Revert "Repo restructure"

This reverts commit 4f186c9.
DataINCITE · Oct 24, 2022 · 2e9293a6664ceed4f1c42e8964de0f3a67411577 · 2e9293a
1 parent c1b03a5
commit 2e9293a6664ceed4f1c42e8964de0f3a67411577
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Showing 111 changed files with 37 additions and 825 deletions.
diff --git a/data/cellchat/CellChatDB.csv → CellChatDB.csv b/data/cellchat/CellChatDB.csv → CellChatDB.csv
diff --git a/...ression/DEgenes_MtvsWt_2mo_6celltypes.rds → DEgenes_MtvsWt_2mo_6celltypes.rds b/...ression/DEgenes_MtvsWt_2mo_6celltypes.rds → DEgenes_MtvsWt_2mo_6celltypes.rds
diff --git a/...on/DEgenes_MtvsWt_2mo_other8celltypes.rds → DEgenes_MtvsWt_2mo_other8celltypes.rds b/...on/DEgenes_MtvsWt_2mo_other8celltypes.rds → DEgenes_MtvsWt_2mo_other8celltypes.rds
diff --git a/...ssion/DEgenes_MtvsWt_4mo_allcelltypes.rds → DEgenes_MtvsWt_4mo_allcelltypes.rds b/...ssion/DEgenes_MtvsWt_4mo_allcelltypes.rds → DEgenes_MtvsWt_4mo_allcelltypes.rds
diff --git a/...ression/DEgenes_MtvsWt_6mo_6celltypes.rds → DEgenes_MtvsWt_6mo_6celltypes.rds b/...ression/DEgenes_MtvsWt_6mo_6celltypes.rds → DEgenes_MtvsWt_6mo_6celltypes.rds
diff --git a/...on/DEgenes_MtvsWt_6mo_other8celltypes.rds → DEgenes_MtvsWt_6mo_other8celltypes.rds b/...on/DEgenes_MtvsWt_6mo_other8celltypes.rds → DEgenes_MtvsWt_6mo_other8celltypes.rds
diff --git a/...ial-expression/DEgenes_MtvsWt_Ast_2mo.rds → DEgenes_MtvsWt_Ast_2mo.rds b/...ial-expression/DEgenes_MtvsWt_Ast_2mo.rds → DEgenes_MtvsWt_Ast_2mo.rds
diff --git a/...ial-expression/DEgenes_MtvsWt_Ast_6mo.rds → DEgenes_MtvsWt_Ast_6mo.rds b/...ial-expression/DEgenes_MtvsWt_Ast_6mo.rds → DEgenes_MtvsWt_Ast_6mo.rds
diff --git a/...l-expression/DEgenes_MtvsWt_ExDp1_2mo.rds → DEgenes_MtvsWt_ExDp1_2mo.rds b/...l-expression/DEgenes_MtvsWt_ExDp1_2mo.rds → DEgenes_MtvsWt_ExDp1_2mo.rds
diff --git a/...l-expression/DEgenes_MtvsWt_ExDp1_6mo.rds → DEgenes_MtvsWt_ExDp1_6mo.rds b/...l-expression/DEgenes_MtvsWt_ExDp1_6mo.rds → DEgenes_MtvsWt_ExDp1_6mo.rds
diff --git a/...l-expression/DEgenes_MtvsWt_ExDp2_2mo.rds → DEgenes_MtvsWt_ExDp2_2mo.rds b/...l-expression/DEgenes_MtvsWt_ExDp2_2mo.rds → DEgenes_MtvsWt_ExDp2_2mo.rds
diff --git a/...l-expression/DEgenes_MtvsWt_ExDp2_6mo.rds → DEgenes_MtvsWt_ExDp2_6mo.rds b/...l-expression/DEgenes_MtvsWt_ExDp2_6mo.rds → DEgenes_MtvsWt_ExDp2_6mo.rds
diff --git a/...l-expression/DEgenes_MtvsWt_ExM-U_2mo.rds → DEgenes_MtvsWt_ExM-U_2mo.rds b/...l-expression/DEgenes_MtvsWt_ExM-U_2mo.rds → DEgenes_MtvsWt_ExM-U_2mo.rds
diff --git a/...l-expression/DEgenes_MtvsWt_ExM-U_6mo.rds → DEgenes_MtvsWt_ExM-U_6mo.rds b/...l-expression/DEgenes_MtvsWt_ExM-U_6mo.rds → DEgenes_MtvsWt_ExM-U_6mo.rds
diff --git a/...ial-expression/DEgenes_MtvsWt_ExM_2mo.rds → DEgenes_MtvsWt_ExM_2mo.rds b/...ial-expression/DEgenes_MtvsWt_ExM_2mo.rds → DEgenes_MtvsWt_ExM_2mo.rds
diff --git a/...ial-expression/DEgenes_MtvsWt_ExM_6mo.rds → DEgenes_MtvsWt_ExM_6mo.rds b/...ial-expression/DEgenes_MtvsWt_ExM_6mo.rds → DEgenes_MtvsWt_ExM_6mo.rds
diff --git a/...ial-expression/DEgenes_MtvsWt_ExN_2mo.rds → DEgenes_MtvsWt_ExN_2mo.rds b/...ial-expression/DEgenes_MtvsWt_ExN_2mo.rds → DEgenes_MtvsWt_ExN_2mo.rds
diff --git a/...ial-expression/DEgenes_MtvsWt_ExN_6mo.rds → DEgenes_MtvsWt_ExN_6mo.rds b/...ial-expression/DEgenes_MtvsWt_ExN_6mo.rds → DEgenes_MtvsWt_ExN_6mo.rds
diff --git a/...tial-expression/DEgenes_MtvsWt_IP_2mo.rds → DEgenes_MtvsWt_IP_2mo.rds b/...tial-expression/DEgenes_MtvsWt_IP_2mo.rds → DEgenes_MtvsWt_IP_2mo.rds
diff --git a/...tial-expression/DEgenes_MtvsWt_IP_6mo.rds → DEgenes_MtvsWt_IP_6mo.rds b/...tial-expression/DEgenes_MtvsWt_IP_6mo.rds → DEgenes_MtvsWt_IP_6mo.rds
diff --git a/...l-expression/DEgenes_MtvsWt_InCGE_2mo.rds → DEgenes_MtvsWt_InCGE_2mo.rds b/...l-expression/DEgenes_MtvsWt_InCGE_2mo.rds → DEgenes_MtvsWt_InCGE_2mo.rds
diff --git a/...l-expression/DEgenes_MtvsWt_InCGE_6mo.rds → DEgenes_MtvsWt_InCGE_6mo.rds b/...l-expression/DEgenes_MtvsWt_InCGE_6mo.rds → DEgenes_MtvsWt_InCGE_6mo.rds
diff --git a/...l-expression/DEgenes_MtvsWt_InMGE_2mo.rds → DEgenes_MtvsWt_InMGE_2mo.rds b/...l-expression/DEgenes_MtvsWt_InMGE_2mo.rds → DEgenes_MtvsWt_InMGE_2mo.rds
diff --git a/...l-expression/DEgenes_MtvsWt_InMGE_6mo.rds → DEgenes_MtvsWt_InMGE_6mo.rds b/...l-expression/DEgenes_MtvsWt_InMGE_6mo.rds → DEgenes_MtvsWt_InMGE_6mo.rds
diff --git a/...ial-expression/DEgenes_MtvsWt_OPC_2mo.rds → DEgenes_MtvsWt_OPC_2mo.rds b/...ial-expression/DEgenes_MtvsWt_OPC_2mo.rds → DEgenes_MtvsWt_OPC_2mo.rds
diff --git a/...ial-expression/DEgenes_MtvsWt_OPC_6mo.rds → DEgenes_MtvsWt_OPC_6mo.rds b/...ial-expression/DEgenes_MtvsWt_OPC_6mo.rds → DEgenes_MtvsWt_OPC_6mo.rds
diff --git a/...l-expression/DEgenes_MtvsWt_PgG2M_2mo.rds → DEgenes_MtvsWt_PgG2M_2mo.rds b/...l-expression/DEgenes_MtvsWt_PgG2M_2mo.rds → DEgenes_MtvsWt_PgG2M_2mo.rds
diff --git a/...l-expression/DEgenes_MtvsWt_PgG2M_6mo.rds → DEgenes_MtvsWt_PgG2M_6mo.rds b/...l-expression/DEgenes_MtvsWt_PgG2M_6mo.rds → DEgenes_MtvsWt_PgG2M_6mo.rds
diff --git a/...ial-expression/DEgenes_MtvsWt_PgS_2mo.rds → DEgenes_MtvsWt_PgS_2mo.rds b/...ial-expression/DEgenes_MtvsWt_PgS_2mo.rds → DEgenes_MtvsWt_PgS_2mo.rds
diff --git a/...ial-expression/DEgenes_MtvsWt_PgS_6mo.rds → DEgenes_MtvsWt_PgS_6mo.rds b/...ial-expression/DEgenes_MtvsWt_PgS_6mo.rds → DEgenes_MtvsWt_PgS_6mo.rds
diff --git a/...Egenes_MtvsWt_alltimepts_allcelltypes.csv → DEgenes_MtvsWt_alltimepts_allcelltypes.csv b/...Egenes_MtvsWt_alltimepts_allcelltypes.csv → DEgenes_MtvsWt_alltimepts_allcelltypes.csv
diff --git a/...ial-expression/DEgenes_MtvsWt_oRG_2mo.rds → DEgenes_MtvsWt_oRG_2mo.rds b/...ial-expression/DEgenes_MtvsWt_oRG_2mo.rds → DEgenes_MtvsWt_oRG_2mo.rds
diff --git a/...ial-expression/DEgenes_MtvsWt_oRG_6mo.rds → DEgenes_MtvsWt_oRG_6mo.rds b/...ial-expression/DEgenes_MtvsWt_oRG_6mo.rds → DEgenes_MtvsWt_oRG_6mo.rds
diff --git a/...ial-expression/DEgenes_MtvsWt_vRG_2mo.rds → DEgenes_MtvsWt_vRG_2mo.rds b/...ial-expression/DEgenes_MtvsWt_vRG_2mo.rds → DEgenes_MtvsWt_vRG_2mo.rds
diff --git a/...ial-expression/DEgenes_MtvsWt_vRG_6mo.rds → DEgenes_MtvsWt_vRG_6mo.rds b/...ial-expression/DEgenes_MtvsWt_vRG_6mo.rds → DEgenes_MtvsWt_vRG_6mo.rds
diff --git a/...istributions/FetchDataOutput-AllCells.rds → FetchDataOutput-AllCells.rds b/...istributions/FetchDataOutput-AllCells.rds → FetchDataOutput-AllCells.rds
diff --git a/data/raw/FinalMergedData-downsampled.rds → FinalMergedData-downsampled.rds b/data/raw/FinalMergedData-downsampled.rds → FinalMergedData-downsampled.rds
diff --git a/...rgedData_linesG6A02-G6E11_all_timepts.rds → ...rgedData_linesG6A02-G6E11_all_timepts.rds b/...rgedData_linesG6A02-G6E11_all_timepts.rds → ...rgedData_linesG6A02-G6E11_all_timepts.rds
diff --git a/R/plot_generation.R b/R/plot_generation.R
diff --git a/R/utilities.R b/R/utilities.R
diff --git a/...ne-enrichment/REVIGO_reducedTerms_Ast.rds → REVIGO_reducedTerms_Ast.rds b/...ne-enrichment/REVIGO_reducedTerms_Ast.rds → REVIGO_reducedTerms_Ast.rds
diff --git a/...chment/REVIGO_reducedTerms_Astrocytes.rds → REVIGO_reducedTerms_Astrocytes.rds b/...chment/REVIGO_reducedTerms_Astrocytes.rds → REVIGO_reducedTerms_Astrocytes.rds
diff --git a/...-enrichment/REVIGO_reducedTerms_ExDp1.rds → REVIGO_reducedTerms_ExDp1.rds b/...-enrichment/REVIGO_reducedTerms_ExDp1.rds → REVIGO_reducedTerms_ExDp1.rds
diff --git a/...-enrichment/REVIGO_reducedTerms_ExDp2.rds → REVIGO_reducedTerms_ExDp2.rds b/...-enrichment/REVIGO_reducedTerms_ExDp2.rds → REVIGO_reducedTerms_ExDp2.rds
diff --git a/...ne-enrichment/REVIGO_reducedTerms_ExM.rds → REVIGO_reducedTerms_ExM.rds b/...ne-enrichment/REVIGO_reducedTerms_ExM.rds → REVIGO_reducedTerms_ExM.rds
diff --git a/...ne-enrichment/REVIGO_reducedTerms_ExN.rds → REVIGO_reducedTerms_ExN.rds b/...ne-enrichment/REVIGO_reducedTerms_ExN.rds → REVIGO_reducedTerms_ExN.rds
diff --git a/...ene-enrichment/REVIGO_reducedTerms_IP.rds → REVIGO_reducedTerms_IP.rds b/...ene-enrichment/REVIGO_reducedTerms_IP.rds → REVIGO_reducedTerms_IP.rds
diff --git a/...-enrichment/REVIGO_reducedTerms_InCGE.rds → REVIGO_reducedTerms_InCGE.rds b/...-enrichment/REVIGO_reducedTerms_InCGE.rds → REVIGO_reducedTerms_InCGE.rds
diff --git a/...-enrichment/REVIGO_reducedTerms_InMGE.rds → REVIGO_reducedTerms_InMGE.rds b/...-enrichment/REVIGO_reducedTerms_InMGE.rds → REVIGO_reducedTerms_InMGE.rds
diff --git a/...ne-enrichment/REVIGO_reducedTerms_OPC.rds → REVIGO_reducedTerms_OPC.rds b/...ne-enrichment/REVIGO_reducedTerms_OPC.rds → REVIGO_reducedTerms_OPC.rds
diff --git a/...-enrichment/REVIGO_reducedTerms_PgG2M.rds → REVIGO_reducedTerms_PgG2M.rds b/...-enrichment/REVIGO_reducedTerms_PgG2M.rds → REVIGO_reducedTerms_PgG2M.rds
diff --git a/...ne-enrichment/REVIGO_reducedTerms_PgS.rds → REVIGO_reducedTerms_PgS.rds b/...ne-enrichment/REVIGO_reducedTerms_PgS.rds → REVIGO_reducedTerms_PgS.rds
diff --git a/...ne-enrichment/REVIGO_reducedTerms_oRG.rds → REVIGO_reducedTerms_oRG.rds b/...ne-enrichment/REVIGO_reducedTerms_oRG.rds → REVIGO_reducedTerms_oRG.rds
diff --git a/...ne-enrichment/REVIGO_reducedTerms_vRG.rds → REVIGO_reducedTerms_vRG.rds b/...ne-enrichment/REVIGO_reducedTerms_vRG.rds → REVIGO_reducedTerms_vRG.rds
diff --git a/...-gene-enrichment/REVIGO_simMatrix_Ast.rds → REVIGO_simMatrix_Ast.rds b/...-gene-enrichment/REVIGO_simMatrix_Ast.rds → REVIGO_simMatrix_Ast.rds
diff --git a/...nrichment/REVIGO_simMatrix_Astrocytes.rds → REVIGO_simMatrix_Astrocytes.rds b/...nrichment/REVIGO_simMatrix_Astrocytes.rds → REVIGO_simMatrix_Astrocytes.rds
diff --git a/...ene-enrichment/REVIGO_simMatrix_ExDp1.rds → REVIGO_simMatrix_ExDp1.rds b/...ene-enrichment/REVIGO_simMatrix_ExDp1.rds → REVIGO_simMatrix_ExDp1.rds
diff --git a/...ene-enrichment/REVIGO_simMatrix_ExDp2.rds → REVIGO_simMatrix_ExDp2.rds b/...ene-enrichment/REVIGO_simMatrix_ExDp2.rds → REVIGO_simMatrix_ExDp2.rds
diff --git a/...-gene-enrichment/REVIGO_simMatrix_ExM.rds → REVIGO_simMatrix_ExM.rds b/...-gene-enrichment/REVIGO_simMatrix_ExM.rds → REVIGO_simMatrix_ExM.rds
diff --git a/...-gene-enrichment/REVIGO_simMatrix_ExN.rds → REVIGO_simMatrix_ExN.rds b/...-gene-enrichment/REVIGO_simMatrix_ExN.rds → REVIGO_simMatrix_ExN.rds
diff --git a/...p-gene-enrichment/REVIGO_simMatrix_IP.rds → REVIGO_simMatrix_IP.rds b/...p-gene-enrichment/REVIGO_simMatrix_IP.rds → REVIGO_simMatrix_IP.rds
diff --git a/...ene-enrichment/REVIGO_simMatrix_InCGE.rds → REVIGO_simMatrix_InCGE.rds b/...ene-enrichment/REVIGO_simMatrix_InCGE.rds → REVIGO_simMatrix_InCGE.rds
diff --git a/...ene-enrichment/REVIGO_simMatrix_InMGE.rds → REVIGO_simMatrix_InMGE.rds b/...ene-enrichment/REVIGO_simMatrix_InMGE.rds → REVIGO_simMatrix_InMGE.rds
diff --git a/...-gene-enrichment/REVIGO_simMatrix_OPC.rds → REVIGO_simMatrix_OPC.rds b/...-gene-enrichment/REVIGO_simMatrix_OPC.rds → REVIGO_simMatrix_OPC.rds
diff --git a/...ene-enrichment/REVIGO_simMatrix_PgG2M.rds → REVIGO_simMatrix_PgG2M.rds b/...ene-enrichment/REVIGO_simMatrix_PgG2M.rds → REVIGO_simMatrix_PgG2M.rds
diff --git a/...-gene-enrichment/REVIGO_simMatrix_PgS.rds → REVIGO_simMatrix_PgS.rds b/...-gene-enrichment/REVIGO_simMatrix_PgS.rds → REVIGO_simMatrix_PgS.rds
diff --git a/...-gene-enrichment/REVIGO_simMatrix_oRG.rds → REVIGO_simMatrix_oRG.rds b/...-gene-enrichment/REVIGO_simMatrix_oRG.rds → REVIGO_simMatrix_oRG.rds
diff --git a/...-gene-enrichment/REVIGO_simMatrix_vRG.rds → REVIGO_simMatrix_vRG.rds b/...-gene-enrichment/REVIGO_simMatrix_vRG.rds → REVIGO_simMatrix_vRG.rds
diff --git a/data/cellchat/adjacency_matrix_2m.csv → adjacency_matrix_2m.csv b/data/cellchat/adjacency_matrix_2m.csv → adjacency_matrix_2m.csv
diff --git a/data/cellchat/adjacency_matrix_2v.csv → adjacency_matrix_2v.csv b/data/cellchat/adjacency_matrix_2v.csv → adjacency_matrix_2v.csv
diff --git a/data/cellchat/adjacency_matrix_4m.csv → adjacency_matrix_4m.csv b/data/cellchat/adjacency_matrix_4m.csv → adjacency_matrix_4m.csv
diff --git a/data/cellchat/adjacency_matrix_4v.csv → adjacency_matrix_4v.csv b/data/cellchat/adjacency_matrix_4v.csv → adjacency_matrix_4v.csv
diff --git a/data/cellchat/adjacency_matrix_6m.csv → adjacency_matrix_6m.csv b/data/cellchat/adjacency_matrix_6m.csv → adjacency_matrix_6m.csv
diff --git a/data/cellchat/adjacency_matrix_6v.csv → adjacency_matrix_6v.csv b/data/cellchat/adjacency_matrix_6v.csv → adjacency_matrix_6v.csv
diff --git a/app.R b/app.R
@@ -333,19 +333,19 @@ DotPlot_mod <- function(
 
 
 # full dataset for all other app features
-seurat.all <- readRDS("data/raw/FinalMergedData-downsampled.rds")
+seurat.all <- readRDS("FinalMergedData-downsampled.rds")
 # Switch active identities to cell type labels for plotting
 Idents(seurat.all) <- "CellType"
 
 # Data for main panel 1 bar graph
-celltype_data_with_codes <- readRDS("data/overall-distributions/FetchDataOutput-AllCells.rds") %>% relocate(CellType)
-celltype_props <- readRDS("data/overall-distributions/overall_celltype_props_data.rds")
+celltype_data_with_codes <- readRDS("FetchDataOutput-AllCells.rds") %>% relocate(CellType)
+celltype_props <- readRDS("overall_celltype_props_data.rds")
 
 # Average expression data for Gene Explorer Tab 2 line plots
-res_combined_ann <- readRDS("data/genewise-avgexp-percentexp/average_expression_allcelltypes_timepoints_mtvswt_withpvals.rds")
+res_combined_ann <- readRDS("average_expression_allcelltypes_timepoints_mtvswt_withpvals.rds")
 
 # Marker gene statistics for CellType Explorer Tab 3
-data <- read.csv("data/differential-expression/DEgenes_MtvsWt_alltimepts_allcelltypes.csv")
+data <- read.csv("DEgenes_MtvsWt_alltimepts_allcelltypes.csv")
 
 
 # convert cell type codes to real names
@@ -391,48 +391,48 @@ cLinesList <- c(levels(as.factor(seurat.all$Line)),"All")
 
 # cell-cell communication data
 #cellchat <- readRDS("cellchat.rds")
-cellchat_2m <- readRDS("data/cellchat/cellchat_2M.rds")
-cellchat_2v <- readRDS("data/cellchat/cellchat_2V.rds")
-cellchat_4m <- readRDS("data/cellchat/cellchat_4M.rds")
-cellchat_4v <- readRDS("data/cellchat/cellchat_4V.rds")
-cellchat_6m <- readRDS("data/cellchat/cellchat_6M.rds")
-cellchat_6v <- readRDS("data/cellchat/cellchat_6V.rds")
+cellchat_2m <- readRDS("cellchat_2M.rds")
+cellchat_2v <- readRDS("cellchat_2V.rds")
+cellchat_4m <- readRDS("cellchat_4M.rds")
+cellchat_4v <- readRDS("cellchat_4V.rds")
+cellchat_6m <- readRDS("cellchat_6M.rds")
+cellchat_6v <- readRDS("cellchat_6V.rds")
 
 # cell net pathway data
 #net_df <- read.csv(file = 'net_pathway.csv')
 #net_df$prob <- format(net_df$prob, scientific = TRUE)
 #colnames(net_df) <- c("X", "source", "target", "pathway", "prob", "pval")
 
-net_pathway_2m <- read.csv(file = 'data/cellchat/net_pathway_2m.csv')
+net_pathway_2m <- read.csv(file = 'net_pathway_2m.csv')
 net_pathway_2m$prob <- format(net_pathway_2m$prob, scientific = TRUE)
 colnames(net_pathway_2m) <- c("X", "source", "target", "pathway", "prob", "pval")
 
-net_pathway_2v <- read.csv(file = 'data/cellchat/net_pathway_2v.csv')
+net_pathway_2v <- read.csv(file = 'net_pathway_2v.csv')
 net_pathway_2v$prob <- format(net_pathway_2v$prob, scientific = TRUE)
 colnames(net_pathway_2v) <- c("X", "source", "target", "pathway", "prob", "pval")
 
-net_pathway_4m <- read.csv(file = 'data/cellchat/net_pathway_4m.csv')
+net_pathway_4m <- read.csv(file = 'net_pathway_4m.csv')
 net_pathway_4m$prob <- format(net_pathway_4m$prob, scientific = TRUE)
 colnames(net_pathway_4m) <- c("X", "source", "target", "pathway", "prob", "pval")
 
-net_pathway_4v <- read.csv(file = 'data/cellchat/net_pathway_4v.csv')
+net_pathway_4v <- read.csv(file = 'net_pathway_4v.csv')
 net_pathway_4v$prob <- format(net_pathway_4v$prob, scientific = TRUE)
 colnames(net_pathway_4v) <- c("X", "source", "target", "pathway", "prob", "pval")
 
-net_pathway_6m <- read.csv(file = 'data/cellchat/net_pathway_6m.csv')
+net_pathway_6m <- read.csv(file = 'net_pathway_6m.csv')
 net_pathway_6m$prob <- format(net_pathway_6m$prob, scientific = TRUE)
 colnames(net_pathway_6m) <- c("X", "source", "target", "pathway", "prob", "pval")
 
-net_pathway_6v <- read.csv(file = 'data/cellchat/net_pathway_6v.csv')
+net_pathway_6v <- read.csv(file = 'net_pathway_6v.csv')
 net_pathway_6v$prob <- format(net_pathway_6v$prob, scientific = TRUE)
 colnames(net_pathway_6v) <- c("X", "source", "target", "pathway", "prob", "pval")
 
 # cell pathway names
 #choices <- cellchat@netP$pathways
-pathway_op <- read.csv(file = 'data/cellchat/pathway_choices.csv')
+pathway_op <- read.csv(file = 'pathway_choices.csv')
 
 # signaling pathway annotation
-CellChatDB <- read.csv(file = 'data/cellchat/CellChatDB.csv')
+CellChatDB <- read.csv(file = 'CellChatDB.csv')
 
 # comparative analysis of ccc conditions
 ccc_comparsion_List <- c("tau-V337M organoids at two months", 
@@ -1934,7 +1934,7 @@ server <- function(input, output, session) {
         ct_select <- input$celltype
         ct_code <- ctcode_map[[ct_select]]
 
-        ct_data_to_show <- readRDS(sprintf("data/cell-group-gene-enrichment/celltype_marker_genes_%s.rds",ct_code))
+        ct_data_to_show <- readRDS(sprintf("celltype_marker_genes_%s.rds",ct_code))
         showdata <- tibble::rownames_to_column(ct_data_to_show, "Gene")
         showdata <- showdata %>% dplyr::select(Gene,avg_log2FC,p_val)
         showdata
@@ -1947,7 +1947,7 @@ server <- function(input, output, session) {
 
 
         # File read-in must be here because data depends on a reactive input value
-        reducedTerms <- readRDS(sprintf("data/cell-group-gene-enrichment/REVIGO_reducedTerms_%s.rds",ct_code))
+        reducedTerms <- readRDS(sprintf("REVIGO_reducedTerms_%s.rds",ct_code))
         # treemapPlot(reducedTerms,title=sprintf("Summary of enriched Gene Ontology terms in %s cells, all timepoints.",ct_code),
         #         fontsize.title=10)
         treemapPlot(reducedTerms)
@@ -2554,8 +2554,8 @@ server <- function(input, output, session) {
       req(input$condition_1, input$condition_2)
       cond_1 <- setCCCNames(input$condition_1)
       cond_2 <- setCCCNames(input$condition_2)
-      my_data_1 <- readRDS(sprintf("data/cellchat/cellchat_%s%s.rds",str_extract_all(cond_1, "[0-9]+"), str_extract_all(cond_1, "[aA-zZ]+")))
-      file_names <- paste0('data/cellchat/cellchat_', cond_2, '.rds')
+      my_data_1 <- readRDS(sprintf("cellchat_%s%s.rds",str_extract_all(cond_1, "[0-9]+"), str_extract_all(cond_1, "[aA-zZ]+")))
+      file_names <- paste0('cellchat_', cond_2, '.rds')
       my_data_2 <- readRDS(file_names)
       #my_data_2 <- readRDS(sprintf("cellchat_%s%s.rds",str_extract_all(cond_2, "[0-9]+"), str_extract_all(cond_2, "[aA-zZ]+")))
       name_1 <- as.character(input$condition_1)
@@ -2572,8 +2572,8 @@ server <- function(input, output, session) {
       req(input$condition_1, input$condition_2)
       cond_1 <- setCCCNames(input$condition_1)
       cond_2 <- setCCCNames(input$condition_2)
-      my_data_1 <- readRDS(sprintf("data/cellchat/cellchat_%s%s.rds",str_extract_all(cond_1, "[0-9]+"), str_extract_all(cond_1, "[aA-zZ]+")))
-      file_names <- paste0('data/cellchat/cellchat_', cond_2, '.rds')
+      my_data_1 <- readRDS(sprintf("cellchat_%s%s.rds",str_extract_all(cond_1, "[0-9]+"), str_extract_all(cond_1, "[aA-zZ]+")))
+      file_names <- paste0('cellchat_', cond_2, '.rds')
       my_data_2 <- readRDS(file_names)
       #my_data_2 <- readRDS(sprintf("cellchat_%s%s.rds",str_extract_all(cond_2, "[0-9]+"), str_extract_all(cond_2, "[aA-zZ]+")))
       name_1 <- as.character(input$condition_1)
@@ -2608,10 +2608,10 @@ server <- function(input, output, session) {
       req(input$condition_1, input$condition_2)
       cond_1 <- setCCCNames(input$condition_1)
       cond_2 <- setCCCNames(input$condition_2)
-      my_data_1 <- readRDS(sprintf("data/cellchat/cellchat_%s%s.rds",str_extract_all(cond_1, "[0-9]+"), str_extract_all(cond_1, "[aA-zZ]+")))
+      my_data_1 <- readRDS(sprintf("cellchat_%s%s.rds",str_extract_all(cond_1, "[0-9]+"), str_extract_all(cond_1, "[aA-zZ]+")))
       #my_data_2 <- readRDS(sprintf("cellchat_%s%s.rds",str_extract_all(cond_2, "[0-9]+"), str_extract_all(cond_2, "[aA-zZ]+")))
       if (cond_2 == "2M") {
-        my_data_2 <- readRDS("data/cellchat/cellchat_2M.rds")
+        my_data_2 <- readRDS("cellchat_2M.rds")
         name_1 <- as.character(input$condition_1)
         name_2 <- as.character(input$condition_2)
         object.list <- dplyr::lst(!!name_1 := my_data_1, !!name_2 := my_data_2)
@@ -2628,7 +2628,7 @@ server <- function(input, output, session) {
         }
       }
       if (cond_2 == "2V") {
-        my_data_2 <- readRDS("data/cellchat/cellchat_2V.rds")
+        my_data_2 <- readRDS("cellchat_2V.rds")
         name_1 <- as.character(input$condition_1)
         name_2 <- as.character(input$condition_2)
         object.list <- dplyr::lst(!!name_1 := my_data_1, !!name_2 := my_data_2)
@@ -2645,7 +2645,7 @@ server <- function(input, output, session) {
         }
       }
       if (cond_2 == "4M") {
-        my_data_2 <- readRDS("data/cellchat/cellchat_4M.rds")
+        my_data_2 <- readRDS("cellchat_4M.rds")
         name_1 <- as.character(input$condition_1)
         name_2 <- as.character(input$condition_2)
         object.list <- dplyr::lst(!!name_1 := my_data_1, !!name_2 := my_data_2)
@@ -2662,7 +2662,7 @@ server <- function(input, output, session) {
         }
       }
       if (cond_2 == "4V") {
-        my_data_2 <- readRDS("data/cellchat/cellchat_4V.rds")
+        my_data_2 <- readRDS("cellchat_4V.rds")
         name_1 <- as.character(input$condition_1)
         name_2 <- as.character(input$condition_2)
         object.list <- dplyr::lst(!!name_1 := my_data_1, !!name_2 := my_data_2)
@@ -2679,7 +2679,7 @@ server <- function(input, output, session) {
         }
       }
       if (cond_2 == "6M") {
-        my_data_2 <- readRDS("data/cellchat/cellchat_6M.rds")
+        my_data_2 <- readRDS("cellchat_6M.rds")
         name_1 <- as.character(input$condition_1)
         name_2 <- as.character(input$condition_2)
         object.list <- dplyr::lst(!!name_1 := my_data_1, !!name_2 := my_data_2)
@@ -2696,7 +2696,7 @@ server <- function(input, output, session) {
         }
       }
       if (cond_2 == "6V") {
-        my_data_2 <- readRDS("data/cellchat/cellchat_6V.rds")
+        my_data_2 <- readRDS("cellchat_6V.rds")
         name_1 <- as.character(input$condition_1)
         name_2 <- as.character(input$condition_2)
         object.list <- dplyr::lst(!!name_1 := my_data_1, !!name_2 := my_data_2)
@@ -2733,8 +2733,8 @@ server <- function(input, output, session) {
       req(input$condition_1, input$condition_2)
       cond_1 <- setCCCNames(input$condition_1)
       cond_2 <- setCCCNames(input$condition_2)
-      my_data_1 <- readRDS(sprintf("data/cellchat/cellchat_%s%s.rds",str_extract_all(cond_1, "[0-9]+"), str_extract_all(cond_1, "[aA-zZ]+")))
-      file_names <- paste0('data/cellchat/cellchat_', cond_2, '.rds')
+      my_data_1 <- readRDS(sprintf("cellchat_%s%s.rds",str_extract_all(cond_1, "[0-9]+"), str_extract_all(cond_1, "[aA-zZ]+")))
+      file_names <- paste0('cellchat_', cond_2, '.rds')
       my_data_2 <- readRDS(file_names)
       #my_data_2 <- readRDS(sprintf("cellchat_%s%s.rds",str_extract_all(cond_2, "[0-9]+"), str_extract_all(cond_2, "[aA-zZ]+")))
       name_1 <- as.character(input$condition_1)
@@ -2793,7 +2793,7 @@ server <- function(input, output, session) {
 
     output$VolcanoPlots <- renderPlotly({
       if(input$ct != "All") {
-        allcelltype_data <- read.csv("data/differential-expression/DEgenes_MtvsWt_alltimepts_allcelltypes.csv")
+        allcelltype_data <- read.csv("DEgenes_MtvsWt_alltimepts_allcelltypes.csv")
         celltype_data <- allcelltype_data[allcelltype_data$celltype == input$ct,]
         if(input$time == "All") {
           df_all <- celltype_data %>% 
@@ -2824,7 +2824,7 @@ server <- function(input, output, session) {
 
     output$manhattanplot <- renderPlotly({
       if(input$ct != "All") {
-        allcelltype_data <- read.csv("data/differential-expression/DEgenes_MtvsWt_alltimepts_allcelltypes.csv")
+        allcelltype_data <- read.csv("DEgenes_MtvsWt_alltimepts_allcelltypes.csv")
         celltype_data <- allcelltype_data[allcelltype_data$celltype == input$ct,]
         if(input$time == "All") {
           df_all <- celltype_data %>% 
@@ -2855,7 +2855,7 @@ server <- function(input, output, session) {
 
     output$enrichmentplot <- renderPlot({
       if(input$ct != "All") {
-        allcelltype_data <- read.csv("data/differential-expression/DEgenes_MtvsWt_alltimepts_allcelltypes.csv")
+        allcelltype_data <- read.csv("DEgenes_MtvsWt_alltimepts_allcelltypes.csv")
         celltype_data <- allcelltype_data[allcelltype_data$celltype == input$ct,]
         if(input$time == "All") {
           up = subset(celltype_data, avg_log2FC > 0)

diff --git a/...celltypes_timepoints_mtvswt_withpvals.rds → ...celltypes_timepoints_mtvswt_withpvals.rds b/...celltypes_timepoints_mtvswt_withpvals.rds → ...celltypes_timepoints_mtvswt_withpvals.rds
diff --git a/data/cellchat/cellchat_2M.rds → cellchat_2M.rds b/data/cellchat/cellchat_2M.rds → cellchat_2M.rds
diff --git a/data/cellchat/cellchat_2V.rds → cellchat_2V.rds b/data/cellchat/cellchat_2V.rds → cellchat_2V.rds
diff --git a/data/cellchat/cellchat_4M.rds → cellchat_4M.rds b/data/cellchat/cellchat_4M.rds → cellchat_4M.rds
diff --git a/data/cellchat/cellchat_4V.rds → cellchat_4V.rds b/data/cellchat/cellchat_4V.rds → cellchat_4V.rds
diff --git a/data/cellchat/cellchat_6M.rds → cellchat_6M.rds b/data/cellchat/cellchat_6M.rds → cellchat_6M.rds
diff --git a/data/cellchat/cellchat_6V.rds → cellchat_6V.rds b/data/cellchat/cellchat_6V.rds → cellchat_6V.rds
diff --git a/...-enrichment/celltype_marker_genes_Ast.rds → celltype_marker_genes_Ast.rds b/...-enrichment/celltype_marker_genes_Ast.rds → celltype_marker_genes_Ast.rds
diff --git a/...nrichment/celltype_marker_genes_ExDp1.rds → celltype_marker_genes_ExDp1.rds b/...nrichment/celltype_marker_genes_ExDp1.rds → celltype_marker_genes_ExDp1.rds
diff --git a/...nrichment/celltype_marker_genes_ExDp2.rds → celltype_marker_genes_ExDp2.rds b/...nrichment/celltype_marker_genes_ExDp2.rds → celltype_marker_genes_ExDp2.rds
diff --git a/...-enrichment/celltype_marker_genes_ExM.rds → celltype_marker_genes_ExM.rds b/...-enrichment/celltype_marker_genes_ExM.rds → celltype_marker_genes_ExM.rds
diff --git a/...-enrichment/celltype_marker_genes_ExN.rds → celltype_marker_genes_ExN.rds b/...-enrichment/celltype_marker_genes_ExN.rds → celltype_marker_genes_ExN.rds
diff --git a/...e-enrichment/celltype_marker_genes_IP.rds → celltype_marker_genes_IP.rds b/...e-enrichment/celltype_marker_genes_IP.rds → celltype_marker_genes_IP.rds
diff --git a/...nrichment/celltype_marker_genes_InCGE.rds → celltype_marker_genes_InCGE.rds b/...nrichment/celltype_marker_genes_InCGE.rds → celltype_marker_genes_InCGE.rds
diff --git a/...nrichment/celltype_marker_genes_InMGE.rds → celltype_marker_genes_InMGE.rds b/...nrichment/celltype_marker_genes_InMGE.rds → celltype_marker_genes_InMGE.rds
diff --git a/...-enrichment/celltype_marker_genes_OPC.rds → celltype_marker_genes_OPC.rds b/...-enrichment/celltype_marker_genes_OPC.rds → celltype_marker_genes_OPC.rds
diff --git a/...nrichment/celltype_marker_genes_PgG2M.rds → celltype_marker_genes_PgG2M.rds b/...nrichment/celltype_marker_genes_PgG2M.rds → celltype_marker_genes_PgG2M.rds
diff --git a/...-enrichment/celltype_marker_genes_PgS.rds → celltype_marker_genes_PgS.rds b/...-enrichment/celltype_marker_genes_PgS.rds → celltype_marker_genes_PgS.rds
diff --git a/...-enrichment/celltype_marker_genes_oRG.rds → celltype_marker_genes_oRG.rds b/...-enrichment/celltype_marker_genes_oRG.rds → celltype_marker_genes_oRG.rds
diff --git a/...-enrichment/celltype_marker_genes_vRG.rds → celltype_marker_genes_vRG.rds b/...-enrichment/celltype_marker_genes_vRG.rds → celltype_marker_genes_vRG.rds