update README

Author: stemangiola

README.md

@@ -6,7 +6,7 @@ tidyHeatmap
 [![Lifecycle:maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html)
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.02472/status.svg)](https://doi.org/10.21105/joss.02472)
 <!-- badges: end -->
- 
+
 ## Citation
 
 Mangiola et al., (2020). tidyHeatmap: an R package for modular heatmap
@@ -47,10 +47,10 @@ as graphical engine.
 | Function            | Description                                                                 |
 |---------------------|-----------------------------------------------------------------------------|
 | `heatmap`           | Plots base heatmap                                                          |
-| `add_tile`          | Adds tile annotation to the heatmap                                         |
-| `add_point`         | Adds point annotation to the heatmap                                        |
-| `add_bar`           | Adds bar annotation to the heatmap                                          |
-| `add_line`          | Adds line annotation to the heatmap                                         |
+| `annotation_tile`   | Adds tile annotation to the heatmap                                         |
+| `annotation_point`  | Adds point annotation to the heatmap                                        |
+| `annotation_bar`    | Adds bar annotation to the heatmap                                          |
+| `annotation_line`   | Adds line annotation to the heatmap                                         |
 | `layer_point`       | Adds layer of symbols on top of the heatmap                                 |
 | `layer_square`      | Adds layer of symbols on top of the heatmap                                 |
 | `layer_diamond`     | Adds layer of symbols on top of the heatmap                                 |
@@ -141,7 +141,7 @@ mtcars
 mtcars_heatmap <- 
     mtcars_tidy |> 
     heatmap(`Car name`, Property, Value,    scale = "row"   ) |>
-    add_tile(hp)
+    annotation_tile(hp)
 
 mtcars_heatmap
 ```
@@ -169,7 +169,7 @@ mtcars_tidy_groupings =
 mtcars_tidy_groupings |> 
     group_by(vs, property_group) |>
     heatmap(`Car name`, Property, Value,    scale = "row"   ) |>
-    add_tile(hp)
+    annotation_tile(hp)
 ```
 
 ![](man/fragments/figures/unnamed-chunk-9-1.png)<!-- -->
@@ -191,7 +191,7 @@ mtcars_tidy_groupings |>
             c("#b58b4c", "#74a6aa")
         )
     ) |>
-    add_tile(hp)
+    annotation_tile(hp)
 ```
 
 ![](man/fragments/figures/unnamed-chunk-10-1.png)<!-- -->
@@ -289,6 +289,11 @@ mtcars_tidy |>
     )
 ```
 
+    ## Warning: `add_tile()` was deprecated in tidyHeatmap 1.9.0.
+    ## Please use `annotation_tile()` instead
+    ## This warning is displayed once every 8 hours.
+    ## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
+
 ![](man/fragments/figures/unnamed-chunk-16-1.png)<!-- -->
 
 We can use grid::colorRamp2 function for tile annotation for specific
@@ -302,7 +307,7 @@ mtcars_tidy |>
         Value,  
         scale = "row"
     ) |>
-    add_tile(
+    annotation_tile(
         hp, 
         palette = circlize::colorRamp2(c(0, 100, 200, 300), viridis::magma(4))
     )
@@ -321,8 +326,8 @@ tidyHeatmap::pasilla |>
         .value = `count normalised adjusted`,   
         scale = "row"
     ) |>
-    add_tile(condition) |>
-    add_tile(activation)
+    annotation_tile(condition) |>
+    annotation_tile(activation)
 ```
 
 ![](man/fragments/figures/unnamed-chunk-18-1.png)<!-- -->
@@ -340,8 +345,8 @@ tidyHeatmap::pasilla |>
         scale = "row",
         show_heatmap_legend = FALSE
     ) |>
-    add_tile(condition, show_legend = FALSE) |>
-    add_tile(activation, show_legend = FALSE)
+    annotation_tile(condition, show_legend = FALSE) |>
+    annotation_tile(activation, show_legend = FALSE)
 ```
 
 ![](man/fragments/figures/unnamed-chunk-19-1.png)<!-- -->
@@ -368,11 +373,11 @@ pasilla_plus |>
         .value = `count normalised adjusted`,   
         scale = "row"
     ) |>
-    add_tile(condition) |>
-    add_point(activation) |>
-    add_tile(act) |>
-    add_bar(size) |>
-    add_line(age)
+    annotation_tile(condition) |>
+    annotation_point(activation) |>
+    annotation_tile(act) |>
+    annotation_bar(size) |>
+    annotation_line(age)
 ```
 
 ![](man/fragments/figures/unnamed-chunk-20-1.png)<!-- -->
@@ -390,11 +395,11 @@ pasilla_plus |>
         .value = `count normalised adjusted`,   
         scale = "row"
     ) |>
-    add_tile(condition, size = unit(0.3, "cm"), annotation_name_gp= gpar(fontsize = 8)) |>
-    add_point(activation, size = unit(0.3, "cm"),   annotation_name_gp= gpar(fontsize = 8)) |>
-    add_tile(act, size = unit(0.3, "cm"),   annotation_name_gp= gpar(fontsize = 8)) |>
-    add_bar(size, size = unit(0.3, "cm"),   annotation_name_gp= gpar(fontsize = 8)) |>
-    add_line(age, size = unit(0.3, "cm"),   annotation_name_gp= gpar(fontsize = 8))
+    annotation_tile(condition, size = unit(0.3, "cm"),  annotation_name_gp= gpar(fontsize = 8)) |>
+    annotation_point(activation, size = unit(0.3, "cm"),    annotation_name_gp= gpar(fontsize = 8)) |>
+    annotation_tile(act, size = unit(0.3, "cm"),    annotation_name_gp= gpar(fontsize = 8)) |>
+    annotation_bar(size, size = unit(0.3, "cm"),    annotation_name_gp= gpar(fontsize = 8)) |>
+    annotation_line(age, size = unit(0.3, "cm"),    annotation_name_gp= gpar(fontsize = 8))
 ```
 
 ![](man/fragments/figures/unnamed-chunk-21-1.png)<!-- -->

man/fragments/figures/unnamed-chunk-20-1.png

@@ -41,6 +41,7 @@ Function | Description
 `save_pdf` | Saves the PDF of the heatmap
 `+` | Integrate heatmaps side-by-side
 `as_ComplexHeatmap` | Convert the tidyHeatmap output to ComplexHeatmap for non-standard "drawing"
+`group_by` | Applied to the input dataset, groups heatpmap rows/columns
 
 ## Installation