update

src/chromatinhd/data/peakcounts/plot.py

@@ -104,6 +104,10 @@ def extract_peaks(peaks_bed, promoter, peakcaller):
         peaks = peaks.rename(columns={"name": "cluster"})
         peaks["cluster"] = peaks["cluster"].astype(int)
 
+    if peakcaller == "rolling_500":
+        peaks["start"] = peaks["start"] + 250
+        peaks["end"] = peaks["end"] + 250
+
     if len(peaks) > 0:
         peaks["peak"] = peaks["chrom"] + ":" + peaks["start"].astype(str) + "-" + peaks["end"].astype(str)
         peaks = center_peaks(peaks, promoter)
@@ -337,7 +341,7 @@ def _plot_peaks(ax, plotdata, y, lw=0.5, fc="#555"):
                 peak["end"] - peak["start"],
                 1,
                 fc=fc,
-                lw=0,
+                lw=0.5,
             )
             ax.add_patch(rect)
             # ax.plot([peak["start"]] * 2, [y, y + 1], color="grey", lw=lw)

src/chromatinhd/grid/__init__.py

@@ -1,2 +1,2 @@
 from .grid import Grid, Figure, Panel, Wrap, Ax
-from .broken import Broken, BrokenGrid
+from .broken import Broken, BrokenGrid, Breaking

src/chromatinhd/grid/broken.py

@@ -7,7 +7,7 @@
 @dataclasses.dataclass
 class Breaking:
     regions: pd.DataFrame
-    gap: int
+    gap: int = 0.1
     resolution: int = 5000
 
     @property
@@ -29,7 +29,11 @@ def __init__(self, breaking, height=0.5, margin_height=0.0, *args, **kwargs):
         regions["ix"] = np.arange(len(regions))
 
         for i, (region, region_info) in enumerate(regions.iterrows()):
-            subpanel_width = region_info["width"] / breaking.resolution
+            if "resolution" in region_info.index:
+                resolution = region_info["resolution"]
+            else:
+                resolution = breaking.resolution
+            subpanel_width = region_info["width"] / resolution
             panel, ax = self.add_right(
                 Panel((subpanel_width, height + 1e-4)),
             )

src/chromatinhd/grid/grid.py

@@ -59,13 +59,21 @@ def height(self):
             h += AXIS_HEIGHT
         return h
 
+    @height.setter
+    def height(self, value):
+        self.dim = (self.dim[0], value)
+
     @property
     def width(self):
         w = self.dim[0]
         if self.ax.axison:
             w += AXIS_WIDTH
         return w
 
+    @width.setter
+    def width(self, value):
+        self.dim = (value, self.dim[1])
+
     def align(self):
         pass
 
@@ -218,9 +226,7 @@ def __getitem__(self, key):
 
     def get_bottom_left_corner(self):
         nrow = (len(self.elements) - 1) // self.ncol
-        print(len(self.elements))
         ix = (nrow) * self.ncol
-        print(nrow, self.ncol, ix)
         return self.elements[ix]
         # return self.elements[self.ncol * ((len(self.elements) % self.ncol) - 1)]
 

src/chromatinhd/models/pred/interpret/censorers.py

@@ -61,7 +61,7 @@ def __call__(self, data):
 
 
 class MultiWindowCensorer:
-    def __init__(self, window, window_sizes=(50, 100, 200, 500), relative_stride=0.5):
+    def __init__(self, window, window_sizes=(25, 50, 100, 200, 500), relative_stride=0.5):
         design = [{"window": "control"}]
         for window_size in window_sizes:
             cuts = np.arange(*window, step=int(window_size * relative_stride))

src/chromatinhd/models/pred/interpret/regionmultiwindow.py

@@ -60,8 +60,6 @@ def create(
 
         regions = fragments.regions.var.index
 
-        print(len(folds))
-
         coords_pointed = {
             regions.name: regions,
             "fold": pd.Index(range(len(folds)), name="fold"),
@@ -305,8 +303,6 @@ def _interpolate(self, region):
         effects = np.stack(effects)
         losts = np.stack(losts)
 
-        print(deltacors.min())
-
         scores_statistical = []
         for i in range(deltacors.shape[1]):
             if deltacors.shape[0] > 1:

src/chromatinhd/models/pred/model/__init__.py

@@ -1,2 +1,3 @@
 from . import additive
 from . import nonadditive
+from . import better as multiscale