updated documentation

docs/build/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: bb1eb5e0e5c901ebcfc674ab6a6d6864
+config: b970ada4cb3d5597f4d7b000044e4c6b
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/_sources/rnalysis.filtering.CountFilter.ma_plot.rst.txt

@@ -0,0 +1,6 @@
+rnalysis.filtering.CountFilter.ma\_plot
+=======================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: CountFilter.ma_plot

docs/build/_sources/rnalysis.filtering.CountFilter.normalize_median_of_ratios.rst.txt

@@ -0,0 +1,6 @@
+rnalysis.filtering.CountFilter.normalize\_median\_of\_ratios
+============================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: CountFilter.normalize_median_of_ratios

docs/build/_sources/rnalysis.filtering.CountFilter.normalize_rle.rst.txt

@@ -0,0 +1,6 @@
+rnalysis.filtering.CountFilter.normalize\_rle
+=============================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: CountFilter.normalize_rle

docs/build/_sources/rnalysis.filtering.CountFilter.normalize_tmm.rst.txt

@@ -0,0 +1,6 @@
+rnalysis.filtering.CountFilter.normalize\_tmm
+=============================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: CountFilter.normalize_tmm

docs/build/_sources/rnalysis.filtering.CountFilter.normalize_to_quantile.rst.txt

@@ -0,0 +1,6 @@
+rnalysis.filtering.CountFilter.normalize\_to\_quantile
+======================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: CountFilter.normalize_to_quantile

docs/build/_sources/rnalysis.filtering.CountFilter.normalize_to_rpm.rst.txt

@@ -3,4 +3,4 @@ rnalysis.filtering.CountFilter.normalize\_to\_rpm
 
 .. currentmodule:: rnalysis.filtering
 
-.. automethod:: CountFilter.normalize_to_rpm_htseqcount
+.. automethod:: CountFilter.normalize_to_rpm

docs/build/_sources/rnalysis.filtering.CountFilter.normalize_to_rpm_htseqcount.rst.txt

@@ -0,0 +1,6 @@
+rnalysis.filtering.CountFilter.normalize\_to\_rpm\_htseqcount
+=============================================================
+
+.. currentmodule:: rnalysis.filtering
+
+.. automethod:: CountFilter.normalize_to_rpm_htseqcount

docs/build/_sources/rnalysis.filtering.CountFilter.rst.txt

@@ -5,17 +5,17 @@
 
 .. autoclass:: CountFilter
 
-
-
-
+   
+   
+   
     .. automethod:: __init__
+
+
 
-
-
-
+
 .. autosummary::
     :toctree: .
-
+    
     CountFilter.biotypes
     CountFilter.box_plot
     CountFilter.clustergram
@@ -34,7 +34,13 @@
     CountFilter.from_folder
     CountFilter.head
     CountFilter.intersection
+    CountFilter.ma_plot
     CountFilter.majority_vote_intersection
+    CountFilter.normalize_median_of_ratios
+    CountFilter.normalize_rle
+    CountFilter.normalize_tmm
+    CountFilter.normalize_to_quantile
+    CountFilter.normalize_to_rpm
     CountFilter.normalize_to_rpm_htseqcount
     CountFilter.normalize_with_scaling_factors
     CountFilter.number_filters
@@ -59,4 +65,5 @@
     CountFilter.transform
     CountFilter.union
     CountFilter.violin_plot
-
+
+

docs/build/_sources/user_guide.rst.txt

@@ -505,7 +505,21 @@ There are a few filtering operations unique to CountFilter. Those include 'filte
 
 Normalizing reads with CountFilter
 ------------------------------------
-:term:`CountFilter` offers two methods for normalizing reads: supply user-defined scaling factors, or normalize to reads per million (RPM). Data normalized in other methods (such as RPKM) can be used as input for CountFilter, but it cannot perform such normalization methods on its own.
+:term:`CountFilter` offers two methods for normalizing reads: normalize with one of the pre-made normalization methods *RNAlysis* supplies, or using user-defined scaling factors. Data normalized in other methods (such as RPKM) can be used as input for CountFilter as well.
+
+*RNAlysis* supplies the following normalization methods:
+
+* Relative Log Expression (RLE - 'normalize_rle'), used by default by R's DESeq2
+* Trimmed Mean of M-values (TMM - 'normalize_tmm'), used by default by R's edgeR
+* Quantile normalization, a generalization of Upper Quantile normalization (UQ - 'normalize_quantile'), used by default by R's Limma
+* Median of Ratios Normalization (MRN - 'normalize_mrn')
+* Reads Per Million (RPM - 'normalize_to_rpm')
+
+To normalize a :term:`CountFilter` with one of these functions, simply call the function with your preferred parameters, if there are any. For example::
+
+    >>> counts = filtering.CountFilter('tests/test_files/counted.csv')
+    >>> counts.normalize_rle()
+    Normalized the values of 22 features. Normalized inplace.
 
 To normalize a :term:`CountFilter` with user-generated scaling factors, we need a `csv` table with the size factor for each sample:
 
@@ -518,7 +532,8 @@ To normalize a :term:`CountFilter` with user-generated scaling factors, we need
 We would then supply the function with the path to the scaling factors file::
 
     >>> counts = filtering.CountFilter('tests/test_files/counted.csv')
-    >>> counts.normalize with_scaling_factors('scaling_factors.csv')
+    >>> counts.normalize_with_scaling_factors('scaling_factors.csv')
+    Normalized the values of 22 features. Normalized inplace.
 
 The resulting :term:`CountFilter` object will be normalized with the scaling factors (dividing the value of each column by the value of the corresponding scaling factor).
 
@@ -544,6 +559,7 @@ We would then supply the normalization function with the path to the special cou
 
     >>> counts = CountFilter("tests/test_files/counted.csv")
     >>> counts.normalize_to_rpm_htseqcount("tests/test_files/uncounted.csv")
+    Normalized the values of 22 features. Normalized inplace.
 
 The resulting :term:`CountFilter` object will be normalized to RPM with the formula (1,000,000 * reads in cell) / (sum of aligned reads + __no_feature + __ambiguous + __alignment_no_unique)
 

docs/build/_static/documentation_options.js

@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '3.0.1',
+    VERSION: '3.1.0',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',