Merge pull request #61 from torres-alexis/NF-RCP-typo-fix

NF_RCP: Remove whitespace in by_docker_image.config
Remove circles on ERCC analysis box and whisker plots

Author: asaravia-butler

RNAseq/Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-F.md

@@ -2118,7 +2118,7 @@ ddf['Avg Mix1 CPM/ Avg Mix2 CPM'] = (ddf['Avg Mix1 CPM'] / ddf['Avg Mix2 CPM'])
 ## Multi-sample ERCC analyses
 ### Create box and whisker plots of the log(2) CPM for each ERCC detected in group A in Mix 1 and Mix 2 spiked samples
 
-a = sns.catplot(x="ERCC ID", y="log2 Count per million", order=groupA[::-1], hue="Mix",data=merged_ercc[merged_ercc['ERCC ID'].isin(groupA)], kind="box", col="ERCC group", height=5, aspect=1, palette=sns.color_palette(['blue', 'orange']))
+a = sns.catplot(x="ERCC ID", y="log2 Count per million", order=groupA[::-1], hue="Mix",data=merged_ercc[merged_ercc['ERCC ID'].isin(groupA)], kind="box", col="ERCC group", height=5, aspect=1, palette=sns.color_palette(['blue', 'orange']), showfliers=False)
 a.set_xticklabels(rotation=90)
 plt.text(23,2.5,"Mix1/ Mix2 = 4")
 
@@ -2133,7 +2133,7 @@ print('Number of ERCC detected in group A (out of 23) =', adf['Avg Mix1 CPM/ Avg
 
 ### Create box and whisker plots of the log(2) CPM for each ERCC detected in group B in Mix 1 and Mix 2 spiked samples
 
-b = sns.catplot(x="ERCC ID", y="log2 Count per million", order=groupB[::-1], hue="Mix", data=merged_ercc[merged_ercc['ERCC ID'].isin(groupB)], kind="box", col="ERCC group", height=5, aspect=1, palette=sns.color_palette(['blue', 'orange']))
+b = sns.catplot(x="ERCC ID", y="log2 Count per million", order=groupB[::-1], hue="Mix", data=merged_ercc[merged_ercc['ERCC ID'].isin(groupB)], kind="box", col="ERCC group", height=5, aspect=1, palette=sns.color_palette(['blue', 'orange']), showfliers=False)
 b.set_xticklabels(rotation=90)
 plt.text(23,2.5,"Mix1/ Mix2 = 1")
 
@@ -2149,7 +2149,7 @@ print('Number of ERCC detected in group B (out of 23) =', bdf['Avg Mix1 CPM/ Avg
 
 ### Create box and whisker plots of the log(2) CPM for each ERCC detected in group C in Mix 1 and Mix 2 spiked samples
 
-c = sns.catplot(x="ERCC ID", y="log2 Count per million", order=groupC[::-1], hue="Mix", data=merged_ercc[merged_ercc['ERCC ID'].isin(groupC)], kind="box", col="ERCC group", height=5, aspect=1, palette=sns.color_palette(['blue', 'orange']))
+c = sns.catplot(x="ERCC ID", y="log2 Count per million", order=groupC[::-1], hue="Mix", data=merged_ercc[merged_ercc['ERCC ID'].isin(groupC)], kind="box", col="ERCC group", height=5, aspect=1, palette=sns.color_palette(['blue', 'orange']), showfliers=False)
 c.set_xticklabels(rotation=90)
 plt.text(23,2.5,"Mix1/ Mix2 = 0.67")
 
@@ -2165,7 +2165,7 @@ print('Number of ERCC detected in group C (out of 23) =', cdf['Avg Mix1 CPM/ Avg
 
 ### Create box and whisker plots of the log(2) CPM for each ERCC detected in group D in Mix 1 and Mix 2 spiked samples
 
-d = sns.catplot(x="ERCC ID", y="log2 Count per million", order=groupD[::-1], hue="Mix", data=merged_ercc[merged_ercc['ERCC ID'].isin(groupD)], col="ERCC group", kind="box", height=5, aspect=1, palette=sns.color_palette(['blue', 'orange']))
+d = sns.catplot(x="ERCC ID", y="log2 Count per million", order=groupD[::-1], hue="Mix", data=merged_ercc[merged_ercc['ERCC ID'].isin(groupD)], col="ERCC group", kind="box", height=5, aspect=1, palette=sns.color_palette(['blue', 'orange']), showfliers=False)
 d.set_xticklabels(rotation=90)
 plt.text(23,2.5,"Mix1/ Mix2 = 0.5")
 

RNAseq/Workflow_Documentation/NF_RCP-F/workflow_code/bin/combined_ercc_analysis.ipynb

@@ -391,7 +391,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "a = sns.catplot(x=\"ERCC ID\", y=\"log2 Count per million\", order=groupA[::-1], hue=\"Mix\",data=merged_ercc[merged_ercc['ERCC ID'].isin(groupA)], kind=\"box\", col=\"ERCC group\", height=5, aspect=1, palette=sns.color_palette(['blue', 'orange']))\n",
+    "a = sns.catplot(x=\"ERCC ID\", y=\"log2 Count per million\", order=groupA[::-1], hue=\"Mix\",data=merged_ercc[merged_ercc['ERCC ID'].isin(groupA)], kind=\"box\", col=\"ERCC group\", height=5, aspect=1, palette=sns.color_palette(['blue', 'orange']), showfliers=False)\n",
     "a.set_xticklabels(rotation=90)\n",
     "plt.text(23,2.5,\"Mix1/ Mix2 = 4\")"
    ]
@@ -430,7 +430,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "b = sns.catplot(x=\"ERCC ID\", y=\"log2 Count per million\", order=groupB[::-1], hue=\"Mix\", data=merged_ercc[merged_ercc['ERCC ID'].isin(groupB)], kind=\"box\", col=\"ERCC group\", height=5, aspect=1, palette=sns.color_palette(['blue', 'orange']))\n",
+    "b = sns.catplot(x=\"ERCC ID\", y=\"log2 Count per million\", order=groupB[::-1], hue=\"Mix\", data=merged_ercc[merged_ercc['ERCC ID'].isin(groupB)], kind=\"box\", col=\"ERCC group\", height=5, aspect=1, palette=sns.color_palette(['blue', 'orange']), showfliers=False)\n",
     "b.set_xticklabels(rotation=90)\n",
     "plt.text(23,2.5,\"Mix1/ Mix2 = 1\")"
    ]
@@ -470,7 +470,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "c = sns.catplot(x=\"ERCC ID\", y=\"log2 Count per million\", order=groupC[::-1], hue=\"Mix\", data=merged_ercc[merged_ercc['ERCC ID'].isin(groupC)], kind=\"box\", col=\"ERCC group\", height=5, aspect=1, palette=sns.color_palette(['blue', 'orange']))\n",
+    "c = sns.catplot(x=\"ERCC ID\", y=\"log2 Count per million\", order=groupC[::-1], hue=\"Mix\", data=merged_ercc[merged_ercc['ERCC ID'].isin(groupC)], kind=\"box\", col=\"ERCC group\", height=5, aspect=1, palette=sns.color_palette(['blue', 'orange']), showfliers=False)\n",
     "c.set_xticklabels(rotation=90)\n",
     "plt.text(23,2.5,\"Mix1/ Mix2 = 0.67\")"
    ]
@@ -510,7 +510,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "d = sns.catplot(x=\"ERCC ID\", y=\"log2 Count per million\", order=groupD[::-1], hue=\"Mix\", data=merged_ercc[merged_ercc['ERCC ID'].isin(groupD)], col=\"ERCC group\", kind=\"box\", height=5, aspect=1, palette=sns.color_palette(['blue', 'orange']))\n",
+    "d = sns.catplot(x=\"ERCC ID\", y=\"log2 Count per million\", order=groupD[::-1], hue=\"Mix\", data=merged_ercc[merged_ercc['ERCC ID'].isin(groupD)], col=\"ERCC group\", kind=\"box\", height=5, aspect=1, palette=sns.color_palette(['blue', 'orange']), showfliers=False)\n",
     "d.set_xticklabels(rotation=90)\n",
     "plt.text(23,2.5,\"Mix1/ Mix2 = 0.5\")"
    ]

RNAseq/Workflow_Documentation/NF_RCP-F/workflow_code/config/software/by_docker_image.config

@@ -45,7 +45,7 @@ process {
         container = "quay.io/biocontainers/rsem:1.3.1--pl526r341h4f16992_0"
     }
 
-    withName: 'RUNSHEET_FROM_GLDS |GENERATE_MD5SUMS|UPDATE_ISA_TABLES|SOFTWARE_VERSIONS' {
+    withName: 'RUNSHEET_FROM_GLDS|GENERATE_MD5SUMS|UPDATE_ISA_TABLES|SOFTWARE_VERSIONS' {
         container = "quay.io/j_81/dp_tools:1.3.4"
     }