Fixed paths

NBISweden · Jan 14, 2024 · 929c830 · 929c830
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commit 929c830
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Showing 22 changed files with 26 additions and 20 deletions.
diff --git a/compiled/labs/bioc/bioc_02_dimred.qmd b/compiled/labs/bioc/bioc_02_dimred.qmd
@@ -30,6 +30,7 @@ suppressPackageStartupMessages({
 ``` {r}
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"
 path_file <- "data/covid/results/bioc_covid_qc.rds"
+if (!dir.exists(dirname(path_file))) dir.create(dirname(path_file), recursive = TRUE)
 if (!file.exists(path_file)) download.file(url = file.path(path_data, "covid/results/bioc_covid_qc.rds"), destfile = path_file)
 sce <- readRDS(path_file)
 ```

diff --git a/compiled/labs/bioc/bioc_03_integration.qmd b/compiled/labs/bioc/bioc_03_integration.qmd
@@ -57,6 +57,7 @@ reticulate::py_discover_config()
 ``` {r}
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"
 path_file <- "data/covid/results/bioc_covid_qc_dr.rds"
+if (!dir.exists(dirname(path_file))) dir.create(dirname(path_file), recursive = TRUE)
 if (!file.exists(path_file)) download.file(url = file.path(path_data, "covid/results/bioc_covid_qc_dr.rds"), destfile = path_file)
 sce <- readRDS(path_file)
 print(reducedDims(sce))

diff --git a/compiled/labs/bioc/bioc_04_clustering.qmd b/compiled/labs/bioc/bioc_04_clustering.qmd
@@ -36,6 +36,7 @@ suppressPackageStartupMessages({
 ``` {r}
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"
 path_file <- "data/covid/results/bioc_covid_qc_dr_int.rds"
+if (!dir.exists(dirname(path_file))) dir.create(dirname(path_file), recursive = TRUE)
 if (!file.exists(path_file)) download.file(url = file.path(path_data, "covid/results/bioc_covid_qc_dr_int.rds"), destfile = path_file)
 sce <- readRDS(path_file)
 print(reducedDims(sce))

diff --git a/compiled/labs/bioc/bioc_05_dge.qmd b/compiled/labs/bioc/bioc_05_dge.qmd
@@ -40,6 +40,7 @@ suppressPackageStartupMessages({
 ``` {r}
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"
 path_file <- "data/covid/results/bioc_covid_qc_dr_int_cl.rds"
+if (!dir.exists(dirname(path_file))) dir.create(dirname(path_file), recursive = TRUE)
 if (!file.exists(path_file)) download.file(url = file.path(path_data, "covid/results/bioc_covid_qc_dr_int_cl.rds"), destfile = path_file)
 sce <- readRDS(path_file)
 print(reducedDims(sce))

diff --git a/compiled/labs/bioc/bioc_06_celltyping.qmd b/compiled/labs/bioc/bioc_06_celltyping.qmd
@@ -53,6 +53,7 @@ Let's read in the saved Covid-19 data object from the clustering step.
 ``` {r}
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"
 path_file <- "data/covid/results/bioc_covid_qc_dr_int_cl.rds"
+if (!dir.exists(dirname(path_file))) dir.create(dirname(path_file), recursive = TRUE)
 if (!file.exists(path_file)) download.file(url = file.path(path_data, "covid/results/bioc_covid_qc_dr_int_cl.rds"), destfile = path_file)
 alldata <- readRDS(path_file)
 ```

diff --git a/compiled/labs/seurat/seurat_02_dimred.qmd b/compiled/labs/seurat/seurat_02_dimred.qmd
@@ -32,8 +32,8 @@ suppressPackageStartupMessages({
 
 ``` {r}
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"
-
 path_file <- "data/covid/results/seurat_covid_qc.rds"
+if (!dir.exists(dirname(path_file))) dir.create(dirname(path_file), recursive = TRUE)
 if (!file.exists(path_file)) download.file(url = file.path(path_data, "covid/results/seurat_covid_qc.rds"), destfile = path_file)
 alldata <- readRDS(path_file)
 ```

diff --git a/compiled/labs/seurat/seurat_03_integration.qmd b/compiled/labs/seurat/seurat_03_integration.qmd
@@ -56,6 +56,7 @@ reticulate::py_discover_config()
 ``` {r}
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"
 path_file <- "data/covid/results/seurat_covid_qc_dr.rds"
+if(!dir.exists(dirname(path_file))) dir.create(dirname(path_file), recursive = TRUE)
 if (!file.exists(path_file)) download.file(url = file.path(path_data, "covid/results/seurat_covid_qc_dr.rds"), destfile = path_file)
 alldata <- readRDS(path_file)
 print(names(alldata@reductions))

diff --git a/compiled/labs/seurat/seurat_04_clustering.qmd b/compiled/labs/seurat/seurat_04_clustering.qmd
@@ -34,6 +34,7 @@ suppressPackageStartupMessages({
 ``` {r}
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"
 path_file <- "data/covid/results/seurat_covid_qc_dr_int.rds"
+if (!dir.exists(dirname(path_file))) dir.create(dirname(path_file), recursive = TRUE)
 if (!file.exists(path_file)) download.file(url = file.path(path_data, "covid/results/seurat_covid_qc_dr_int.rds"), destfile = path_file)
 alldata <- readRDS(path_file)
 print(names(alldata@reductions))

diff --git a/compiled/labs/seurat/seurat_05_dge.qmd b/compiled/labs/seurat/seurat_05_dge.qmd
@@ -41,6 +41,7 @@ suppressPackageStartupMessages({
 ``` {r}
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"
 path_file <- "data/covid/results/seurat_covid_qc_dr_int_cl.rds"
+if (!dir.exists(dirname(path_file))) dir.create(dirname(path_file), recursive = TRUE)
 if (!file.exists(path_file)) download.file(url = file.path(path_data, "covid/results/seurat_covid_qc_dr_int_cl.rds"), destfile = path_file)
 alldata <- readRDS(path_file)
 ```

diff --git a/compiled/labs/seurat/seurat_06_celltyping.qmd b/compiled/labs/seurat/seurat_06_celltyping.qmd
@@ -52,6 +52,7 @@ Let's read in the saved Covid-19 data object from the clustering step.
 ``` {r}
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"
 path_file <- "data/covid/results/seurat_covid_qc_dr_int_cl.rds"
+if (!dir.exists(dirname(path_file))) dir.create(dirname(path_file), recursive = TRUE)
 if (!file.exists(path_file)) download.file(url = file.path(path_data, "covid/results/seurat_covid_qc_dr_int_cl.rds"), destfile = path_file)
 alldata <- readRDS(path_file)
 ```

diff --git a/compiled/labs/seurat/seurat_07_trajectory.qmd b/compiled/labs/seurat/seurat_07_trajectory.qmd
@@ -60,14 +60,8 @@ You can download the files we prepared with these commands:
 
 ``` {r}
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"
-
-path_marrow <- "./data/trajectory"
-if (!dir.exists(path_marrow)) dir.create(path_marrow, recursive = T)
-
-path_results <- "data/results/trajectory"
-if (!dir.exists(path_results)) dir.create(path_results, recursive = T)
-
 path_file <- "data/trajectory/trajectory_seurat_filtered.rds"
+if (!dir.exists(dirname(path_file))) dir.create(dirname(path_file), recursive = TRUE)
 if (!file.exists(path_file)) download.file(url = file.path(path_data, "trajectory/trajectory_seurat_filtered.rds"), destfile = path_file)
 ```
 
@@ -547,7 +541,7 @@ Before computing differential gene expression, sometimes it is a good idea to ma
 
 
 
-```lxk
+```fhi
 #| eval: false
 
 # SEURAT
@@ -565,7 +559,7 @@ Since we are not interested in the effects of the batches in this example, but o
 
 
 
-```lxk
+```fhi
 #| eval: false
 
 # Get the gene means and standard deviation
@@ -592,7 +586,7 @@ Let's compare how the normalized data compares to the batch-corrected one.
 
 
 
-```lxk
+```fhi
 #| eval: false
 
 par(mfrow = c(3, 3))
@@ -626,7 +620,7 @@ Let's also take a closer inspection on the UMAPs:
 
 
 
-```lxk
+```fhi
 #| eval: false
 
 par(mfrow = c(4, 5), mar = c(.1, .1, 2, 1))

diff --git a/labs/bioc/bioc_02_dimred.qmd b/labs/bioc/bioc_02_dimred.qmd
@@ -26,6 +26,7 @@ suppressPackageStartupMessages({
 ```{r}
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"
 path_file <- "data/covid/results/bioc_covid_qc.rds"
+if (!dir.exists(dirname(path_file))) dir.create(dirname(path_file), recursive = TRUE)
 if (!file.exists(path_file)) download.file(url = file.path(path_data, "covid/results/bioc_covid_qc.rds"), destfile = path_file)
 sce <- readRDS(path_file)
 ```

diff --git a/labs/bioc/bioc_03_integration.qmd b/labs/bioc/bioc_03_integration.qmd
@@ -41,6 +41,7 @@ reticulate::py_discover_config()
 ```{r}
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"
 path_file <- "data/covid/results/bioc_covid_qc_dr.rds"
+if (!dir.exists(dirname(path_file))) dir.create(dirname(path_file), recursive = TRUE)
 if (!file.exists(path_file)) download.file(url = file.path(path_data, "covid/results/bioc_covid_qc_dr.rds"), destfile = path_file)
 sce <- readRDS(path_file)
 print(reducedDims(sce))

diff --git a/labs/bioc/bioc_04_clustering.qmd b/labs/bioc/bioc_04_clustering.qmd
@@ -28,6 +28,7 @@ suppressPackageStartupMessages({
 ```{r}
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"
 path_file <- "data/covid/results/bioc_covid_qc_dr_int.rds"
+if (!dir.exists(dirname(path_file))) dir.create(dirname(path_file), recursive = TRUE)
 if (!file.exists(path_file)) download.file(url = file.path(path_data, "covid/results/bioc_covid_qc_dr_int.rds"), destfile = path_file)
 sce <- readRDS(path_file)
 print(reducedDims(sce))

diff --git a/labs/bioc/bioc_05_dge.qmd b/labs/bioc/bioc_05_dge.qmd
@@ -29,6 +29,7 @@ suppressPackageStartupMessages({
 ```{r}
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"
 path_file <- "data/covid/results/bioc_covid_qc_dr_int_cl.rds"
+if (!dir.exists(dirname(path_file))) dir.create(dirname(path_file), recursive = TRUE)
 if (!file.exists(path_file)) download.file(url = file.path(path_data, "covid/results/bioc_covid_qc_dr_int_cl.rds"), destfile = path_file)
 sce <- readRDS(path_file)
 print(reducedDims(sce))

diff --git a/labs/bioc/bioc_06_celltyping.qmd b/labs/bioc/bioc_06_celltyping.qmd
@@ -35,6 +35,7 @@ suppressPackageStartupMessages({
 ```{r}
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"
 path_file <- "data/covid/results/bioc_covid_qc_dr_int_cl.rds"
+if (!dir.exists(dirname(path_file))) dir.create(dirname(path_file), recursive = TRUE)
 if (!file.exists(path_file)) download.file(url = file.path(path_data, "covid/results/bioc_covid_qc_dr_int_cl.rds"), destfile = path_file)
 alldata <- readRDS(path_file)
 ```

diff --git a/labs/seurat/seurat_02_dimred.qmd b/labs/seurat/seurat_02_dimred.qmd
@@ -28,8 +28,8 @@ suppressPackageStartupMessages({
 
 ```{r}
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"
-
 path_file <- "data/covid/results/seurat_covid_qc.rds"
+if (!dir.exists(dirname(path_file))) dir.create(dirname(path_file), recursive = TRUE)
 if (!file.exists(path_file)) download.file(url = file.path(path_data, "covid/results/seurat_covid_qc.rds"), destfile = path_file)
 alldata <- readRDS(path_file)
 ```

diff --git a/labs/seurat/seurat_03_integration.qmd b/labs/seurat/seurat_03_integration.qmd
@@ -40,6 +40,7 @@ reticulate::py_discover_config()
 ```{r}
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"
 path_file <- "data/covid/results/seurat_covid_qc_dr.rds"
+if(!dir.exists(dirname(path_file))) dir.create(dirname(path_file), recursive = TRUE)
 if (!file.exists(path_file)) download.file(url = file.path(path_data, "covid/results/seurat_covid_qc_dr.rds"), destfile = path_file)
 alldata <- readRDS(path_file)
 print(names(alldata@reductions))

diff --git a/labs/seurat/seurat_04_clustering.qmd b/labs/seurat/seurat_04_clustering.qmd
@@ -26,6 +26,7 @@ suppressPackageStartupMessages({
 ```{r}
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"
 path_file <- "data/covid/results/seurat_covid_qc_dr_int.rds"
+if (!dir.exists(dirname(path_file))) dir.create(dirname(path_file), recursive = TRUE)
 if (!file.exists(path_file)) download.file(url = file.path(path_data, "covid/results/seurat_covid_qc_dr_int.rds"), destfile = path_file)
 alldata <- readRDS(path_file)
 print(names(alldata@reductions))

diff --git a/labs/seurat/seurat_05_dge.qmd b/labs/seurat/seurat_05_dge.qmd
@@ -30,6 +30,7 @@ suppressPackageStartupMessages({
 ```{r}
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"
 path_file <- "data/covid/results/seurat_covid_qc_dr_int_cl.rds"
+if (!dir.exists(dirname(path_file))) dir.create(dirname(path_file), recursive = TRUE)
 if (!file.exists(path_file)) download.file(url = file.path(path_data, "covid/results/seurat_covid_qc_dr_int_cl.rds"), destfile = path_file)
 alldata <- readRDS(path_file)
 ```

diff --git a/labs/seurat/seurat_06_celltyping.qmd b/labs/seurat/seurat_06_celltyping.qmd
@@ -34,6 +34,7 @@ suppressPackageStartupMessages({
 ```{r}
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"
 path_file <- "data/covid/results/seurat_covid_qc_dr_int_cl.rds"
+if (!dir.exists(dirname(path_file))) dir.create(dirname(path_file), recursive = TRUE)
 if (!file.exists(path_file)) download.file(url = file.path(path_data, "covid/results/seurat_covid_qc_dr_int_cl.rds"), destfile = path_file)
 alldata <- readRDS(path_file)
 ```

diff --git a/labs/seurat/seurat_07_trajectory.qmd b/labs/seurat/seurat_07_trajectory.qmd
@@ -52,14 +52,8 @@ You can download the files we prepared with these commands:
 
 ```{r}
 path_data <- "https://export.uppmax.uu.se/naiss2023-23-3/workshops/workshop-scrnaseq"
-
-path_marrow <- "./data/trajectory"
-if (!dir.exists(path_marrow)) dir.create(path_marrow, recursive = T)
-
-path_results <- "data/results/trajectory"
-if (!dir.exists(path_results)) dir.create(path_results, recursive = T)
-
 path_file <- "data/trajectory/trajectory_seurat_filtered.rds"
+if (!dir.exists(dirname(path_file))) dir.create(dirname(path_file), recursive = TRUE)
 if (!file.exists(path_file)) download.file(url = file.path(path_data, "trajectory/trajectory_seurat_filtered.rds"), destfile = path_file)
 ```