tidyomics · zhanchen · Mar 12, 2025 · Mar 12, 2025 · Mar 12, 2025
diff --git a/NAMESPACE b/NAMESPACE
@@ -5,6 +5,8 @@ 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(tidy_message)
 importClassesFrom(SummarizedExperiment,SummarizedExperiment)
 importFrom(S4Vectors,coolcat)
 importFrom(S4Vectors,metadata)

diff --git a/R/tidyprint_message.R b/R/tidyprint_message.R
@@ -0,0 +1,45 @@
+#' Print styled tidyprint messages
+#'
+#' @param message A character string containing the message to display.
+#' @param type The type of message to display ("info", "success", "warning", "danger"). Defaults to "info".
+#' @export
+#' @examples
+#' tidy_message("Loading data...", type = "info")
+#' tidy_message("Data loaded successfully!", type = "success")
+tidy_message <- function(message, type = c("info", "success", "warning", "danger")) {
+  type <- match.arg(type, choices = c("info", "success", "warning", "danger"))
+
+  calling_package <- utils::packageName(parent.frame())
+  prefix_package <- ifelse(is.null(calling_package), "Console", calling_package)
+
+  # prefix <- switch(
+  #   type,
+  #   info = paste0(prefix_package, " says"),
+  #   success = paste0(prefix_package, " success"),
+  #   warning = paste0(prefix_package, " warning"),
+  #   danger = paste0(prefix_package, " error")
+  # )
+
+  prefix = paste0(prefix_package, " says")
+
+  style_fun <- switch(
+    type,
+    info = cli::cli_alert_info,
+    success = cli::cli_alert_success,
+    warning = cli::cli_alert_warning,
+    danger = cli::cli_alert_danger
+  )
+
+  style_fun("{prefix}: {message}")
+}
+
+#' Test tidy_message function
+#' @export
+#' @examples
+#' test_tidy_message()
+test_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")
+  tidy_message("Operation failed.", type = "danger")
+}
diff --git a/README.md b/README.md
@@ -7,11 +7,13 @@ tidyprint
 
 <!-- badges: end -->
 
-**tidyprint** is an R package that provides multiple printing styles for
-`SummarizedExperiment` objects. You can choose among:
+**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 diplay:
 
-1.  **SummarizedExperiment** (default): Standard R/SummarizedExperiment
-    printing style.
+1.  **SummarizedExperiment**: Standard R/SummarizedExperiment printing
+    style.
 
 2.  **tidyprint_1**: Newly designed tibble abstraction, combines styles
     from **tidySummarizedExperiment** and **plyxp**
@@ -27,17 +29,17 @@ it easy to switch between these printing styles.
 
 ## 1. Installation
 
-You need the \`\` package to install from GitHub. If you don’t have it,
-install via:
+You need the `remotes` package to install from GitHub. If you don’t have
+it, install via:
 
 ``` r
-install.packages("devtools")
+install.packages("remotes")
 ```
 
 Then install **tidyprint** from GitHub:
 
 ``` r
-devtools::install_github("tidyomics/tidyprint")
+remotes::install_github("tidyomics/tidyprint")
 ```
 
 ------------------------------------------------------------------------
@@ -126,24 +128,6 @@ se_airway %>% print(design = "tidyprint_1")
 #> 309552 ENSG00000283123 SRR1039521  |  0       |   |  treated N061011  GSM1275875
 ```
 
-You can also limit the number of displayed rows by setting `n_print` (or
-a similar argument in your code):
-
-``` r
-
-se_airway %>% print(design = "tidyprint_1", n_print = 5)
-#> # 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
-#>        --------------- ---------- --  ---    --  --  ------- -------  ----------
-#> 309551 ENSG00000283120 SRR1039521  |  0       |   |  treated N061011  GSM1275875
-#> 309552 ENSG00000283123 SRR1039521  |  0       |   |  treated N061011  GSM1275875
-```
-
 ### 2.4 **tidySummarizedExperiment**
 
 Use the “tidySummarizedExperiment” design to view your data in a
@@ -194,20 +178,21 @@ se_airway %>% print(design = "plyxp")
 #> 10 ENSG00000283123 SRR1039521  |       0  |   |  treated N061011  GSM1275875
 ```
 
-You can also limit the number of displayed rows by setting `n_print` (or
-a similar argument in your code):
+# 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.
 
 ``` r
 
-se_airway %>% print(design = "plyxp", n_print = 5)
-#> # A tibble: 5 × 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 ENSG00000283120 SRR1039521  |       0  |   |  treated N061011  GSM1275875
-#> 5 ENSG00000283123 SRR1039521  |       0  |   |  treated N061011  GSM1275875
+test_tidy_message()
+#> ℹ tidyprint says: This is an informational message send within tidyprint package.
+#> ✔ tidyprint says: Operation completed successfully!
+#> ! tidyprint says: Potential issue detected.
+#> ✖ tidyprint says: Operation failed.
 ```
 
 ## Session info

diff --git a/man/test_tidy_message.Rd b/man/test_tidy_message.Rd
diff --git a/man/tidy_message.Rd b/man/tidy_message.Rd
diff --git a/tests/testthat/test-print_methods.R b/tests/testthat/test-print_methods.R
@@ -55,3 +55,8 @@ test_that("tidyprint_1 print works", {
 test_that("Invalid design throws an error", {
   expect_error(print(se_airway, design = "invalidDesign"), "should be one of")
 })
+
+# test for message
+test_that("tidy_message works correctly", {
+  expect_message(tidy_message("Test info message"), "says: Test info message")
+})
diff --git a/vignettes/Introduction.Rmd b/vignettes/Introduction.Rmd
@@ -57,9 +57,9 @@ find_figure <- function(names){
 
 <!-- badges: end -->
 
-**tidyprint** is an R package that provides multiple printing styles for `SummarizedExperiment` objects. You can choose among:
+**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 diplay:
 
-1.  **SummarizedExperiment** (default): Standard R/SummarizedExperiment printing style.
+1.  **SummarizedExperiment**: Standard R/SummarizedExperiment printing style.
 
 2.  **tidyprint_1**: Newly designed tibble abstraction, combines styles from **tidySummarizedExperiment** and **plyxp**
 
@@ -73,16 +73,16 @@ Depending on your workflow and desired console output, `tidyprint` makes it easy
 
 ## 1. Installation
 
-You need the \`\` package to install from GitHub. If you don’t have it, install via:
+You need the `remotes` package to install from GitHub. If you don’t have it, install via:
 
 ```{r eval=FALSE}
-install.packages("devtools")
+install.packages("remotes")
 ```
 
 Then install **tidyprint** from GitHub:
 
 ```{r eval=FALSE}
-devtools::install_github("tidyomics/tidyprint")
+remotes::install_github("tidyomics/tidyprint")
 ```
 
 ------------------------------------------------------------------------
@@ -137,15 +137,6 @@ se_airway %>% print(design = "tidyprint_1")
 
 ```
 
-You can also limit the number of displayed rows by setting `n_print` (or a similar argument in your code):
-
-```{r}
-
-se_airway %>% print(design = "tidyprint_1", n_print = 5)
-
-```
-
-
 
 ### 2.4 **tidySummarizedExperiment**
 
@@ -169,14 +160,17 @@ se_airway %>% print(design = "plyxp")
 
 ```
 
-You can also limit the number of displayed rows by setting `n_print` (or a similar argument in your code):
+# 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.
 
 ```{r}
 
-se_airway %>% print(design = "plyxp", n_print = 5)
+test_tidy_message()
 
 ```
 
+
 ## Session info
 
 ```{r}

diff --git a/vignettes/Introduction.html b/vignettes/Introduction.html
@@ -362,11 +362,13 @@ <h1 class="title toc-ignore">tidyprint</h1>
 <!-- badges: start -->
 <p><a href="https://lifecycle.r-lib.org/articles/stages.html#experimental"><img src="data:image/svg+xml;base64,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" alt="Lifecycle:experimental" /></a></p>
 <!-- badges: end -->
-<p><strong>tidyprint</strong> is an R package that provides multiple
-printing styles for <code>SummarizedExperiment</code> objects. You can
-choose among:</p>
+<p><strong>tidyprint</strong> is an R package that provides a
+centralised tidy display strategy for biological data
+(e.g. SummarizedExperiment), and centralised messaging styles for the
+<code>tidyomics</code> packages. To facilitate the discussion about data
+display, we compare here four data diplay:</p>
 <ol style="list-style-type: decimal">
-<li><p><strong>SummarizedExperiment</strong> (default): Standard
+<li><p><strong>SummarizedExperiment</strong>: Standard
 R/SummarizedExperiment printing style.</p></li>
 <li><p><strong>tidyprint_1</strong>: Newly designed tibble abstraction,
 combines styles from <strong>tidySummarizedExperiment</strong> and
@@ -382,11 +384,11 @@ <h1 class="title toc-ignore">tidyprint</h1>
 <hr />
 <div id="installation" class="section level2">
 <h2>1. Installation</h2>
-<p>You need the `` package to install from GitHub. If you don’t have it,
-install via:</p>
-<pre class="r"><code>install.packages(&quot;devtools&quot;)</code></pre>
+<p>You need the <code>remotes</code> package to install from GitHub. If
+you don’t have it, install via:</p>
+<pre class="r"><code>install.packages(&quot;remotes&quot;)</code></pre>
 <p>Then install <strong>tidyprint</strong> from GitHub:</p>
-<pre class="r"><code>devtools::install_github(&quot;tidyomics/tidyprint&quot;)</code></pre>
+<pre class="r"><code>remotes::install_github(&quot;tidyomics/tidyprint&quot;)</code></pre>
 <hr />
 </div>
 <div id="demo" class="section level2">
@@ -461,20 +463,6 @@ <h3>2.3 <strong>tidyprint_1</strong></h3>
 #&gt; 309550 ENSG00000283119 SRR1039521  |  0       |   |  treated N061011  GSM1275875
 #&gt; 309551 ENSG00000283120 SRR1039521  |  0       |   |  treated N061011  GSM1275875
 #&gt; 309552 ENSG00000283123 SRR1039521  |  0       |   |  treated N061011  GSM1275875</code></pre>
-<p>You can also limit the number of displayed rows by setting
-<code>n_print</code> (or a similar argument in your code):</p>
-<pre class="r"><code>
-se_airway %&gt;% print(design = &quot;tidyprint_1&quot;, n_print = 5)
-#&gt; # A SummarizedExperiment-tibble abstraction:
-#&gt; # Features=38694 | Samples=8 | Assays=counts
-#&gt;        .features       .samples   `|` counts `|` `|` dex     celltype geo_id    
-#&gt;        &lt;chr&gt;           &lt;chr&gt;      &lt;|&gt; &lt;chr&gt;  &lt;|&gt; &lt;|&gt; &lt;chr&gt;   &lt;chr&gt;    &lt;chr&gt;     
-#&gt; 1      ENSG00000000003 SRR1039508  |  723     |   |  control N61311   GSM1275862
-#&gt; 2      ENSG00000000005 SRR1039508  |  0       |   |  control N61311   GSM1275862
-#&gt; 3      ENSG00000000419 SRR1039508  |  467     |   |  control N61311   GSM1275862
-#&gt;        --------------- ---------- --  ---    --  --  ------- -------  ----------
-#&gt; 309551 ENSG00000283120 SRR1039521  |  0       |   |  treated N061011  GSM1275875
-#&gt; 309552 ENSG00000283123 SRR1039521  |  0       |   |  treated N061011  GSM1275875</code></pre>
 </div>
 <div id="tidysummarizedexperiment" class="section level3">
 <h3>2.4 <strong>tidySummarizedExperiment</strong></h3>
@@ -519,20 +507,21 @@ <h3>2.5 <strong>plyxp</strong></h3>
 #&gt;  8 ENSG00000283119 SRR1039521  |       0  |   |  treated N061011  GSM1275875
 #&gt;  9 ENSG00000283120 SRR1039521  |       0  |   |  treated N061011  GSM1275875
 #&gt; 10 ENSG00000283123 SRR1039521  |       0  |   |  treated N061011  GSM1275875</code></pre>
-<p>You can also limit the number of displayed rows by setting
-<code>n_print</code> (or a similar argument in your code):</p>
-<pre class="r"><code>
-se_airway %&gt;% print(design = &quot;plyxp&quot;, n_print = 5)
-#&gt; # A tibble: 5 × 9
-#&gt;   .features       .samples   `|` counts `|` `|` dex     celltype geo_id    
-#&gt;   &lt;chr&gt;           &lt;chr&gt;      &lt;|&gt;  &lt;dbl&gt; &lt;|&gt; &lt;|&gt; &lt;chr&gt;   &lt;chr&gt;    &lt;chr&gt;     
-#&gt; 1 ENSG00000000003 SRR1039508  |     723  |   |  control N61311   GSM1275862
-#&gt; 2 ENSG00000000005 SRR1039508  |       0  |   |  control N61311   GSM1275862
-#&gt; 3 ENSG00000000419 SRR1039508  |     467  |   |  control N61311   GSM1275862
-#&gt; 4 ENSG00000283120 SRR1039521  |       0  |   |  treated N061011  GSM1275875
-#&gt; 5 ENSG00000283123 SRR1039521  |       0  |   |  treated N061011  GSM1275875</code></pre>
 </div>
 </div>
+<div id="messaging-function" class="section level1">
+<h1>Messaging function</h1>
+<p>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.</p>
+<pre class="r"><code>
+test_tidy_message()
+#&gt; ℹ tidyprint says: This is an informational message send within tidyprint package.
+#&gt; ✔ tidyprint says: Operation completed successfully!
+#&gt; ! tidyprint says: Potential issue detected.
+#&gt; ✖ tidyprint says: Operation failed.</code></pre>
 <div id="session-info" class="section level2">
 <h2>Session info</h2>
 <pre class="r"><code>
@@ -592,6 +581,7 @@ <h2>Session info</h2>
 #&gt; [55] knitr_1.49                  htmltools_0.5.8.1          
 #&gt; [57] rmarkdown_2.29              compiler_4.4.0</code></pre>
 </div>
+</div>