Fix S7 zenodo table names (#1756)

* g to i

* h to g

* i to h

* README notices that files arent in github

* only 1 of those files

analyses/immune-deconv/03-quantiseq-at-threshold.Rmd

@@ -37,7 +37,7 @@ quantiseq_file <- file.path(quantiseq_dir, "results", "quantiseq_deconv-output-t
 quantiseq_plot_pdf <- file.path(quantiseq_dir, "plots", "tumor-purity-threshold_quantiseq-cancer-groups.pdf")
 
 # output plot data CSV file for Zenodo upload
-figS7i_csv <- file.path("results", "figure-S7i-data.csv")
+figS7h_csv <- file.path("results", "figure-S7h-data.csv")
 ```
 
 
@@ -170,7 +170,7 @@ quantiseq_df %>%
   dplyr::select(Kids_First_Biospecimen_ID, dplyr::everything()) %>%
   # arrange on biospecimen
   dplyr::arrange(Kids_First_Biospecimen_ID) %>%
-  readr::write_csv(figS7i_csv)
+  readr::write_csv(figS7h_csv)
 ```
 
 

analyses/transcriptomic-dimension-reduction/06-umap-tumor-purity-threshold.Rmd

@@ -62,7 +62,7 @@ umap_threshold_file <- file.path(
 umap_pdf <- file.path("plots", "umap_tumor-purity-threshold.pdf")
 
 # output plot data CSV file for Zenodo upload
-figS7h_csv <- file.path(dim_red_dir, "results", "figure-S7h-data.csv")
+figS7g_csv <- file.path(dim_red_dir, "results", "figure-S7g-data.csv")
 ```
 
 And read in and prepare the files:
@@ -199,7 +199,7 @@ umap_thresholded %>%
   # arrange
   dplyr::arrange(Kids_First_Biospecimen_ID) %>%
   # export
-  readr::write_csv(figS7h_csv)
+  readr::write_csv(figS7g_csv)
 ```
 
 

figures/scripts/figS7-tp53-telomerase-tumor-purity-threshold.R

@@ -27,7 +27,7 @@ palette_dir <- file.path(root_dir, "figures", "palettes")
 
 # Zenodo CSV output directory and file path
 zenodo_tables_dir <- file.path(root_dir, "tables", "zenodo-upload")
-figS7g_csv <- file.path(zenodo_tables_dir, "figure-S7g-data.csv")
+figS7i_csv <- file.path(zenodo_tables_dir, "figure-S7i-data.csv")
 
 # Output PDF filenames
 output_pdf <- file.path(output_dir, "tp53_telomerase_boxplots_tumor-purity-threshold.pdf")
@@ -257,6 +257,6 @@ plot_df %>%
   # arrange on RNA ID column, but bring both to front
   dplyr::select(Kids_First_Biospecimen_ID, Kids_First_Biospecimen_ID_DNA, everything()) %>%
   dplyr::arrange(Kids_First_Biospecimen_ID) %>%
-  readr::write_csv(figS7g_csv)
+  readr::write_csv(figS7i_csv)
 
 

tables/copy-zenodo-tables.sh

@@ -37,8 +37,8 @@ cp "${ANALYSIS_DIR}/tp53_nf1_score/results/tumor-purity-threshold/figure-S7d-dat
 cp "${ANALYSIS_DIR}/tp53_nf1_score/results/tumor-purity-threshold/figure-S7e-data.csv" "${OUTDIR}/figure-S7e-data.csv"
 cp "${ANALYSIS_DIR}/tp53_nf1_score/results/tumor-purity-threshold/figure-S7f-data.csv" "${OUTDIR}/figure-S7f-data.csv"
 
-# Figure S7H: Tumor purity thresholded UMAP
-cp "${ANALYSIS_DIR}/transcriptomic-dimension-reduction/results/figure-S7h-data.csv" "${OUTDIR}/figure-S7h-data.csv"
+# Figure S7G: Tumor purity thresholded UMAP
+cp "${ANALYSIS_DIR}/transcriptomic-dimension-reduction/results/figure-S7g-data.csv" "${OUTDIR}/figure-S7g-data.csv"
 
-# Figure S7I: Tumor purity thresholded quanTIseq results
-cp "${ANALYSIS_DIR}/immune-deconv/results/figure-S7i-data.csv" "${OUTDIR}/figure-S7i-data.csv"
+# Figure S7H: Tumor purity thresholded quanTIseq results
+cp "${ANALYSIS_DIR}/immune-deconv/results/figure-S7h-data.csv" "${OUTDIR}/figure-S7h-data.csv"

tables/zenodo-upload/README.md

@@ -101,7 +101,7 @@ Where applicable, all tables are ordered by either `sample_id` or `Kids_First_Bi
 
 | Figure Panel(s) | Filename | Brief Description | Notes on Tabular Data |
 |--------|-------------|--------------------|-------------------------|
-|   S2A-C    |  `figure-S2a-S2b-S2c-data.csv`   | Correlations, distributions, and UpSet plot of mutation VAFs from variant callers for PBTA data, respectively   | This compressed file contains data for all three panels S2A, S2B, and S2C. Caution: Uncompressed, this file is ~3.9 GB.|
+|   S2A-C    |  `figure-S2a-S2b-S2c-data.csv`   | Correlations, distributions, and UpSet plot of mutation VAFs from variant callers for PBTA data, respectively   | This compressed file contains data for all three panels S2A, S2B, and S2C. Caution: Uncompressed, this file is ~3.9 GB. <br><br> Note that this file is only available in Zenodo, not in the OpenPBTA GitHub repository, due to size.|
 |   S3D-F     |   `figure-S2d-S2e-S2f-data.csv`    |  Correlations, distributions, and UpSet of mutation VAFs from variant callers for TCGA data, respectively       | This compressed file contains data for all three panels S2D, S2E, and S2F. Uncompressed, this file is 13MB.            |
 |   S2G     |   `figure-S2g-data.csv`          |  Distributions of VAFs from Lancet calls on PBTA data for tumors with WGS and WXS   |
 |   S2H     |   `figure-S2h-data.csv`         |  Cumulative distribution TMB plots for PBTA cancer groups          |