diff options
| -rw-r--r-- | wqflask/wqflask/templates/wgcna_results.html | 2 | ||||
| -rwxr-xr-x | wqflask/wqflask/views.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/wgcna/wgcna_analysis.py | 14 |
3 files changed, 11 insertions, 7 deletions
diff --git a/wqflask/wqflask/templates/wgcna_results.html b/wqflask/wqflask/templates/wgcna_results.html index 9592c25f..b8a4a4f5 100644 --- a/wqflask/wqflask/templates/wgcna_results.html +++ b/wqflask/wqflask/templates/wgcna_results.html @@ -12,7 +12,7 @@ {% endfor %} </table> <h2>WGCNA module plot</h2> - <a href="{{ results['imgurl'] }}"> + <a href="/tmp/{{ results['imgurl'] }}"> <img alt="Embedded Image" src="data:image/png;base64, {% for elem in results['imgdata'] -%} {% print("%c"|format(elem)) %} diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 73899316..dc199ab2 100755 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -96,7 +96,7 @@ def tmp_page(img_path): print("img_path:", img_path) initial_start_vars = request.form print("initial_start_vars:", initial_start_vars) - imgfile = open('/home/zas1024/tmp/' + img_path, 'rb') + imgfile = open(webqtlConfig.TMPDIR + img_path, 'rb') imgdata = imgfile.read() imgB64 = imgdata.encode("base64") bytesarray = array.array('B', imgB64) diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py index 74bb6f8e..9ab7950b 100644 --- a/wqflask/wqflask/wgcna/wgcna_analysis.py +++ b/wqflask/wqflask/wgcna/wgcna_analysis.py @@ -7,6 +7,7 @@ import rpy2.robjects as ro # R Objects import rpy2.rinterface as ri from base import webqtlConfig # For paths and stuff +from utility import webqtlUtil # Random number for the image import base64 import array @@ -97,22 +98,24 @@ class WGCNA(object): # Create block wise modules using WGCNA network = self.r_blockwiseModules(rM, power = 6, verbose = 3) + # Save the network for the GUI self.results['network'] = network # How many modules and how many gene per module ? print(r_table(network[1])) # The iconic WCGNA plot of the modules in the hanging tree - self.results['imgurl'] = webqtlConfig.TMPDIR + "WGCNAoutput.png" - r_png(self.results['imgurl']) + self.results['imgurl'] = webqtlUtil.genRandStr("WGCNAoutput_") + ".png" + self.results['imgloc'] = webqtlConfig.TMPDIR + self.results['imgurl'] + r_png(self.results['imgloc']) mergedColors = self.r_labels2colors(network[1]) - self.r_plotDendroAndColors(network[5][0], mergedColors, "Module colors",dendroLabels = False, hang = 0.03, addGuide = True, guideHang = 0.05) + self.r_plotDendroAndColors(network[5][0], mergedColors, "Module colors", dendroLabels = False, hang = 0.03, addGuide = True, guideHang = 0.05) r_dev_off() sys.stdout.flush() def render_image(self, results): - print("pre-loading imgage results:", self.results['imgurl']) - imgfile = open(self.results['imgurl'], 'rb') + print("pre-loading imgage results:", self.results['imgloc']) + imgfile = open(self.results['imgloc'], 'rb') imgdata = imgfile.read() imgB64 = imgdata.encode("base64") bytesarray = array.array('B', imgB64) @@ -124,6 +127,7 @@ class WGCNA(object): template_vars["input"] = self.input template_vars["results"] = self.results self.render_image(results) + sys.stdout.flush() #r_sink(type = "message") # This restores R output to the stdout/stderr #r_sink() # We should end the Rpy session more or less return(dict(template_vars)) |