Merge pull request #48 from finddx/sample-classification

summarise_function fix write.csv

DESCRIPTION

@@ -38,4 +38,5 @@ Config/fusen/version: 0.6.0
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
+

R/samples_distributed_summary.R

@@ -117,7 +117,7 @@ samples_distributed_summary <- function(df,
       stop("please provide a path to save your file")
     }
     stopifnot("Directory provided does not exists"= dir.exists(dirname(path_name)))
-    utils::write.csv(dff, file = path_name)
+    utils::write.csv(dff, file = path_name, row.names = FALSE)
   }
   dff 
 

dev/config_fusen.yaml

@@ -137,3 +137,4 @@ sample_selections.Rmd:
     check: true
     document: true
     overwrite: ask
+    clean: ask

dev/sample_selections.Rmd

@@ -1418,7 +1418,7 @@ samples_distributed_summary <- function(df,
       stop("please provide a path to save your file")
     }
     stopifnot("Directory provided does not exists"= dir.exists(dirname(path_name)))
-    utils::write.csv(dff, file = path_name)
+    utils::write.csv(dff, file = path_name, row.names = FALSE)
   }
   dff 
   

vignettes/sample-selections-vignette.Rmd

@@ -14,20 +14,22 @@ knitr::opts_chunk$set(
 )
 ```
 
-```{r setup}
+```{r}
 library(findBiobankR)
 ```
 
 <!-- WARNING - This vignette is generated by {fusen} from dev/sample_selections.Rmd: do not edit by hand -->
 
+
+
 <!--
 You need to run the 'description' chunk in the '0-dev_history.Rmd' file before continuing your code there.
 -->
 
 
-
 # convert_os_df_to_wide 
 
+
 ```{r example-convert_os_df_to_wide}
 library(data.table)
 library(dplyr)
@@ -49,8 +51,18 @@ clin_specs  <- convert_os_df_to_wide(clinical_df = tb_data,
 knitr::kable(clin_specs[1:10, ])
 ```
 
+
+
+
+
+
+
+
 # select_one_aliquot
 
+
+
+
 ```{r example-select_one_aliquot}
 library(data.table)
 library(dplyr)
@@ -89,8 +101,16 @@ samples_list <- list(c("TB0990100010101001", "TB0990100010101002", "TB0990100010
 select_one_aliquot(samples_list, aliquot_number = 2)
 ```
 
+
+
+
+
+
+
+
 # select_many_aliquots
 
+
 ```{r example-select_many_aliquots}
 
 samples_list <- list(c("TB0990100010101001", "TB0990100010101002", "TB0990100010101003"),
@@ -107,22 +127,20 @@ aliquots_selected <- select_many_aliquots(samples_list,
 aliquots_selected
 ```
 
-# select_and_shuffle_dt
 
-
 
+# select_and_shuffle_dt
+
 
-
 ```{r example-select_and_shuffle_dt}
 #select_and_shuffle_dt()
 ```
 
 
-
 
-
 # select_patients_per_group
 
+
 ```{r example-select_patients_per_group}
 
 library(data.table)
@@ -156,6 +174,8 @@ clin_specs_2 <- select_patients_per_group(df = clin_specs,
 
 ```
 
+
+
 # selected_aliquots_df
 
 ```{r example-selected_aliquots_df}
@@ -187,6 +207,8 @@ selected_aliquots_df(clin_specs,
                      ppid_col = "ppid")
 ```
 
+
+
 # make_clean_os_names
 
 ```{r example-make_clean_os_names}
@@ -201,6 +223,8 @@ nms_os <- c("Participant_PPID", "Visit_Visit Site",
 make_clean_os_names(nms_os)
 ```
 
+
+
 # read_os_data
 
 ```{r example-read_os_data}
@@ -209,8 +233,12 @@ tb_specs <- system.file("extdata", "tb_specs.csv",
 read_os_data(path_name = tb_specs)
 ```
 
+
+
+
 # append_check_col
 
+
 ```{r example-append_check_col}
 
 library(data.table)
@@ -256,6 +284,10 @@ df_send <- append_check_col(selected_samples = selected_samples,
 df_send
 ```
 
+
+
+
+
 # process_save_selected_aliquots
 
 ```{r example-process_save_selected_aliquots}
@@ -311,6 +343,9 @@ process_save_selected_aliquots(file_path = path_name,
 
 ```
 
+
+
+
 # create_save_workbook
 
 ```{r example-create_save_workbook}
@@ -340,6 +375,11 @@ unlink(path_name)
 
 ```
 
+
+
+
+
+
 # gen_clinical_data
 
 ```{r example-gen_clinical_data}
@@ -396,8 +436,11 @@ gen_clinical_data(clinical_data = tb_data,
 
 ```
 
+
+
 # samples_distributed_summary
 
+
 ```{r example-samples_distributed_summary}
 library(data.table)
 library(dplyr)
@@ -461,28 +504,23 @@ samples_distributed_summary(df =list_dfs$clinical_data ,
                             order_col = "Total")
 ```
 
-# mark_all_duplicates
 
-
 
-
 
+# mark_all_duplicates
+
+
 ```{r example-mark_all_duplicates}
 
 vec <- c("apple", "banana", "apple", "cherry", "banana")
 mark_all_duplicates(vec)
 ```
 
 
-
 
-
 # create_folders
-
 
-
 
-
 ```{r example-create_folders}
 path_name <- tempfile(pattern = "main_folder") %>%
     normalizePath(winslash = "/")
@@ -495,7 +533,11 @@ create_folders(path_name, c("archive", "temp", "shared"), "_dir")
 ```
 
 
-
 
 
 
+
+
+
+
+