Fixing guides

README.Rmd

@@ -37,13 +37,15 @@ install_github("leonardojo/ggPlantmap")
 
 ## ggPlantmap useful guides (HIGHLY RECOMMENDED!)
 
-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. 
+**(NEW)** Here is a [practical guide](https://github.com/leonardojo/ggPlantmap/blob/main/guides/guide_practical_sc.md) on how to work with ggPlantmap to explore single-cell data
+
+I created a step-by-step [user guide](https://github.com/leonardojo/ggPlantmap/blob/main/guides/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.
+I also created a [step-by-step guide with tips](https://github.com/leonardojo/ggPlantmap/blob/main/guides/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.
+Finally, here are some [instructions](https://github.com/leonardojo/ggPlantmap/blob/main/guides/contributetoggPlantmap.md) on how your newly created ggPlantmap can be included in the package.
 
 ## What is a ggPlantmap?
 

README.md

@@ -1,7 +1,7 @@
 
 # ggPlantmap <img src="man/figures/hex.png" align="right" height="250"/>
 
-###### Version 1.0.0
+###### Version 1.1.0
 
 ###### Author: Leonardo Jo (<l.jo@uu.nl>)
 
@@ -40,20 +40,24 @@ install_github("leonardojo/ggPlantmap")
 
 ## ggPlantmap useful guides (HIGHLY RECOMMENDED!)
 
+**(NEW)** Here is a [practical
+guide](https://github.com/leonardojo/ggPlantmap/blob/main/guides/guide_practical_sc.md)
+on how to work with ggPlantmap to explore single-cell data
+
 I created a step-by-step [user
-guide](https://github.com/leonardojo/ggPlantmap/blob/main/ggPlantmap.userguide.md)
+guide](https://github.com/leonardojo/ggPlantmap/blob/main/guides/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)
+tips](https://github.com/leonardojo/ggPlantmap/blob/main/guides/TutorialforXMLfile.pdf)
 on how to create your own ggPlantmap.
 
 Finally, here are some
-[instructions](https://github.com/leonardojo/ggPlantmap/blob/main/contributetoggPlantmap.md)
+[instructions](https://github.com/leonardojo/ggPlantmap/blob/main/guides/contributetoggPlantmap.md)
 on how your newly created ggPlantmap can be included in the package.
 
 ## What is a ggPlantmap?

guides/contributetoggPlantmap.Rmd → guides/contributetoggPlantmap2.Rmd

@@ -2,24 +2,22 @@
 output: github_document
 ---
 
-```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE)
-```
-# Contribute to ggPlantmap <img src="man/figures/hex.png" align="right" height="200"/>
+# Contribute to ggPlantmap <img src="https://github.com/leonardojo/ggPlantmap/blob/main/man/figures/hex.png" align="right" height="200"/>
 
 ## Create your own ggPlantmap!
 ### Anything you can trace, you can create!
 
-We created a [step-by-step guide with tips](https://github.com/leonardojo/ggPlantmap/blob/main/TutorialforXMLfile.pdf) on how to create your own ggPlantmap. With our described method, users can generate new ggPlantmaps without the necessity of high-resolution images and advanced coding skills. The ggPlantmap package is an open-source project, encouraging community contributions and creation of maps that will be continuously loaded into the package. We encourage users to extend its functionality to meet specific research requirements and to better display plant biological data. Its compatibility with R, one of the most comprehensive programing languages in plant biology, makes it a versatile and accessible tool for the plant science community.
+We created a [step-by-step guide with tips](https://github.com/leonardojo/ggPlantmap/blob/main/guides/TutorialforXMLfile.pdf) on how to create your own ggPlantmap. With our described method, users can generate new ggPlantmaps without the necessity of high-resolution images and advanced coding skills. The ggPlantmap package is an open-source project, encouraging community contributions and creation of maps that will be continuously loaded into the package. We encourage users to extend its functionality to meet specific research requirements and to better display plant biological data. Its compatibility with R, one of the most comprehensive programing languages in plant biology, makes it a versatile and accessible tool for the plant science community.
 
 ## How can my ggPlantmap be included in the package?
 
-<img src="man/figures/contributetoggPlantmap.png" align="center" height="500"/>
+<img src="https://github.com/leonardojo/ggPlantmap/blob/main/man/figures/contributetoggPlantmap.png" align="center" height="500"/>
 
 If you create a new ggPlantmap and want it to be included in the package, please save your new map as a tab-delimited text file using the following code:
 ```{r, eval=F}
-your.ggPlantmap <- XML.to.ggPlantmap("ggPlantmap.xml")
-write.table(your.ggPlantmap,"ggPm.Species.Tissue.Type.txt",sep="\t",header=T)
+library(ggPlantmap)
+your.ggPlantmap <- XML.to.ggPlantmap("data/ggPm.sample.xml")
+write.table(your.ggPlantmap,"data/ggPm.Species.Tissue.Type.txt",sep="\t",col.names=T)
 ```
 
 ### We then ask you to send this table (l.jo@uu.nl) along with the following information:

guides/data/contributetoggPlantmap.Rmd

@@ -0,0 +1,47 @@
+---
+output: github_document
+---
+```{r, echo = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "images/userguide-"
+)
+```
+# Contribute to ggPlantmap
+
+## Create your own ggPlantmap!
+### Anything you can trace, you can create!
+
+We created a [step-by-step guide with tips](https://github.com/leonardojo/ggPlantmap/blob/main/guides/TutorialforXMLfile.pdf) on how to create your own ggPlantmap. With our described method, users can generate new ggPlantmaps without the necessity of high-resolution images and advanced coding skills. The ggPlantmap package is an open-source project, encouraging community contributions and creation of maps that will be continuously loaded into the package. We encourage users to extend its functionality to meet specific research requirements and to better display plant biological data. Its compatibility with R, one of the most comprehensive programing languages in plant biology, makes it a versatile and accessible tool for the plant science community.
+
+## How can my ggPlantmap be included in the package?
+<p>
+<img src="https://github.com/leonardojo/ggPlantmap/blob/f7f426ecf5ee8f53a4603f125dcde6620c9f9edc/man/figures/hex.png" align="center" height="500"/>
+</p>
+If you create a new ggPlantmap and want it to be included in the package, please save your new map as a tab-delimited text file using the following code:
+```{r, eval=F}
+library(ggPlantmap)
+your.ggPlantmap <- XML.to.ggPlantmap("data/ggPm.sample.xml")
+write.table(your.ggPlantmap,"data/ggPm.Species.Tissue.Type.txt",sep="\t",col.names=T)
+```
+
+### We then ask you to send this table (l.jo@uu.nl) along with the following information:
+##### Species:
+##### Tissue: (Ex: Root, Leaf, Stem, Seed)
+##### Type: (Ex: Cross-section, longitudinal view, diagram, top view)
+##### Description: (Short summary of the ggPlantmap, Ex: Cross-section of maturation zone region of Arabidopsis thaliana roots)
+##### Layer levels: (Ex: cell types, zones, etc)
+##### DOI link to the reference image: (If the map was based on previous published data, we asked that you send the DOI link of the reference image)
+##### Author name:
+##### Author contact email:
+
+We will test your ggPlantmap and include in the package in future updates,
+If you have any suggestions or questions, please feel free to contact us,
+
+Thank you for your help!
+
+Leonardo Jo (l.jo@uu.nl)
+
+
+

guides/contributetoggPlantmap.md → guides/data/contributetoggPlantmap.md

@@ -1,12 +1,12 @@
 
-# Contribute to ggPlantmap <img src="man/figures/hex.png" align="right" height="200"/>
+# Contribute to ggPlantmap
 
 ## Create your own ggPlantmap!
 
 ### Anything you can trace, you can create!
 
 We created a [step-by-step guide with
-tips](https://github.com/leonardojo/ggPlantmap/blob/main/TutorialforXMLfile.pdf)
+tips](https://github.com/leonardojo/ggPlantmap/blob/main/guides/TutorialforXMLfile.pdf)
 on how to create your own ggPlantmap. With our described method, users
 can generate new ggPlantmaps without the necessity of high-resolution
 images and advanced coding skills. The ggPlantmap package is an
@@ -20,15 +20,18 @@ community.
 
 ## How can my ggPlantmap be included in the package?
 
-<img src="man/figures/contributetoggPlantmap.png" align="center" height="500"/>
+<p>
+<img src="https://github.com/leonardojo/ggPlantmap/blob/f7f426ecf5ee8f53a4603f125dcde6620c9f9edc/man/figures/hex.png" align="center" height="500"/>
+</p>
 
 If you create a new ggPlantmap and want it to be included in the
 package, please save your new map as a tab-delimited text file using the
 following code:
 
 ``` r
-your.ggPlantmap <- XML.to.ggPlantmap("ggPlantmap.xml")
-write.table(your.ggPlantmap,"ggPm.Species.Tissue.Type.txt",sep="\t",header=T)
+library(ggPlantmap)
+your.ggPlantmap <- XML.to.ggPlantmap("data/ggPm.sample.xml")
+write.table(your.ggPlantmap,"data/ggPm.Species.Tissue.Type.txt",sep="\t",col.names=T)
 ```
 
 ### We then ask you to send this table (<l.jo@uu.nl>) along with the following information: