Added boxplot for sizes.

README.md

@@ -24,11 +24,11 @@ cd PrioritizationCNAs
         - Set cancer_type and date_data to download Firehose data or provide own input file.
         - Provide the remainder files related to the tumor type of the input file.
 
-6. Run the pipeline from the directory containing the Snakefile:
+6. Run the pipeline shell script, which will create the required conda environment and run snakemake (recommended when snakemake is not installed yet):
 ```
 bash run_pipeline.sh
 ```
-    Or manually create an environment for the pipeline, install the required packages and run snakemake:
+    Or manually install the required packages and run snakemake:
 ```
 conda install -c bioconda snakemake=4.4.0
 conda install -c conda-forge matplotlib-venn=0.11.5

Snakefile

@@ -39,8 +39,8 @@ onerror:
 rule all:
     """Define desired output from pipeline."""
     input:
-        "Samplesize/Report.txt",
-        #"Reports/Tools.txt"
+        #"Samplesize/Report.txt",
+        "Reports/Results.html"
         #"Reports/Segments.txt",
         #"GO/comparison.txt"
 

config.yaml

 #Directories to be specified
-workdir: /home/bftan/CNA_results        #directory to write output
-gisticdir: /home/bftan/Tools/GISTIC2    #directory to install GISTIC2
+#workdir: /home/bftan/CNA_results        #directory to write output
+#gisticdir: /home/bftan/Tools/GISTIC2    #directory to install GISTIC2
 
-#workdir: /home/beatrice/CNA_analysis
-#gisticdir: /home/beatrice/CNA_analysis/run_gistic2
+workdir: /home/beatrice/CNA_analysis
+gisticdir: /home/beatrice/CNA_analysis/run_gistic2
 
 #Input details to download from firehose
 cancer_type: SKCM

rules/RecurrentRegions.smk

@@ -115,7 +115,15 @@ rule report_tools:
 rule report:
     """Write html report on segmentation file."""
     input:
-        seg="Reports/Segments.txt"
+        seg="Reports/Segments.txt",
+        tools="Reports/Tools.txt",
+        table_regions="Reports/Recurrent_regions.txt",
+        genes_both="Reports/Genes_both.txt",
+        genes_gistic="Reports/Genes_GISTIC2.txt",
+        genes_rubic="Reports/Genes_RUBIC.txt",
+        overlap="Reports/Overlap_genes.txt",
+        venn="Reports/Venn_overlap_genes.png",
+        swarmplot="Reports/Swarmplot_sizes.png"
     output:
         html="Reports/Results.html"
     run:

scripts/Reports.py

@@ -166,7 +166,7 @@ class ReportTools:
     def make_swarmplot_sizes(self, parsed_results, out_plot):
         """Make swarmplot of the sizes of recurrent regions detected by either GISTIC2 or RUBIC."""
         sizes, sizes_zoomed = [], []
-        tool = 'GISTIC2'
+        tool = 'GISTIC2.0'
         for tool_results in parsed_results:
             amp_sizes, del_sizes = [], []
             for cnv in tool_results:
@@ -181,29 +181,20 @@ class ReportTools:
         self.make_swarmplot_log_sizes(df, out_plot)
 
     def make_swarmplot_log_sizes(self, size_list, plot_file):
-        sns.set_style("whitegrid")
+        sns.set_style("white")
         f, ax = plt.subplots(figsize=(7, 7))
         ax.set(yscale="log")
-        g = sns.swarmplot(x="Tool", y="Size", hue="CNV type", data=size_list, size=5)
-        g.set(xlabel='Tool', ylabel='Log size of recurrent regions', fontsize=25)
+        g = sns.boxplot(x="Tool", y="Size", hue="CNV type", data=size_list, whis=np.inf, palette="deep")
+        g = sns.swarmplot(x="Tool", y="Size", split=True, hue="CNV type", data=size_list, size=5, palette={"Amplification": "#3f3f3f", "Deletion": "#3f3f3f"})
+        sns.despine()
+        g.set_xlabel("Tool",fontsize=16)
+        g.set_ylabel("Log size of recurrent regions",fontsize=16)
+        g.tick_params(labelsize=12)
+        handles, labels = g.get_legend_handles_labels()
+        plt.legend(handles[0:2], labels[:2], fontsize=12)
         plt.savefig(plot_file, dpi=300)
         plt.close()
 
-#    def make_swarmplot_sizes(self, size_list, plot_file):
-#        plotnr = 1
-#        for data in sizes, sizes_zoomed:
-#            df = pd.DataFrame(data, columns=labels)
-#            plt.subplot(2, 1, plotnr)
-#            g = sns.swarmplot(x="Size", y="Tool", hue="Type", data=df, size=3)
-#            if plotnr == 2:
-#                g.set(xlim=(-10000, None))
-#                g.legend_.remove()
-#            else:
-#                g.set(xlim=(-1000000, None))
-#            plotnr = 2
-#        plt.savefig(out_plot, dpi=300)
-#        plt.close()
-
     def venn_overlap(self, gene_lists, out_venn):
         """Compare the genes detected by GISTIC and those by RUBIC."""
         venn2([set(gene_lists[0]), set(gene_lists[1])], set_labels = ('GISTIC2', 'RUBIC'))
@@ -373,6 +364,8 @@ class ReportSizes:
         png_file = os.path.join(plot_dir, y_axis.replace(" ", "_") + ".png")
         plt.savefig(png_file, dpi=300)
 
+#    def test_signficance(list_one, list_two):
+
 
 class ReportControl:
     """Make a report on analyses using control samples or without using them."""