renumbers tables

csbg · Mar 9, 2023 · a6108ca · a6108ca
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diff --git a/README.md b/README.md
@@ -1,28 +1,3 @@
-TODO
-
-- rename figures:
-  - 3c use new version
-  - 3f/g use old versions
-  - 4b -> S4b
-  - 4c -> 4b
-  - 4d -> 4c
-  - 4e -> 4d
-  - S1b -> S1c
-  - S1c -> S1d
-  - S1d -> S1e
-  - S4b -> S4c
-  - S5d+e -> S5d
-- rename tables
-  - S4 -> S5
-  - S5 -> S6
-  - S6 -> S4
-  - S7 -> S8
-  - S8 -> S7
-- upload R objects to Zenodo
-- add CITATION.cff (after manuscript has been published)
-
-
-
 # Dissecting the cellular architecture of neuroblastoma bone marrow metastasis using single-cell transcriptomics and epigenomics unravels the role of monocytes at the metastatic niche
 
 ## Folders
@@ -63,9 +38,9 @@ Create a folder `data_raw` that will contain raw data in the following subfolder
     - `GSM4654672_T200_gene_cell_exprs_table.xls.gz`
     - `GSM4654673_T214_gene_cell_exprs_table.xls.gz`
     - `GSM4654674_T230_gene_cell_exprs_table.xls.gz`
-- `snp_array`: Extract the contents of `snp_array.tgz` provided in Zenodo repository [https://doi.org/10.5281/zenodo.7707614]
+- `snp_array`: Extract the contents of `snp_array.tgz` provided in Zenodo repository https://doi.org/10.5281/zenodo.7707614
 
-Optionally, obtain intermediary data: Extract the contents of `R_data_generated.tgz` from Zenodo repository [https://doi.org/10.5281/zenodo.7707614] to folder `data_generated`.
+Optionally, obtain intermediary data: Extract the contents of `R_data_generated.tgz` from Zenodo repository https://doi.org/10.5281/zenodo.7707614 to folder `data_generated`.
 
 
 
@@ -108,8 +83,8 @@ Run these R scripts in arbitrary order to generate publication figures and table
 
 - [plot_figure_1_S1.R](plot_figure_1_S1.R) - includes Tables S2, S3, and S10
 - [plot_figure_2_S2.R](plot_figure_2_S2.R)
-- [plot_figure_3_S3.R](plot_figure_3_S3.R) - includes Table S6
-- [plot_figure_4_S4_S7b.R](plot_figure_4_S4_S7b.R) - includes Tables S4 and S5
+- [plot_figure_3_S3.R](plot_figure_3_S3.R) - includes Table S4
+- [plot_figure_4_S4_S7b.R](plot_figure_4_S4_S7b.R) - includes Tables S5 and S6
 - [plot_figure_S5_S7c.R](plot_figure_S5_S7c.R) - includes Table S7 and S8
 - [plot_figures_revision.R](plot_figures_revision.R) – plots for the reply to reviewers
 

diff --git a/plot_figure_3_S3.R b/plot_figure_3_S3.R
@@ -465,7 +465,7 @@ plot_netvisual()
 
 # Tables ------------------------------------------------------------------
 
-## S6 ----
+## S4 ----
 
 sig_data %>% 
   select(
@@ -479,4 +479,4 @@ sig_data %>%
     Pathway = pathway_name,
     "Type of interaction" = annotation
   ) %>%
-  save_table("S6_ccc", sheet_name = "Interactions")
+  save_table("S4_ccc", sheet_name = "Interactions")
diff --git a/plot_figure_4_S4_S7b.R b/plot_figure_4_S4_S7b.R
@@ -755,7 +755,7 @@ ggsave_publication("S7b_gsea", width = 8, height = 10.8)
 
 # Tables ------------------------------------------------------------------
 
-## S4 ----
+## S5 ----
 
 gene_pathways <- 
   CellChatDB.human$interaction %>% 
@@ -803,11 +803,11 @@ dge$results_wide_filtered %>%
   left_join(gene_pathways, by = c(gene = "Gene")) %>%
   split(.$cell_type) %>%
   map(select, !cell_type) %>%
-  save_table("S4_dge")
+  save_table("S5_dge")
 
 
 
-## S5 ----
+## S6 ----
 
 dge$gsea %>% 
   arrange(db, comparison, cell_type, desc(NES)) %>%
@@ -831,4 +831,4 @@ dge$gsea %>%
   ) %>%
   split(.$`Cell type`) %>%
   map(select, !`Cell type`) %>%
-  save_table("S5_gsea")
+  save_table("S6_gsea")
diff --git a/plot_figure_S5_S7c.R b/plot_figure_S5_S7c.R
@@ -540,8 +540,6 @@ ggsave_publication("S7c_IL10", type = "png",
 
 # Tables ------------------------------------------------------------------
 
-## S7 ----
-
 gene_pathways <- 
   CellChatDB.human$interaction %>% 
   as_tibble() %>% 
@@ -566,24 +564,9 @@ rename_columns <- function(s) {
   )
 }
 
-dge_my$results_wide_filtered %>% 
-  arrange(comparison, cell_type, desc(logFC)) %>%
-  mutate(
-    logFC = logFC / log(2),  # nebula returns natural log fold changes
-    comparison = rename_contrast_long_alt(comparison),
-  ) %>%
-  select(!c(p, frq, frq_ref, direction)) %>%
-  pivot_wider(names_from = comparison, values_from = c(logFC, p_adj)) %>%
-  relocate(1, 2, 3, 7, 4, 8, 5, 9, 6, 10) %>%
-  rename_with(rename_columns) %>%
-  left_join(gene_pathways, by = c(gene = "Gene")) %>%
-  split(.$cell_type) %>%
-  map(select, !cell_type) %>%
-  save_table("S7_dge_myeloid")
-
 
 
-## S8 ----
+## S7 ----
 
 dge_my$gsea %>% 
   arrange(db, comparison, cell_type, desc(NES)) %>%
@@ -606,4 +589,23 @@ dge_my$gsea %>%
   ) %>%
   split(.$`Cell type`) %>%
   map(select, !`Cell type`) %>%
-  save_table("S8_gsea_myeloid")
+  save_table("S7_gsea_myeloid")
+
+
+
+## S8 ----
+
+dge_my$results_wide_filtered %>% 
+  arrange(comparison, cell_type, desc(logFC)) %>%
+  mutate(
+    logFC = logFC / log(2),  # nebula returns natural log fold changes
+    comparison = rename_contrast_long_alt(comparison),
+  ) %>%
+  select(!c(p, frq, frq_ref, direction)) %>%
+  pivot_wider(names_from = comparison, values_from = c(logFC, p_adj)) %>%
+  relocate(1, 2, 3, 7, 4, 8, 5, 9, 6, 10) %>%
+  rename_with(rename_columns) %>%
+  left_join(gene_pathways, by = c(gene = "Gene")) %>%
+  split(.$cell_type) %>%
+  map(select, !cell_type) %>%
+  save_table("S8_dge_myeloid")