update to v2.0.6

brie/__init__.py

@@ -7,7 +7,7 @@
 at https://brie.readthedocs.io/.
 """
 
-from ._cli import cli
+# from ._cli import cli
 from .version import __version__
 
 # direct classes or functions

brie/bin/brie_main.py

@@ -0,0 +1,13 @@
+
+from ..version import __version__
+
+def main():
+    print("Welcome to BRIE v%s! Command lines available:\n " %(__version__))
+    print("brie-count\n    Counting reads for exon-skipping events from "
+          "per cell bam files")
+    print("brie-quant\n    Quantify splicing ratio and detecting differential "
+          "splicing\n")
+
+
+if __name__ == "__main__":
+    main()

brie/plot/LRtest_plot.py

@@ -20,24 +20,58 @@ def LRT_basic(LRT_res):
     plt.show()
 
 
-def volcano(adata, x="cell_coeff", y="pval", index=0, score_red=0.0001, 
-            n_anno=10, anno_id='index', log_y=True, adjust=True):
+def volcano(adata, x="cell_coeff", y="ELBO_gain", index=0, score_red=4, 
+            n_anno=10, anno_id='index', log_y=None, clip_y_min=0, adjust=True):
     """Volcano plot for p values and weights
+
+    Parameters
+    ----------
+    adata: AnnData
+        The input AnnData, containing varm[x] and varm[y]
+    x: str
+        The tag in adata.varm for presenting in x-axis
+    y: str
+        The tag in adata.varm for presenting in y-axis
+    index: int
+        The index to present, used as adata.varm[x|y][:, index]
+    score_red: float
+        The cutoff score for highlighting in red
+    n_anno: int
+        Number of top hits to add names
+    anno_id: str
+        The tag id of the adata.var to use as var name
+    log_y: bool
+        If True, show y axis as log scale
+    clip_y_min: float
+        Clipping y at lower bound
+    adjust: bool
+        If True, adjust the annotation position
+
+    Examples
+    --------
+    brie.pl.volcano(adata, x="cell_coeff", y="ELBO_gain", score_red=4)
+    brie.pl.volcano(adata, x="cell_coeff", y="pval", score_red=0.0001)
+    brie.pl.volcano(adata, x="cell_coeff", y="FDR", score_red=0.0001)
     """
     xval = adata.varm[x][:, index]
     yval = adata.varm[y][:, index]
+
+    if clip_y_min is not None:
+        yval[yval < clip_y_min] = clip_y_min
 
-    if log_y:
-        idx = yval < score_red
-        idx_anno = np.argsort(yval)[:n_anno]
-        y_label = "-log10(%s)" %(y)
-
-        yval = -np.log10(yval)
-    else:
+    if y == 'ELBO_gain':
         idx = yval > score_red
         idx_anno = np.argsort(yval)[-n_anno:]
         y_label = str(y)
-
+    else:
+        idx = yval < score_red
+        idx_anno = np.argsort(yval)[:n_anno]
+        if log_y is None or log_y is True:
+            y_label = "-log10(%s)" %(y)
+            yval = -np.log10(yval)
+        else:
+            y_label = str(y)
+
     plt.scatter(xval[~idx], yval[~idx], color="gray")
     plt.scatter(xval[idx], yval[idx], color="firebrick")
 

brie/utils/count.py

@@ -144,7 +144,7 @@ def SE_probability(gene, rlen=75, edge_hang=10, junc_hang=2):
     """
     # check SE event
     if _check_SE_event(gene) == False:
-        print("This is not exon-skipping event!")
+        print("This is not exon-skipping event: %s! %(gene.geneID)")
         exit()
 
     l1, l2, l3 = gene.trans[0].exons[:, 1] - gene.trans[0].exons[:, 0]
@@ -186,7 +186,7 @@ def SE_effLen(gene, rlen=75, edge_hang=10, junc_hang=2):
     """
     # check SE event
     if _check_SE_event(gene) == False:
-        print("This is not exon-skipping event!")
+        print("This is not exon-skipping event: %s! %(gene.geneID)")
         exit()
 
     l1, l2, l3 = gene.trans[0].exons[:, 1] - gene.trans[0].exons[:, 0]

brie/version.py

@@ -1,2 +1,2 @@
-__version__ = "2.0.5"
+__version__ = "2.0.6"
 

setup.py

@@ -44,6 +44,7 @@
     entry_points={
         'console_scripts': [
             # 'brie = brie:_cli.cli',
+            'brie = brie.bin.brie_main:main',
             'brie-count = brie.bin.count:main',
             'brie-quant = brie.bin.quant:main',
             'brie1 = brie.version1.brie:main',