Corrected typo in samples metadata

NEWS.md

@@ -5,3 +5,5 @@
 - Package here has been removed from dependencies (not needed).
 
 - `where()` function now imported from tidyselect instead of dplyr (as it required a newer version of dplyr).
+
+- Fixed typo in samples metadata file, samples with no value for "rnaseq_batch" variable now have `NA` rather than `"BNA"` values. 

R/so2pls.R

@@ -777,8 +777,8 @@ so2pls_plot_cv_sparsity <- function(cv_res) {
     ggplot2::theme_bw() +
     ggplot2::theme(
       plot.title = ggplot2::element_text(hjust = 0.5),
-      legend.position = "bottom",
-      legend.title.align = 0.5
+      legend.title = ggplot2::element_text(hjust = 0.5),
+      legend.position = "bottom"
     ) +
     ggplot2::labs(
       title = paste0("Mean covariance between joint scores"),

data-raw/example_dataset_li2022.R

@@ -404,7 +404,10 @@ smeta_df <- samples_raw_df |>
       gender == 1 ~ "female"
     ),
     feedlot = paste0("F", feedlot),
-    rnaseq_batch = paste0("B", rnaseq_batch)
+    rnaseq_batch = case_when(
+      is.na(rnaseq_batch) ~ NA_character_,
+      TRUE ~ paste0("B", rnaseq_batch)
+    )
   )
 
 

inst/extdata/samples_info.csv

@@ -137,9 +137,9 @@ U6679,F4,male,BRD,17,B2,0.187151,0.812839,1e-5,K3
 O5245,F4,female,BRD,7,B2,0.108729,1e-5,0.891261,K1
 O5076,F4,female,BRD,11,B2,0.341252,0.608248,0.050501,K3
 O5108,F4,female,BRD,13,B2,1e-5,0.065019,0.934971,K1
-P4744,F3,male,BRD,38,BNA,0.124324,0.82208,0.053596,K3
-P4772,F3,male,Control,46,BNA,0.225694,0.518568,0.255738,K3
-R8953,F1,female,Control,21,BNA,0.31024,0.154271,0.53549,K1
-U5416,F4,male,Control,53,BNA,0.763865,0.115527,0.120608,K2
+P4744,F3,male,BRD,38,NA,0.124324,0.82208,0.053596,K3
+P4772,F3,male,Control,46,NA,0.225694,0.518568,0.255738,K3
+R8953,F1,female,Control,21,NA,0.31024,0.154271,0.53549,K1
+U5416,F4,male,Control,53,NA,0.763865,0.115527,0.120608,K2
 R9518,F2,male,Control,NA,B1,NA,NA,NA,NA
 R9909,F2,male,Control,NA,B1,NA,NA,NA,NA