwig_track,instance_name="bigwig"):
+        group2scales={}
+        group2scaletype={}
+        for t in self.tracks_list:
+            if isinstance(t,instance):
+                if t.scale=="custom":
+                    if t.scale_max=="": t.scale_max=None
+                    if t.scale_max is None: raise KnownException("Please provide the scale_max parameter if you use a custom scale.")
+                    if isinstance(t.scale_max,str) and "," in t.scale_max:
+                        try:t.scale_max=[float(x) for x in t.scale_max.split(",")]
+                        except: raise KnownException("The scale_max parameter in a "+instance_name+" track should be a number (or a list of numbers separated by commas): "+str(self.scale_max))
+                    else:
+                        try: t.scale_max=[float(t.scale_max)]
+                        except: raise KnownException("The scale_max parameter in a "+instance_name+" track should be a number: "+str(self.scale_max))
+                elif t.scale=="auto":
+                    t.scale_max=t.compute_max(self.regions,per_region=False)
+                elif t.scale=="group auto":
+                    if not hasattr(t,"group"): raise KnownException("Please provide the group parameter, if you use the group auto scale.")
+                    maximum=t.compute_max(self.regions,per_region=False)
+                    if t.group in group2scaletype:
+                        if group2scaletype[t.group]!="group auto": raise KnownException("Please use the same scale (group auto or group auto per region) for all bigwig tracks of the same group.")
+                    else: group2scaletype[t.group]="group auto"
+                    if t.group in group2scales: group2scales[t.group] = max(maximum,group2scales[t.group])
+                    else: group2scales[t.group] = maximum
+                elif t.scale=="auto per region":
+                    t.scale_max= t.compute_max(self.regions,per_region=True)
+                elif t.scale=="group auto per region":
+                    if not hasattr(t,"group"): raise KnownException("Please provide the group parameter, if you use the group auto per region scale.")
+                    if t.group in group2scaletype:
+                        if group2scaletype[t.group]!="group auto per region": raise KnownException("Please use the same scale (group auto or group auto per region) for all bigwig tracks of the same group.")
+                    else: group2scaletype[t.group]="group auto per region"
+                    maxima=t.compute_max(self.regions,per_region=True)
+                    if t.group in group2scales: group2scales[t.group] = [max(group2scales[t.group][i],maxima[i]) for i in range(len(maxima))]
+                    else: group2scales[t.group] = maxima
+                else:
+                    raise KnownException("Invalid scale for "+instance_name+" track: "+str(t.scale)+". Must be auto, auto per region, group auto, group auto per region, or custom.")
+
+        for t in self.tracks_list:
+            if isinstance(t,instance):
+                if t.scale=="group auto" or t.scale=="group auto per region":
+                    t.scale_max=group2scales[t.group]
+                if len(t.scale_max)>1 and t.scale_pos!="none": t.scale_pos="corner all"
+
+
+
 def figeno_make(config=None,config_file=None,warnings=[]):
     if config is None and config_file is None: raise Exception("ERROR: a config or a config_file is required for figeno_make.")
     tp = tracks_plot(config=config,config_file=config_file)

figeno/gui/package.json

@@ -1,6 +1,6 @@
 {
   "name": "figeno",
-  "version": "1.3.3",
+  "version": "1.4.0",
   "private": true,
   "homepage": "./",
   "dependencies": {

figeno/gui/src/App.js

@@ -158,12 +158,15 @@ export default function App() {
         t.bedmethyls = t.bedmethyls.map((b)=>{const newBed={...b};delete newBed.id; return newBed;})
       }
       else if (t.type=="bigwig" || t.type=="coverage"){
-        if (t.scale=="auto"){
+        if (t.scale!="custom"){
           delete t.scale_max;
         }
+        if (t.scale!="group auto" && t.scale!="group auto per region"){
+          delete t.group;
+        }
       }
       else if (t.type=="hic"){
-        if (t.scale=="auto"){
+        if (t.scale!="auto"){
           delete t.scale_min;
           delete t.scale_max;
         }

figeno/gui/src/Track.jsx

@@ -244,7 +244,9 @@ function BigWigTrack({track,set_value,openColorPanel, setFileDialogData,setFileD
                     <label htmlFor={"scale"+track.id}>Scale:</label>
                     <select id={"scale"+track.id} value={track.scale} onChange={(e) =>{set_value("scale",e.target.value)}}> 
                                 <option className="dropDownOption" key="auto" value="auto">auto</option>
+                                <option className="dropDownOption" key="group auto" value="group auto">group auto</option>
                                 <option className="dropDownOption" key="auto per region" value="auto per region">auto per region</option>
+                                <option className="dropDownOption" key="group auto per region" value="group auto per region">group auto per region</option>
                                 <option className="dropDownOption" key="custom"  value="custom">custom</option>
                     </select>
                 </div>
@@ -254,6 +256,13 @@ function BigWigTrack({track,set_value,openColorPanel, setFileDialogData,setFileD
                     <input id={"scale_max"+track.id} style={{width:"3em"}} value={track.scale_max} onChange={(e) => set_value("scale_max",e.target.value)} ></input>
                 </div>):""
                 }
+                {(track.scale=="group auto" || track.scale=="group auto per region")?(
+                    <div className='formItem'>
+                    <label htmlFor={"group"+track.id}>Group:</label>
+                    <input id={"group"+track.id} style={{width:"3em"}} value={track.group} onChange={(e) => set_value("group",e.target.value)} ></input>
+                </div>):""
+                }
+
                 <div className='formItem'>
                     <label htmlFor={"scale_pos"+track.id}>Scale pos:</label>
                     <select id={"scale_pos"+track.id} value={track.scale_pos} onChange={(e) =>{set_value("scale_pos",e.target.value)}}> 
@@ -294,7 +303,9 @@ function CoverageTrack({track,set_value,openColorPanel, setFileDialogData,setFil
                     <label htmlFor={"scale"+track.id}>Scale:</label>
                     <select id={"scale"+track.id} value={track.scale} onChange={(e) =>{set_value("scale",e.target.value)}}> 
                                 <option className="dropDownOption" key="auto" value="auto">auto</option>
+                                <option className="dropDownOption" key="group auto" value="group auto">group auto</option>
                                 <option className="dropDownOption" key="auto per region" value="auto per region">auto per region</option>
+                                <option className="dropDownOption" key="group auto per region" value="group auto per region">group auto per region</option>
                                 <option className="dropDownOption" key="custom"  value="custom">custom</option>
                     </select>
                 </div>
@@ -304,6 +315,12 @@ function CoverageTrack({track,set_value,openColorPanel, setFileDialogData,setFil
                     <input id={"scale_max"+track.id} style={{width:"3em"}} value={track.scale_max} onChange={(e) => set_value("scale_max",e.target.value)} ></input>
                 </div>):""
                 }
+                {(track.scale=="group auto" || track.scale=="group auto per region")?(
+                    <div className='formItem'>
+                    <label htmlFor={"group"+track.id}>Group:</label>
+                    <input id={"group"+track.id} style={{width:"3em"}} value={track.group} onChange={(e) => set_value("group",e.target.value)} ></input>
+                </div>):""
+                }
                 <div className='formItem'>
                     <label htmlFor={"scale_pos"+track.id}>Scale pos:</label>
                     <select id={"scale_pos"+track.id} value={track.scale_pos} onChange={(e) =>{set_value("scale_pos",e.target.value)}}> 

figeno/gui/src/TracksContainer.jsx

@@ -57,6 +57,7 @@ export const defaultTrackValues={
         n_bins:500,
         scale:"auto",
         scale_max:"",
+        group:"1",
         scale_pos:"corner",
         upside_down:false
     },
@@ -72,6 +73,7 @@ export const defaultTrackValues={
         n_bins:500,
         scale:"auto",
         scale_max:"",
+        group:"1",
         scale_pos:"corner",
         upside_down:false
     },