snp_arrow only draws if focus snp is set

.travis.yml

@@ -3,7 +3,7 @@ language: python
 python: 
   - 2.7
 
-
+install: "pip install -r requirements.txt"
 env: 
   global:
     - NOSE_ARGS="not slow"

genda/eQTL/plotting.py

@@ -8,11 +8,10 @@
 import matplotlib.pyplot as plt
 from statsmodels.graphics.regressionplots import abline_plot
 
-from genda.plotting import (should_not_plot, snp_arrow)
+from genda.plotting import (snp_arrow)
 from genda import calculate_minor_allele_frequency, calculate_ld
 
 
-
 class gene_reference(object):
     """
     """
@@ -188,17 +187,11 @@ def plot_eQTL(meQTL, gene_name, annotation, dosage, ax=None,
     ### Actual scatter #############################
     im = ax.scatter(pos, adj_pv, s=dosage_maf, c = color1)
     #:TODO make the arrow into a funciton
-    ax = snp_arrow(snpx, snp_pv, snp, ax)
+    if focus_snp:
+        ax = snp_arrow(snpx, snp_pv, snp, ax)
+    else: pass
     ax.set_ylabel(r'$-log_{10}$ eQTL p-value')
     ax.set_xlabel(r'Position (Mb)')
-    if should_not_plot(gene_annot):
-        pass
-        '''
-        patch = add_gene_bounderies(ax, gene_annot, 
-                gene_name, x_scale)
-        ax.add_patch(patch)
-        '''
-    else: pass
     if symbol:
         gene_name = symbol
     if ax_orig:

genda/plotting/annotation.py

@@ -1,6 +1,7 @@
 
 
-def snp_arrow(pos, height, snpid, ax, hadjust = 0.0,**kwargs):
+def snp_arrow(pos, height, snpid, ax, hadjust = 0.0,
+        **kwargs):
     """ Draws an arrow pointing at a SNP in 
     a Manhattan plot