Added information for y-axis(Using a modified RPKM). Show Y-axis labe…

…l now.

README.md

@@ -22,6 +22,12 @@ Installation
 The package, rmats2sashimiplot is installed by typing:
 
     python setup.py install
+
+### Update ###
+To update rmats2sashimiplot, please download (or git pull) latest version from Github and type in:
+
+    pip uninstall rmats2sashimiplot
+    python setup.py install
 
 Usage
 -----
@@ -97,7 +103,7 @@ Using grouping function:
 
 ### Grouping
 
-By using this function, user can divide their samples into different groups. Our program will calculate average inclusion level, average read depth and average number of junction-spanning reads of each group and display them in sashimi plot.
+By using this function, user can divide their samples into different groups. rmats2sashimiplot calculates the average inclusion level, the average read depth and the average number of junction-spanning reads of each group and display them in sashimi plot.
 It's extremely helpful when you need to do comparisons between different groups of samples.
 
 
@@ -137,7 +143,7 @@ Each line stand for a group, which consists of *group name* and *index* of bam f
 
 ***Important notes:*** Index starts from 1. And the order of bam files corresponds to the order we specified in --b1/b2/s1/s2, i.e. concatenate --b1 and --b2 (or --s1 and --s2 if you're using them.). User can confirm this order by checking variable `bam_files` in `sashimi_plot_settings.txt`(under Sashimi_index_* folder.)
 
-Index should be seperated by `','`. And use `'-'` to express a sequence.
+Index should be seperated by `','`. And use `'-'` to specify a sequence.
 
 **Eg:**
 
@@ -169,6 +175,19 @@ http://www.mimg.ucla.edu/faculty/xing/rmats2sashimiplot/testData.tar
 
 All output sashimiplot pdf files are in Sashimi_plot folder
 
+### FAQ
+
+Q: What does the y-axis represent?
+
+A: MISO is the actual plotting backend of rmats2sashimiplot, so they have almost the same mechanism of plotting. The y-axis represents a modified RPKM value.
+
+![images](https://github.com/Xinglab/rmats2sashimiplot/blob/master/img/RPKM.png)
+
+Q: How does rmats2sashimiplot calculate junction count, read density(modified RPKM) and inclusion level in the grouping mode?
+
+A: rmats2sashimiplot uses a modified Sashimi plot proposed by SplicePlot(Wu, Nance, & Montgomery, 2014). Briefly, rmats2sashimiplot calculates the average read depth and the average number of junction-spanning reads for groups.
+
+
 Contacts and bug reports
 ------------------------
 Yi Xing

src/rmats2sashimiplot/rmats2sashimiplot.py

@@ -121,7 +121,7 @@ def conf_setting_file(options, gene_no_str=None, gene_symbol=None, events_name_l
         setting["nxticks"] = 11
     else:
         setting["nxticks"] = 6
-    setting["show_ylabel"] = False
+    setting["show_ylabel"] = True
     setting["show_xlabel"] = True
     setting["plot_title"] = "\"gene symbol\""
     setting["plot_label"] = "plot_label"