fix bug plotflagstats

frangiPANe/generate_stats.py

@@ -275,6 +275,20 @@ def dashboard_fastq(csv, total_size, group_file, output_dir):
     plt.savefig(os.path.join(output_dir,f"sample_reads_base_ratio.png"))
     plt.close()
 
+def plot_flagstat(stat_file, output_png):
+
+    df_bam_stat = pd.read_csv(stat_file, index_col=False, sep=",")
+    df_bam_stat.sort_values(by=['sample'], inplace=True)
+
+    plt.figure()  # figsize=(12, 5))
+    ratio = sns.scatterplot(x='sample', y='value', hue='variable', data=pd.melt(df_bam_stat, 'sample'))
+    ratio.set(xlabel="sample", ylabel="ratio")
+    ratio.set_title("Read mapped ratio ")
+    plt.legend(bbox_to_anchor=(1.01, 1), borderaxespad=0);
+    plt.savefig(output_png)
+    plt.close()
+
+
 def dashboard_flagstat(stat_file, df_group, output_png):
 
     df_bam_stat = pd.read_csv(stat_file, index_col=False, sep=",")

frangiPANe/snakefiles/plot_mapping.smk

 rule plot_mapping:
     input:
         csv = rules.merge_flagstat.output.stat_file,
-        group=f"{frangipane_obj.path_group}",
     output: 
         png_mapping=f"{frangipane_obj.path_stat_plot}/mapping_read_ratio-{frangipane_obj.reference_basename}.png",
     log:
@@ -19,4 +18,13 @@ rule plot_mapping:
 --------------------
 """
     run:
-        gs.dashboard_flagstat(input.csv,input.group,output.png_mapping)
\ No newline at end of file
+        df_bam_stat = pd.read_csv(input.csv,index_col=False,sep=",")
+        df_bam_stat.sort_values(by=['sample'],inplace=True)
+
+        plt.figure()  # figsize=(12, 5))
+        ratio = sns.scatterplot(x='sample',y='value',hue='variable',data=pd.melt(df_bam_stat,'sample'))
+        ratio.set(xlabel="sample",ylabel="ratio")
+        ratio.set_title("Read mapped ratio ")
+        plt.legend(bbox_to_anchor=(1.01, 1),borderaxespad=0);
+        plt.savefig(output.png_mapping)
+        plt.close()