Merge pull request #33 from CenterForMedicalGeneticsGhent/genderforce

v1.0.3

README.md

@@ -30,17 +30,18 @@ bins from non-informative ones.
 
 ### Installation
 
-Stable releases can be installed using [Conda](https://conda.io/docs/). This is the preferred option since
-Conda takes care of all necessary dependencies.
+Stable releases can be installed using [Conda](https://conda.io/docs/). This option takes care of all necessary
+dependencies.
 ```bash
 
 conda install -f -c conda-forge -c bioconda wisecondorx
 ```
 
-Alternatively, WisecondorX can be installed using the python Setuptools library.
+Alternatively, WisecondorX can be installed through pip install. This option ascertains the latest version is downloaded,
+yet it does not install R dependencies.  
 ```bash
 
-python setup.py install
+pip install -U git+https://github.com/CenterForMedicalGeneticsGhent/WisecondorX
 ```
 
 ### Running WisecondorX

setup.py

@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 from setuptools import setup, find_packages
 
-version = '1.0.2'
+version = '1.0.3'
 dl_version = 'master' if 'dev' in version else '{}'.format(version)
 
 setup(

wisecondorX/include/plotter.R

@@ -204,8 +204,8 @@ for (ab in input$results_c){
   start = as.integer(info[2]) + chr.ends[chr] + 1
   end = as.integer(info[3]) + chr.ends[chr]
   height = as.double(info[5])
+  rect(start, height, end, 0, col=color.XX[dot.cols[start] == color.X], border=color.XX[dot.cols[start] == color.X], lwd=0.1)
   segments(start, height, end, height, col=lighter.grey, lwd=5 * mean(dot.cex[start:end], na.rm=T), lty=1)
-  rect(start, height, end, 0, col=color.XX[dot.cols[start] == color.X], border=NA)
 }
 
 # boxplots
@@ -232,7 +232,7 @@ if(any(is.infinite(c(y.sex.down, y.sex.up)))){
 
 par(mar=c(2.5,3,1,1))
 boxplot(box.list[23:length(chrs)], ylim=c(y.sex.down, y.sex.up), 
-        bg=black, axes=F, outpch=16, ylab=expression('log'[2]*'(ratio)'))
+        bg=black, axes=F, outpch=16, ylab='')
 
 par(xpd=NA)
 text(1:(length(chrs) - 22), par("usr")[3], labels=labels[23:length(chrs)], srt=45, pos=1)
@@ -308,7 +308,7 @@ for (c in chrs){
     start = as.integer(info[2]) + chr.ends[chr] + 1
     end = as.integer(info[3]) + chr.ends[chr]
     height = as.double(info[5])
-    rect(start, height, end, 0, col=color.XX[dot.cols[start] == color.X], border=NA)
+    rect(start, height, end, 0, col=color.XX[dot.cols[start] == color.X],border=color.XX[dot.cols[start] == color.X], lwd=0.1)
     segments(start, height, end, height, col=lighter.grey, lwd=6 * mean(dot.cex[start:end], na.rm=T), lty=1)
   }
 

wisecondorX/main.py

@@ -140,6 +140,8 @@ def tool_test(args):
 
     if not ref_file['is_nipt']:
         actual_gender = predict_gender(sample, ref_file['trained_cutoff'])
+        if args.gender:
+            actual_gender = args.gender
         sample = gender_correct(sample, actual_gender)
     else:
         actual_gender = 'F'