PTMMap relative paths

CNIC-Proteomics · Oct 24, 2024 · aa5e060 · aa5e060
1 parent ff4afb1
commit aa5e060
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Showing 3 changed files with 27 additions and 13 deletions.
diff --git a/2_ReportLimma_wo_GUI/app_wo_GUI.R b/2_ReportLimma_wo_GUI/app_wo_GUI.R
@@ -4,7 +4,7 @@ library("logging")
 library("yaml")
 
 # Get get arguments
-#configPath <- "D:\\ReportAnalysis\\test\\test7_Andrea\\2_ReportLimma_wo_GUI\\limma_params.yaml"
+# configPath <- "D:\\ReportAnalysis\\2_ReportLimma_wo_GUI\\test\\test4\\limma_params_HFpEF_01.yaml"
 args = commandArgs(trailingOnly=TRUE)
 configPath <- args[1]
 

diff --git a/4_qTableReport/qReportMaker.py b/4_qTableReport/qReportMaker.py
@@ -389,20 +389,26 @@ def qReportDesign(config, quan, qTableD, contrast):
         q2info.columns = pd.MultiIndex.from_tuples([qTableD.columns[0] if n==0 else (i,'','') for n,i in enumerate(q2info.columns)])
         qTableD = pd.merge(q2info, qTableD, how='right', on=[qTableD.columns[0]])
 
-    if config['plotFolder'] and os.path.exists(config['plotFolder'][0]):
+    if config['plotFolder']:# and os.path.exists(config['plotFolder'][0]):
         qTableD = qTableD[[qTableD.columns[0]]].rename(columns={'':'NoFilt'}).join(qTableD)
-        plotted_q = [os.path.splitext(i)[0] for i in os.listdir(config['plotFolder'][0])]
+
+        ptmMapPath = config['plotFolder'][0] if config['plotFolder'][0] else os.path.join(config['outfolder'], f'PTMMaps/{contrast}/plots')
+        plotted_q = [os.path.splitext(i)[0] for i in os.listdir(ptmMapPath)]
+
+        ptmMapPathExcel = config['plotFolder'][0] if config['plotFolder'][0] else f'../../../PTMMaps/{contrast}/plots'
         qTableD[qTableD.columns[0]] = \
-            [f"=HYPERLINK(\"{os.path.join(config['plotFolder'][0], i)}.html\", \"{i}\")" if i in plotted_q else '' if i=='Sum' else i for i in qTableD.iloc[:, 0]]
+            [f"=HYPERLINK(\"{os.path.join(ptmMapPathExcel, i)}.html\", \"{i}\")" if i in plotted_q else '' if i=='Sum' else i for i in qTableD.iloc[:, 0]]
 
-        if len(config['plotFolder'])>1 and os.path.exists(config['plotFolder'][1]):
+        if len(config['plotFolder'])>1: #and os.path.exists(config['plotFolder'][1]):
             qTableD = qTableD[[qTableD.columns[1]]].rename(columns={'':'Filt'}).join(qTableD)
-            plotted_q = [os.path.splitext(i)[0] for i in os.listdir(config['plotFolder'][1])]
+
+            ptmMapPath = config['plotFolder'][1] if config['plotFolder'][1] else os.path.join(config['outfolder'], f'PTMMaps/{contrast}/plots_FDR')
+            plotted_q = [os.path.splitext(i)[0] for i in os.listdir(ptmMapPath)]
+
+            ptmMapPathExcel = config['plotFolder'][1] if config['plotFolder'][1] else f'../../../PTMMaps/{contrast}/plots_FDR'
             qTableD[qTableD.columns[0]] = \
-                [f"=HYPERLINK(\"{os.path.join(config['plotFolder'][1], i)}.html\", \"{i}\")" if i in plotted_q else '' if i=='Sum' else i for i in qTableD.iloc[:, 0]]
+                [f"=HYPERLINK(\"{os.path.join(ptmMapPathExcel, i)}.html\", \"{i}\")" if i in plotted_q else '' if i=='Sum' else i for i in qTableD.iloc[:, 0]]
 
-
-
     return qTableD
 
 
@@ -451,8 +457,12 @@ def qReportMergeUpDown(params):
             df_out = pd.DataFrame()
             for col in dfup_wo.columns:
                 if 'sig' in col[1]:
-                    df_out[('up', *col)] = dfup_wo[col]
-                    df_out[('down', *col)] = dfdo_wo[col]
+                    if col[1] == 'NMsig':
+                        df_out[('up (NM decreased)', *col)] = dfup_wo[col]
+                        df_out[('down (NM increased)', *col)] = dfdo_wo[col]
+                    else:
+                        df_out[('up', *col)] = dfup_wo[col]
+                        df_out[('down', *col)] = dfdo_wo[col]
                 elif 'Hypergeom' in col[0]:
                     df_out[('up', *col)] = dfup_wo[col]
                     df_out[('down', *col)] = dfdo_wo[col]

diff --git a/4_qTableReport/qReportMaker.yaml b/4_qTableReport/qReportMaker.yaml
@@ -178,9 +178,13 @@ values_pivot: x-PSM
 # Plot path: Path to the folder containing Cristina Plots
 # - /Path/to/CompletePlot
 # - /Path/to/FilteredPlot
+
+# Leave it blank to use default folder:
+#   - [outfolder]/PTMMaps/{groups}/plots
+#   - [outfolder]/PTMMaps/{groups}/plots_FDR
 plotFolder: 
-    - D:\CNIC\Scripts\ReportStats\test\Plots
-    - D:\CNIC\Scripts\ReportStats\test\Plots_FDR
+    - 
+    - 
 
 n_cpu: 8