updated report docs for pipeline_rrbs, pep8 changes

CGATPipelines/pipeline_docs/pipeline_rrbs/pipeline.rst

@@ -5,12 +5,15 @@ RRBS pipeline
 Contents:
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 4
 
-   pipeline/SummaryPlots.rst
    pipeline/QC.rst
    pipeline/Coverage.rst
-
+   pipeline/summaryPlots.rst
+   pipeline/summaryPlots/ReadPositionsMethylationBias.rst
+   pipeline/summaryPlots/MethylationBySample.rst
+   pipeline/summaryPlots/Heatmaps.rst
+
 .. errorlist::
 
 

CGATPipelines/pipeline_docs/pipeline_rrbs/pipeline/ReadPositionsMethylationBias.rst

@@ -0,0 +1,39 @@
+========
+Coverage
+========
+========
+Summary Plots
+========
+
+Methylation frequencies across the read length
+==============================================
+
+The following plots show the average methylation value for each read
+position, split by cytosine context, with one plot per sample. The
+purpose of these plots is to identify systematic bias in bisulphite
+conversion, for example, 3' bias. Note: read positions are taken from
+the methylation caller which may be instructed to ignore the first n
+bases from each read, in which case the read positions will be shifted
+along by n.
+
+.. report:: SummaryPlots.readPositionMethylationBias
+   :render: gallery-plot
+
+   Plots can be downloaded using the links below each plot
+
+Difference in methylation frequency across the read length
+==========================================================
+
+The following plot(s) presents the difference in methylation between a
+pair of treatments groups. It is assumed that most CpGs will remain
+unchanged between treatment pairs and the median difference will
+therefore be 0 with bioligical and technical variation resulting in a
+normal distribution around zero. The purpose of this plot is to
+identify instances of unexpectdly high variance which may be due to
+systematic technical variation, for example, sequencing errors. The
+whiskers contain the 99% of the data. Outliers are not shown. 
+
+.. report:: SummaryPlots.readPositionMethylationDiff
+   :render: gallery-plot
+
+   Plots can be downloaded using the links below each plot

CGATPipelines/pipeline_docs/pipeline_rrbs/pipeline/SummaryPlots.rst

@@ -0,0 +1,11 @@
+========
+Summary Plots
+========
+
+.. toctree::
+   :maxdepth: 4
+
+   pipeline/summaryPlots/ReadPositionsMethylationBias.rst
+   pipeline/summaryPlots/MethylationBySample.rst
+   pipeline/summaryPlots/Heatmaps.rst
+

CGATPipelines/pipeline_docs/pipeline_rrbs/pipeline/summaryPlots/Heatmaps.rst

@@ -0,0 +1,43 @@
+=====================
+Correlations, heatmaps and clustering
+=====================
+
+Global correlation
+==========================
+The following plots are correlations between treatment groups for all
+CpGs, split by CpG island / Non-CpG island.
+
+.. report:: SummaryPlots.correlations
+   :render: gallery-plot
+
+   High resolution plots can be downloaded using the links below each plot
+
+Spearman's correlation heatmaps
+==========================
+
+The following plots are heatmaps of spearman's rho values for all
+possible pairwise comparisons. The samples are ordered by treatment
+group and are not clustered. For clustering see the plots in the next
+section. Heatmaps are split by CpG island / Non-CpG island.
+
+.. report:: SummaryPlots.heatmaps
+   :render: gallery-plot
+
+   High resolution plots can be downloaded using the links below each plot
+
+
+Hierachical clustering
+==========================
+
+The following plots are hierarchical clusterings of the samples based
+on pairwise spearman's rank correlations. Clusterings are split by are
+split by CpG island / Non-CpG island. Distance between samples is
+represented by height on the y-axis. The clustering has been
+bootstrapped to estimate how strongly the data support the
+cluster. The numbers in green are the bootstrap probabilities.
+
+.. report:: SummaryPlots.clustering
+   :render: gallery-plot
+
+   High resolution plots can be downloaded using the links below each plot
+

CGATPipelines/pipeline_docs/pipeline_rrbs/pipeline/summaryPlots/MethylationBySample.rst

@@ -0,0 +1,13 @@
+
+Distribution of Methylation frequencies
+==========================
+
+The following plots present the distribution of methylation values
+split by sample and CpG island / Non-CpGI island. The first plots show
+the distribution per sample. The later plots show the distribution for
+the mean methylation values across treatment groups
+
+.. report:: SummaryPlots.methylationSample
+   :render: gallery-plot
+
+   High resolution plots can be downloaded using the links below each plot

CGATPipelines/pipeline_docs/pipeline_rrbs/pipeline/summaryPlots/ReadPositionsMethylationBias.rst

@@ -0,0 +1,32 @@
+
+Methylation frequencies across the read length
+==============================================
+
+The following plots show the average methylation value for each read
+position, split by cytosine context, with one plot per sample. The
+purpose of these plots is to identify systematic bias in bisulphite
+conversion, for example, 3' bias. Note: read positions are taken from
+the methylation caller which may be instructed to ignore the first n
+bases from each read, in which case the read positions will be shifted
+along by n.
+
+.. report:: SummaryPlots.readPositionMethylationBias
+   :render: gallery-plot
+
+   Plots can be downloaded using the links below each plot
+
+Difference in methylation frequency across the read length
+==========================================================
+
+The following plot(s) presents the difference in methylation between a
+pair of treatments groups. It is assumed that most CpGs will remain
+unchanged between treatment pairs and the median difference will
+therefore be 0 with bioligical and technical variation resulting in a
+normal distribution around zero. The purpose of this plot is to
+identify instances of unexpectdly high variance which may be due to
+systematic technical variation, for example, sequencing errors.
+
+.. report:: SummaryPlots.readPositionMethylationDiff
+   :render: gallery-plot
+
+   Plots can be downloaded using the links below each plot