diff --git a/ctpop_plots/data/cell_locations_ctpop_VH_F_Kidney_L_0603.csv b/ctpop_plots/deprecated-data/cell_locations_ctpop_VH_F_Kidney_L_0603.csv similarity index 100% rename from ctpop_plots/data/cell_locations_ctpop_VH_F_Kidney_L_0603.csv rename to ctpop_plots/deprecated-data/cell_locations_ctpop_VH_F_Kidney_L_0603.csv diff --git a/ctpop_plots/data/old/cell_locations_ctpop_VH_F_Kidney_L.csv b/ctpop_plots/deprecated-data/old/cell_locations_ctpop_VH_F_Kidney_L.csv similarity index 100% rename from ctpop_plots/data/old/cell_locations_ctpop_VH_F_Kidney_L.csv rename to ctpop_plots/deprecated-data/old/cell_locations_ctpop_VH_F_Kidney_L.csv diff --git a/ctpop_plots/FigS6.png b/ctpop_plots/deprecated-exports/FigS6.png similarity index 100% rename from ctpop_plots/FigS6.png rename to ctpop_plots/deprecated-exports/FigS6.png diff --git a/ctpop_plots/as_bar_graphs.png b/ctpop_plots/deprecated-exports/as_bar_graphs.png similarity index 100% rename from ctpop_plots/as_bar_graphs.png rename to ctpop_plots/deprecated-exports/as_bar_graphs.png diff --git a/ctpop_plots/as_bar_graphs_log10.png b/ctpop_plots/deprecated-exports/as_bar_graphs_log10.png similarity index 100% rename from ctpop_plots/as_bar_graphs_log10.png rename to ctpop_plots/deprecated-exports/as_bar_graphs_log10.png diff --git a/ctpop_plots/as_ct_bar_graphs_log10.png b/ctpop_plots/deprecated-exports/as_ct_bar_graphs_log10.png similarity index 100% rename from ctpop_plots/as_ct_bar_graphs_log10.png rename to ctpop_plots/deprecated-exports/as_ct_bar_graphs_log10.png diff --git a/ctpop_plots/fig-4a.pdf b/ctpop_plots/deprecated-exports/fig-4a.pdf similarity index 100% rename from ctpop_plots/fig-4a.pdf rename to ctpop_plots/deprecated-exports/fig-4a.pdf diff --git a/ctpop_plots/fig3a.png b/ctpop_plots/deprecated-exports/fig3a.png similarity index 100% rename from ctpop_plots/fig3a.png rename to ctpop_plots/deprecated-exports/fig3a.png diff --git a/ctpop_plots/figure_3_a.png b/ctpop_plots/deprecated-exports/figure_3_a.png similarity index 100% rename from ctpop_plots/figure_3_a.png rename to ctpop_plots/deprecated-exports/figure_3_a.png diff --git a/ctpop_plots/figure_4_a.png b/ctpop_plots/deprecated-exports/figure_4_a.png similarity index 100% rename from ctpop_plots/figure_4_a.png rename to ctpop_plots/deprecated-exports/figure_4_a.png diff --git a/ctpop_plots/figure_4_bar_graph.png b/ctpop_plots/deprecated-exports/figure_4_bar_graph.png similarity index 100% rename from ctpop_plots/figure_4_bar_graph.png rename to ctpop_plots/deprecated-exports/figure_4_bar_graph.png diff --git a/ctpop_plots/figure_4_top10_bars_for_unity.jpg.png b/ctpop_plots/deprecated-exports/figure_4_top10_bars_for_unity.jpg.png similarity index 100% rename from ctpop_plots/figure_4_top10_bars_for_unity.jpg.png rename to ctpop_plots/deprecated-exports/figure_4_top10_bars_for_unity.jpg.png diff --git a/ctpop_plots/sankey.png b/ctpop_plots/deprecated-exports/sankey.png similarity index 100% rename from ctpop_plots/sankey.png rename to ctpop_plots/deprecated-exports/sankey.png diff --git a/ctpop_plots/DataPreparation.R b/ctpop_plots/deprecated-scripts/DataPreparation.R similarity index 100% rename from ctpop_plots/DataPreparation.R rename to ctpop_plots/deprecated-scripts/DataPreparation.R diff --git a/ctpop_plots/PlotsSlides.R b/ctpop_plots/deprecated-scripts/PlotsSlides.R similarity index 100% rename from ctpop_plots/PlotsSlides.R rename to ctpop_plots/deprecated-scripts/PlotsSlides.R diff --git a/ctpop_plots/ValidationPlots.R b/ctpop_plots/deprecated-scripts/ValidationPlots.R similarity index 100% rename from ctpop_plots/ValidationPlots.R rename to ctpop_plots/deprecated-scripts/ValidationPlots.R diff --git a/ctpop_plots/cosine_similarity.ipynb b/ctpop_plots/deprecated-scripts/cosine_similarity.ipynb similarity index 100% rename from ctpop_plots/cosine_similarity.ipynb rename to ctpop_plots/deprecated-scripts/cosine_similarity.ipynb diff --git a/ctpop_plots/validations.gephi b/ctpop_plots/deprecated-scripts/validations.gephi similarity index 100% rename from ctpop_plots/validations.gephi rename to ctpop_plots/deprecated-scripts/validations.gephi diff --git a/ctpop_plots/vicky_original_cosinesimilarity.ipynb b/ctpop_plots/deprecated-scripts/vicky_original_cosinesimilarity.ipynb similarity index 100% rename from ctpop_plots/vicky_original_cosinesimilarity.ipynb rename to ctpop_plots/deprecated-scripts/vicky_original_cosinesimilarity.ipynb