remove backtick from vertical bars, suppress warnings

NAMESPACE

@@ -1,11 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(as_tibble,SummarizedExperiment)
+S3method(ctl_new_pillar,SE_print_abstraction)
 S3method(ctl_new_rowid_pillar,SE_print_abstraction)
 S3method(print,SummarizedExperiment)
 S3method(tbl_format_header,SE_print_abstraction)
 S3method(tbl_format_header,tidySummarizedExperiment)
-export(test_tidy_message)
+export(demo_tidy_message)
 export(tidy_message)
 importClassesFrom(SummarizedExperiment,SummarizedExperiment)
 importFrom(S4Vectors,coolcat)
@@ -20,10 +21,12 @@ importFrom(cli,col_br_black)
 importFrom(fansi,strwrap_ctl)
 importFrom(methods,setMethod)
 importFrom(pillar,align)
+importFrom(pillar,ctl_new_pillar)
 importFrom(pillar,ctl_new_rowid_pillar)
 importFrom(pillar,get_extent)
 importFrom(pillar,new_pillar)
 importFrom(pillar,new_pillar_shaft)
+importFrom(pillar,pillar)
 importFrom(pillar,pillar_component)
 importFrom(pillar,style_subtle)
 importFrom(pillar,tbl_format_header)

R/plyxp_utlis.R

@@ -22,7 +22,7 @@ vec_phantom <- function(x) {
 }
 
 sep_ <- function(n) {
-  x <- vctrs::vec_rep(" |", times = n)
+  x <- vctrs::vec_rep("|", times = n)
   class(x) <- "|"
   x
 }

R/print_methods.R

@@ -240,16 +240,16 @@ but they do not completely overlap.")
       out_sub <- out[sub_seq, ]
 
       # Compute the max character width for each column
-      separator_row <- sapply(out_sub, function(col) {
+      separator_row <- sapply(out_sub %>% colnames(), function(col) {
         max_width <- max(nchar(as.character(col)), na.rm = TRUE)  # Get max width in the column
         paste(rep("-", max_width), collapse = "")  # Generate a separator of the same length
       })
       # Modify the entire tibble to include a separator row across all columns
-      out_sub <- rbind(
+      out_sub <- suppressWarnings(rbind(
         out_sub[seq_len(top_n),],
         as.list(separator_row),      # Adaptive separator row
         out_sub[(top_n+1):nrow(out_sub), ]
-      )
+      ))
 
 
       # attr(out_sub, "n") <- n

R/tidyprint_1_utlis.R

@@ -53,6 +53,28 @@ ctl_new_rowid_pillar.SE_print_abstraction <- function(controller, x, width, ...)
 
 }
 
+
+#' @importFrom pillar pillar ctl_new_pillar
+#' @export
+ctl_new_pillar.SE_print_abstraction <- function(controller, x, width, ..., title = NULL) {
+
+  if (inherits(x, "|")) {
+    p <- pillar(x, title = "|", ...)
+    class(p$title[[1]]) <- "blank_pillar_title"
+    class(p$type[[1]]) <- "blank_pillar_type"
+    attr(p$type, "width") <- 1L
+    attr(p$type, "min_width") <- 1L
+    attr(p$type[[1]], "width") <- 1L
+    attr(p$type[[1]], "min_width") <- 1L
+    p
+  } else {
+    NextMethod()
+  }
+
+}
+
+
+
 #' @importFrom rlang names2
 #' @importFrom pillar align
 #' @importFrom pillar get_extent

R/tidyprint_message.R

@@ -36,8 +36,8 @@ tidy_message <- function(message, type = c("info", "success", "warning", "danger
 #' Test tidy_message function
 #' @export
 #' @examples
-#' test_tidy_message()
-test_tidy_message <- function() {
+#' demo_tidy_message()
+demo_tidy_message <- function() {
   tidy_message("This is an informational message send within tidyprint package.")
   tidy_message("Operation completed successfully!", type = "success")
   tidy_message("Potential issue detected.", type = "warning")

README.md

@@ -8,9 +8,9 @@ tidyprint
 <!-- badges: end -->
 
 **tidyprint** is an R package that provides a centralised tidy display
-strategy for biological data (e.g. SummarizedExperiment), and
-centralised messaging styles for the `tidyomics` packages. To facilitate
-the discussion about data display, we compare here four data display:
+strategy for biological data (e.g. SummarizedExperiment) and centralised
+messaging styles for the `tidyomics` packages. To facilitate the
+discussion about data display, we compare here four data displays:
 
 1.  **SummarizedExperiment**: Standard R/SummarizedExperiment printing
     style.
@@ -30,7 +30,7 @@ it easy to switch between these printing styles.
 ## 1. Installation
 
 You need the `remotes` package to install from GitHub. If you don’t have
-it, install via:
+it, install it via:
 
 ``` r
 install.packages("remotes")
@@ -106,19 +106,19 @@ plyxp/tidyverse style with tidySummarizedExperiment header:
 se_airway %>% print(design = "tidyprint_1")
 #> # A SummarizedExperiment-tibble abstraction:
 #> # Features=38694 | Samples=8 | Assays=counts
-#>        .features       .samples   `|` counts `|` `|` dex     celltype geo_id    
-#>        <chr>           <chr>      <|> <chr>  <|> <|> <chr>   <chr>    <chr>     
-#> 1      ENSG00000000003 SRR1039508  |  723     |   |  control N61311   GSM1275862
-#> 2      ENSG00000000005 SRR1039508  |  0       |   |  control N61311   GSM1275862
-#> 3      ENSG00000000419 SRR1039508  |  467     |   |  control N61311   GSM1275862
-#> 4      ENSG00000000457 SRR1039508  |  347     |   |  control N61311   GSM1275862
-#> 5      ENSG00000000460 SRR1039508  |  96      |   |  control N61311   GSM1275862
-#>        --------------- ---------- --  ---    --  --  ------- -------  ----------
-#> 309548 ENSG00000283115 SRR1039521  |  0       |   |  treated N061011  GSM1275875
-#> 309549 ENSG00000283116 SRR1039521  |  0       |   |  treated N061011  GSM1275875
-#> 309550 ENSG00000283119 SRR1039521  |  0       |   |  treated N061011  GSM1275875
-#> 309551 ENSG00000283120 SRR1039521  |  0       |   |  treated N061011  GSM1275875
-#> 309552 ENSG00000283123 SRR1039521  |  0       |   |  treated N061011  GSM1275875
+#>        .features       .samples   | counts | | dex     celltype geo_id    
+#>        <chr>           <chr>      | <chr>  | | <chr>   <chr>    <chr>     
+#> 1      ENSG00000000003 SRR1039508 | 723    | | control N61311   GSM1275862
+#> 2      ENSG00000000005 SRR1039508 | 0      | | control N61311   GSM1275862
+#> 3      ENSG00000000419 SRR1039508 | 467    | | control N61311   GSM1275862
+#> 4      ENSG00000000457 SRR1039508 | 347    | | control N61311   GSM1275862
+#> 5      ENSG00000000460 SRR1039508 | 96     | | control N61311   GSM1275862
+#>        ---------       --------   - ------ - - ---     -------- ------    
+#> 309548 ENSG00000283115 SRR1039521 | 0      | | treated N061011  GSM1275875
+#> 309549 ENSG00000283116 SRR1039521 | 0      | | treated N061011  GSM1275875
+#> 309550 ENSG00000283119 SRR1039521 | 0      | | treated N061011  GSM1275875
+#> 309551 ENSG00000283120 SRR1039521 | 0      | | treated N061011  GSM1275875
+#> 309552 ENSG00000283123 SRR1039521 | 0      | | treated N061011  GSM1275875
 ```
 
 ### 2.4 **tidySummarizedExperiment**
@@ -159,16 +159,16 @@ se_airway %>% print(design = "plyxp")
 #> # A tibble: 10 × 9
 #>    .features       .samples   `|` counts `|` `|` dex     celltype geo_id    
 #>    <chr>           <chr>      <|>  <dbl> <|> <|> <chr>   <chr>    <chr>     
-#>  1 ENSG00000000003 SRR1039508  |     723  |   |  control N61311   GSM1275862
-#>  2 ENSG00000000005 SRR1039508  |       0  |   |  control N61311   GSM1275862
-#>  3 ENSG00000000419 SRR1039508  |     467  |   |  control N61311   GSM1275862
-#>  4 ENSG00000000457 SRR1039508  |     347  |   |  control N61311   GSM1275862
-#>  5 ENSG00000000460 SRR1039508  |      96  |   |  control N61311   GSM1275862
-#>  6 ENSG00000283115 SRR1039521  |       0  |   |  treated N061011  GSM1275875
-#>  7 ENSG00000283116 SRR1039521  |       0  |   |  treated N061011  GSM1275875
-#>  8 ENSG00000283119 SRR1039521  |       0  |   |  treated N061011  GSM1275875
-#>  9 ENSG00000283120 SRR1039521  |       0  |   |  treated N061011  GSM1275875
-#> 10 ENSG00000283123 SRR1039521  |       0  |   |  treated N061011  GSM1275875
+#>  1 ENSG00000000003 SRR1039508 |      723 |   |   control N61311   GSM1275862
+#>  2 ENSG00000000005 SRR1039508 |        0 |   |   control N61311   GSM1275862
+#>  3 ENSG00000000419 SRR1039508 |      467 |   |   control N61311   GSM1275862
+#>  4 ENSG00000000457 SRR1039508 |      347 |   |   control N61311   GSM1275862
+#>  5 ENSG00000000460 SRR1039508 |       96 |   |   control N61311   GSM1275862
+#>  6 ENSG00000283115 SRR1039521 |        0 |   |   treated N061011  GSM1275875
+#>  7 ENSG00000283116 SRR1039521 |        0 |   |   treated N061011  GSM1275875
+#>  8 ENSG00000283119 SRR1039521 |        0 |   |   treated N061011  GSM1275875
+#>  9 ENSG00000283120 SRR1039521 |        0 |   |   treated N061011  GSM1275875
+#> 10 ENSG00000283123 SRR1039521 |        0 |   |   treated N061011  GSM1275875
 ```
 
 # 3. Messaging function
@@ -189,17 +189,17 @@ tidyprint::tidy_message('message to print')
 
 You can specify the type of message as
 
-- info (default)
+-   info (default)
 
-- success
+-   success
 
-- warning
+-   warning
 
-- danger
+-   danger
 
 ``` r
 
-test_tidy_message()
+demo_tidy_message()
 #> ℹ tidyprint says: This is an informational message send within tidyprint package.
 #> ✔ tidyprint says: Operation completed successfully!
 #> ! tidyprint says: Potential issue detected.
@@ -214,19 +214,23 @@ function, showing the name of package.
 ``` r
 
 sessionInfo()
-#> R version 4.4.1 (2024-06-14)
-#> Platform: x86_64-apple-darwin20
-#> Running under: macOS Sonoma 14.6.1
+#> R version 4.4.0 (2024-04-24)
+#> Platform: x86_64-pc-linux-gnu
+#> Running under: Red Hat Enterprise Linux 9.4 (Plow)
 #> 
 #> Matrix products: default
-#> BLAS:   /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.0.dylib 
-#> LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
+#> BLAS/LAPACK: FlexiBLAS OPENBLAS;  LAPACK version 3.10.1
 #> 
 #> locale:
-#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
+#>  [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
+#>  [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
+#>  [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
+#>  [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
+#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
+#> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       
 #> 
-#> time zone: Australia/Adelaide
-#> tzcode source: internal
+#> time zone: Australia/Melbourne
+#> tzcode source: system (glibc)
 #> 
 #> attached base packages:
 #> [1] stats     graphics  grDevices utils     datasets  methods   base     
@@ -236,32 +240,32 @@ sessionInfo()
 #> 
 #> loaded via a namespace (and not attached):
 #>  [1] utf8_1.2.4                  sass_0.4.9                 
-#>  [3] generics_0.1.3              SparseArray_1.5.44         
+#>  [3] generics_0.1.3              SparseArray_1.6.2          
 #>  [5] stringi_1.8.4               lattice_0.22-6             
 #>  [7] digest_0.6.37               magrittr_2.0.3             
-#>  [9] evaluate_1.0.3              grid_4.4.1                 
+#>  [9] evaluate_1.0.3              grid_4.4.0                 
 #> [11] fastmap_1.2.0               rprojroot_2.0.4            
-#> [13] jsonlite_1.8.9              Matrix_1.7-0               
-#> [15] GenomeInfoDb_1.41.2         httr_1.4.7                 
+#> [13] jsonlite_1.9.1              Matrix_1.7-3               
+#> [15] GenomeInfoDb_1.42.3         httr_1.4.7                 
 #> [17] fansi_1.0.6                 purrr_1.0.4                
-#> [19] UCSC.utils_1.1.0            jquerylib_0.1.4            
+#> [19] UCSC.utils_1.2.0            jquerylib_0.1.4            
 #> [21] abind_1.4-8                 cli_3.6.4                  
 #> [23] rlang_1.1.5                 crayon_1.5.3               
-#> [25] XVector_0.45.0              Biobase_2.65.1             
+#> [25] XVector_0.46.0              Biobase_2.66.0             
 #> [27] withr_3.0.2                 cachem_1.1.0               
-#> [29] DelayedArray_0.31.14        yaml_2.3.10                
-#> [31] S4Arrays_1.5.11             tools_4.4.1                
-#> [33] GenomeInfoDbData_1.2.13     SummarizedExperiment_1.35.4
-#> [35] BiocGenerics_0.51.3         vctrs_0.6.5                
+#> [29] DelayedArray_0.32.0         yaml_2.3.10                
+#> [31] S4Arrays_1.6.0              tools_4.4.0                
+#> [33] GenomeInfoDbData_1.2.13     SummarizedExperiment_1.36.0
+#> [35] BiocGenerics_0.52.0         vctrs_0.6.5                
 #> [37] R6_2.6.1                    matrixStats_1.5.0          
-#> [39] stats4_4.4.1                lifecycle_1.0.4            
-#> [41] stringr_1.5.1               zlibbioc_1.51.1            
-#> [43] S4Vectors_0.43.2            IRanges_2.39.2             
+#> [39] stats4_4.4.0                lifecycle_1.0.4            
+#> [41] stringr_1.5.1               zlibbioc_1.52.0            
+#> [43] S4Vectors_0.44.0            IRanges_2.40.1             
 #> [45] pkgconfig_2.0.3             pillar_1.10.1              
 #> [47] bslib_0.9.0                 glue_1.8.0                 
-#> [49] xfun_0.50                   tibble_3.2.1               
-#> [51] GenomicRanges_1.57.2        tidyselect_1.2.1           
-#> [53] rstudioapi_0.16.0           MatrixGenerics_1.17.0      
-#> [55] knitr_1.49                  htmltools_0.5.8.1          
-#> [57] rmarkdown_2.29              compiler_4.4.1
+#> [49] xfun_0.51                   tibble_3.2.1               
+#> [51] GenomicRanges_1.58.0        tidyselect_1.2.1           
+#> [53] rstudioapi_0.17.1           MatrixGenerics_1.18.1      
+#> [55] knitr_1.50                  htmltools_0.5.8.1          
+#> [57] rmarkdown_2.29              compiler_4.4.0
 ```

vignettes/Introduction.Rmd

@@ -156,7 +156,6 @@ se_airway %>% print(design = "plyxp")
 
 # 3. Messaging function
 
-
 We integrated a messaging function providing standardized, visually appealing messages for packages within the tidyomics ecosystem. It automatically detects the calling package to provide contextualized messaging, such as "tidyprint says" or "tidybulk says", enhancing consistency and readability across projects.
 
 To use the `tidy_message` function:
@@ -179,7 +178,7 @@ You can specify the type of message as
 
 ```{r}
 
-test_tidy_message()
+demo_tidy_message()
 
 ```