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README.Rmd

@@ -39,6 +39,8 @@ install_github("leonardojo/ggPlantmap")
 
 I created a step-by-step [user guide](https://github.com/leonardojo/ggPlantmap/blob/main/ggPlantmap.userguide.md) to help users navigate through the package. 
 
+Here is a recorded [seminar](https://www.youtube.com/watch?v=TD5m5-CbWTw&t=1402s) with an overview of the package.
+
 I also created a [step-by-step guide with tips](https://github.com/leonardojo/ggPlantmap/blob/main/TutorialforXMLfile.pdf) on how to create your own ggPlantmap.
 
 Finally, here are some [instructions](https://github.com/leonardojo/ggPlantmap/blob/main/contributetoggPlantmap.md) on how your newly created ggPlantmap can be included in the package.
@@ -165,7 +167,11 @@ I would like to acknowledge Kaisa Kajala, Lisa Oskam, Monica Garcia Gomez, Pierr
 
 ## How to cite
 ### Pre-print
-Leonardo Jo, Kaisa Kajala. ggPlantmap: an R package for the  graphic mapping of plant images. Authorea. September 21, 2023.
+
+(current version) Leonardo Jo, Kaisa Kajala. ggPlantmap: an R package for creation of informative and quantitative ggplot maps derived from plant images.
+bioRxiv 2023.11.30.569429; doi: https://doi.org/10.1101/2023.11.30.569429
+
+(previous version) Leonardo Jo, Kaisa Kajala. ggPlantmap: an R package for the  graphic mapping of plant images. Authorea. September 21, 2023.
 DOI: 10.22541/au.169531385.58441696/v1
 
 

README.md

@@ -44,6 +44,10 @@ I created a step-by-step [user
 guide](https://github.com/leonardojo/ggPlantmap/blob/main/ggPlantmap.userguide.md)
 to help users navigate through the package.
 
+Here is a recorded
+[seminar](https://www.youtube.com/watch?v=TD5m5-CbWTw&t=1402s) with an
+overview of the package.
+
 I also created a [step-by-step guide with
 tips](https://github.com/leonardojo/ggPlantmap/blob/main/TutorialforXMLfile.pdf)
 on how to create your own ggPlantmap.
@@ -101,26 +105,25 @@ contribution of the plant research community.
 library(ggPlantmap)
 ggPm.summary
 #> # A tibble: 16 × 9
-#>    ggPlantmap.name   Species Tissue Type  Descr…¹ Layers Image…² Made.by Conta…³
-#>    <chr>             <chr>   <chr>  <chr> <chr>   <chr>  <chr>   <chr>   <chr>  
-#>  1 ggPm.At.roottip.… Arabid… root   cros… Cross-… Cells  https:… Leonar… jo.leo…
-#>  2 ggPm.At.roottip.… Arabid… root   long… Longit… Cells  https:… Leonar… jo.leo…
-#>  3 ggPm.At.3weekros… Arabid… roset… top … Top vi… Leaves https:… Leonar… jo.leo…
-#>  4 ggPm.At.leafepid… Arabid… leaf … top … Top vi… Cells  https:… Leonar… jo.leo…
-#>  5 ggPm.At.leaf.cro… Arabid… leaves cros… Cross-… Cells  https:… Leonar… jo.leo…
-#>  6 ggPm.At.seed.dev… Arabid… seed   deve… Diagra… Cells… https:… Leonar… jo.leo…
-#>  7 ggPm.At.earlyemb… Arabid… embryo deve… Diagra… Cells… https:… Leonar… jo.leo…
-#>  8 ggPm.At.shootape… Arabid… shoot… long… Diagra… Layer… https:… Leonar… jo.leo…
-#>  9 ggPm.At.inflores… Arabid… inflo… cros… Cross-… Cells  https:… Leonar… jo.leo…
-#> 10 ggPm.Sl.root.cro… Solanu… root   cros… Cross-… Cells  https:… Leonar… jo.leo…
-#> 11 ggPm.At.leaf.top… Arabid… leaf   top … Top vi… Leaves http:/… Leonar… jo.leo…
-#> 12 ggPm.At.rootelon… Arabid… root … long… Longit… Cells  https:… Leonar… jo.leo…
-#> 13 ggPm.At.rootmatu… Arabid… root … cros… Cross-… Cells  https:… Leonar… jo.leo…
-#> 14 ggPm.At.flower.d… Arabid… flower diag… Diagra… Tissu… Taiz, … Leonar… jo.leo…
-#> 15 ggPm.At.lateralr… Arabid… later… deve… Diagra… Cells… https:… Leonar… jo.leo…
-#> 16 ggPm.Ms.root.cro… Medica… root   cros… Cross-… Cells  Unpubl… Leonar… jo.leo…
-#> # … with abbreviated variable names ¹​Description, ²​Image.Reference,
-#> #   ³​Contact.Info
+#>    ggPlantmap.name       Species Tissue Type  Description Layers Image.Reference
+#>    <chr>                 <chr>   <chr>  <chr> <chr>       <chr>  <chr>          
+#>  1 ggPm.At.roottip.cros… Arabid… root   cros… Cross-sect… Cells  https://www.fu…
+#>  2 ggPm.At.roottip.long… Arabid… root   long… Longitudin… Cells  https://doi.or…
+#>  3 ggPm.At.3weekrosette… Arabid… roset… top … Top view o… Leaves https://doi.or…
+#>  4 ggPm.At.leafepidermi… Arabid… leaf … top … Top view o… Cells  https://www.na…
+#>  5 ggPm.At.leaf.crossse… Arabid… leaves cros… Cross-sect… Cells  https://doi.or…
+#>  6 ggPm.At.seed.devseri… Arabid… seed   deve… Diagram of… Cells… https://doi.or…
+#>  7 ggPm.At.earlyembryog… Arabid… embryo deve… Diagram of… Cells… https://doi.or…
+#>  8 ggPm.At.shootapex.lo… Arabid… shoot… long… Diagram of… Layer… https://doi.or…
+#>  9 ggPm.At.inflorescenc… Arabid… inflo… cros… Cross-sect… Cells  https://academ…
+#> 10 ggPm.Sl.root.crossse… Solanu… root   cros… Cross-sect… Cells  https://doi.or…
+#> 11 ggPm.At.leaf.topview  Arabid… leaf   top … Top view o… Leaves http://doi.org…
+#> 12 ggPm.At.rootelong.lo… Arabid… root … long… Longitudin… Cells  https://doi.or…
+#> 13 ggPm.At.rootmatur.cr… Arabid… root … cros… Cross-sect… Cells  https://doi.or…
+#> 14 ggPm.At.flower.diagr… Arabid… flower diag… Diagram of… Tissu… Taiz, Lincoln,…
+#> 15 ggPm.At.lateralroot.… Arabid… later… deve… Diagram of… Cells… https://doi.or…
+#> 16 ggPm.Ms.root.crossse… Medica… root   cros… Cross-sect… Cells  Unpublished    
+#> # ℹ 2 more variables: Made.by <chr>, Contact.Info <chr>
 ```
 
 <img src="man/figures/ggPm.someexamples.jpg" align="center" height="500"/>
@@ -201,6 +204,11 @@ for the initial tests of ggPlantmap.
 
 ### Pre-print
 
-Leonardo Jo, Kaisa Kajala. ggPlantmap: an R package for the graphic
-mapping of plant images. Authorea. September 21, 2023. DOI:
-10.22541/au.169531385.58441696/v1
+(current version) Leonardo Jo, Kaisa Kajala. ggPlantmap: an R package
+for creation of informative and quantitative ggplot maps derived from
+plant images. bioRxiv 2023.11.30.569429; doi:
+<https://doi.org/10.1101/2023.11.30.569429>
+
+(previous version) Leonardo Jo, Kaisa Kajala. ggPlantmap: an R package
+for the graphic mapping of plant images. Authorea. September 21, 2023.
+DOI: 10.22541/au.169531385.58441696/v1