updated makefile and figures

Author: jkim810

.DS_Store

@@ -1,11 +1,12 @@
 
 data/*
 figures/*
+figures_backup/*
 images/*
 metadata/*
 documentation/*
 previous_code/*
 results/*
 processed/*
-
+scripts_backup/*
 

.gitignore

@@ -1,4 +1,4 @@
-.PHONY: download spatial celltype similarity utag diff_abundance pca patient
+.PHONY: download spatial celltype t_cell similarity utag diff_abundance pca patient
 
 download:
 	echo not implemented yet
@@ -7,6 +7,15 @@ download:
 celltype:
 	python scripts/celltype_heatmap_info.py
 
+diff_abundance:
+	python scripts/celltype_differential_abundance.py
+
+t_cell:
+	python scripts/t_cell_analysis.py
+
+pca:
+	python scripts/roi_pca_plot.py
+
 spatial:
 	python scripts/spatial_plot.py
 
@@ -17,13 +26,7 @@ similarity:
 	python scripts/sample_similarity.py
 
 utag:
-	python scripts/utag_ue.py
-
-diff_abundance:
-	python scripts/celltype_differential_abundance.py
-	
-pca:
-	python scripts/roi_pca_plot.py
+	python scripts/utag_ue.py	
 
 patient:
 	python scripts/create_patient_density_matrix.py