version 0.1.3

Make text PDF-editable and endpoint-ticks the default

.gitignore

@@ -6,4 +6,5 @@ test_files/
 *_graph.txt
 *_key.txt
 .idea
+.DS_Store
 GBM39KT.py

CycleViz.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
 __author__ = "Jens Luebeck (jluebeck [at] ucsd.edu)"
-__version__ = "0.1.2"
+__version__ = "0.1.3"
 
 import argparse
 from collections import defaultdict
@@ -26,6 +26,7 @@
 
 rcParams['font.family'] = 'sans-serif'
 rcParams['font.sans-serif'] = ['Arial']
+rcParams['pdf.fonttype'] = 42
 
 CV_RESOURCES = os.path.dirname(os.path.abspath(__file__)) + "/resources/"
 print("Using resources in " + CV_RESOURCES)
@@ -1076,7 +1077,7 @@ def construct_cycle_ref_placements(cycle, segSeqD, raw_cycle_length, prev_seg_in
 parser.add_argument("--gene_spacing", help="How far from reference to plot gene names. Default 1.7", type=float,
                     default=1.7)
 parser.add_argument("--tick_type", help="Represent ticks only at segment ends, or throughout ('standard' is default)",
-                    choices=["ends", "standard", "none"], default="standard")
+                    choices=["ends", "standard", "none"], default="ends")
 parser.add_argument("--tick_fontsize", help="font size for genomic position ticks", type=float)
 parser.add_argument("--feature_yaml_list", nargs='+', help="list of the input yamls for bedgraph file feature "
                     "specifying additional data. Will be plotted from inside to outside given the order the filenames "

LinearViz.py

@@ -24,6 +24,8 @@
 
 rcParams['font.family'] = 'sans-serif'
 rcParams['font.sans-serif'] = ['Arial']
+rcParams['pdf.fonttype'] = 42
+
 
 CV_RESOURCES = os.path.dirname(os.path.abspath(__file__)) + "/resources/"
 print("Using resources in " + CV_RESOURCES)

README.md

@@ -1,10 +1,13 @@
 # CycleViz
 
+Latest version: **0.1.3**.
+
 Visualize outputs of [AmpliconArchitect](https://github.com/virajbdeshpande/AmpliconArchitect/) & 
 [AmpliconReconstructor](https://github.com/jluebeck/AmpliconReconstructor) (AR) in Circos-style images. 
-CycleViz can also produce more general visualizations of genomic regions. 
+
+CycleViz can also produce more general circular visualizations of genomic regions using only a bed file. 
 Supports hg19, hg38, and GRCh37. CycleViz is implemented in python and compatible with both python2 and python3. 
-CycleViz has been tested on Ubuntu 16.04+ and MacOS 10+.
+CycleViz has been tested on Ubuntu 16.04 and later, and MacOS 10 and later.
 
 **Examples**: Left, a cycles file visualization without AR-reconstruction data. Right, a cycles file visualization with Bionano data. 
 
@@ -21,22 +24,18 @@ Seperate instructions [are available](#running-cycleviz-with-an-aa-generated-cyc
 Requires matplotlib version 2.0.0 or higher and intervaltree python module, both of which are in some cases 
 non-standard in Conda.
 
-To check your matplotlib version in python, type
-```python
-import matplotlib
-print(matplotlib.__version__)
-```
 
-To upgrade to latest matplotlib from command line, do 
+To install relevant python packages. 
 ```
-pip install --upgrade matplotlib
+pip install intervaltree pyyaml matplotlib
 ```
 
-To install intervaltree python package. 
+If you have matplotlib, but the version is not above 2.0.0, you can try the following:
 ```
-pip install intervaltree
+pip install --upgrade matplotlib
 ```
 
+
 [optional] To get the Microsoft fonts on Ubuntu (CycleViz defaults to Arial font)
 ```bash
 sudo apt-get install ttf-mscorefonts-installer fontconfig