v0.99.2 -- update pkg READMEs to mimic the shiny app README

Author: lcolladotor

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: spatialLIBD
 Title: LIBD Visium spatial transcriptomics human pilot data inspector
-Version: 0.99.1
-Date: 2020-02-26
+Version: 0.99.2
+Date: 2020-02-27
 Authors@R:
     c(
     person("Leonardo", "Collado-Torres", role = c("aut", "cre"), 

NEWS.md

@@ -1,3 +1,7 @@
+# spatialLIBD 0.99.2
+
+* Update main package READMEs to reflect the changes to the shiny web app README.md.
+
 # spatialLIBD 0.99.1
 
 * Added Kristen R Maynard to the DESCRIPTION file.

README.Rmd

@@ -22,6 +22,36 @@ knitr::opts_chunk$set(
 [![Codecov test coverage](https://codecov.io/gh/LieberInstitute/spatialLIBD/branch/master/graph/badge.svg)](https://codecov.io/gh/LieberInstitute/spatialLIBD?branch=master)
 <!-- badges: end -->
 
+Welcome to the `spatialLIBD` project! It is composed by a [shiny](https://shiny.rstudio.com/) web application at [jhubiostatistics.shinyapps.io/spatialLIBD/](https://jhubiostatistics.shinyapps.io/spatialLIBD/), a Bioconductor package at [bioconductor.org/packages/spatialLIBD](http://bioconductor.org/packages/spatialLIBD) (or from [here](http://research.libd.org/spatialLIBD/)), and a [research article](https://www.biorxiv.org/search/maynard%252Bcollado%252Bweber%252Bhicks%252Bmartinowich%252Bjaffe) with the scientific knowledge we drew from this dataset.
+
+The web application allows you to browse the LIBD human dorsolateral pre-frontal cortex (DLPFC) spatial transcriptomics data generated with the 10x Genomics Visium platform. Through the [R/Bioconductor package](https://bioconductor.org/packages/spatialLIBD) you can also download the data as well as visualize your own datasets using this web application. Please check the [bioRxiv pre-print](https://www.biorxiv.org/search/maynard%252Bcollado%252Bweber%252Bhicks%252Bmartinowich%252Bjaffe) for more details about this project.
+
+## Study design
+
+As a quick overview, the data presented here is from portion of the DLPFC that spans six neuronal layers plus white matter (**A**) for a total of three subjects with two pairs of spatially adjacent replicates (**B**). Each dissection of DLPFC was designed to span all six layers plus white matter (**C**). Using this web application you can explore the expression of known genes such as _SNAP25_ (**D**, a neuronal gene), _MOBP_ (**E**, an oligodendrocyte gene), and known layer markers from mouse studies such as _PCP4_ (**F**, a known layer 5 marker gene).
+
+<img src="man/figures/paper_figure1.jpg" align="center" width="800px" />
+
+This web application was built such that we could annotate the spots to layers as you can see under the **spot-level data** tab. Once we annotated each spot to a layer, we compressed the information by a pseudo-bulking approach into **layer-level data**. We then analyzed the expression through a set of models whose results you can also explore through this web application. Finally, you can upload your own gene sets of interest as well as layer enrichment statistics and compare them with our LIBD Human DLPFC Visium dataset.
+
+If you are interested in running this web application locally, you can do so thanks to the `spatialLIBD` R/Bioconductor package that powers this web application as shown below.
+
+```{r run_app, eval = FALSE}
+## Run this web application locally
+spatialLIBD::run_app()
+
+## You will have more control about the length of the
+## session and memory usage.
+
+## You could also use this function to visualize your
+## own data given some requirements described
+## in detail in the package vignette documentation
+## at http://research.libd.org/spatialLIBD/.
+```
+
+
+## R/Bioconductor package
+
 The `spatialLIBD` package contains functions for:
 
 * Accessing the spatial transcriptomics data from the LIBD Human Pilot project ([code on GitHub](https://github.com/LieberInstitute/HumanPilot)) generated with the Visium platform from 10x Genomics. The data is retrieved from [Bioconductor](http://bioconductor.org/)'s `ExperimentHub`.

README.md

@@ -15,6 +15,65 @@ status](http://www.bioconductor.org/shields/build/release/bioc/spatialLIBD.svg)]
 coverage](https://codecov.io/gh/LieberInstitute/spatialLIBD/branch/master/graph/badge.svg)](https://codecov.io/gh/LieberInstitute/spatialLIBD?branch=master)
 <!-- badges: end -->
 
+Welcome to the `spatialLIBD` project\! It is composed by a
+[shiny](https://shiny.rstudio.com/) web application at
+[jhubiostatistics.shinyapps.io/spatialLIBD/](https://jhubiostatistics.shinyapps.io/spatialLIBD/),
+a Bioconductor package at
+[bioconductor.org/packages/spatialLIBD](http://bioconductor.org/packages/spatialLIBD)
+(or from [here](http://research.libd.org/spatialLIBD/)), and a [research
+article](https://www.biorxiv.org/search/maynard%252Bcollado%252Bweber%252Bhicks%252Bmartinowich%252Bjaffe)
+with the scientific knowledge we drew from this dataset.
+
+The web application allows you to browse the LIBD human dorsolateral
+pre-frontal cortex (DLPFC) spatial transcriptomics data generated with
+the 10x Genomics Visium platform. Through the [R/Bioconductor
+package](https://bioconductor.org/packages/spatialLIBD) you can also
+download the data as well as visualize your own datasets using this web
+application. Please check the [bioRxiv
+pre-print](https://www.biorxiv.org/search/maynard%252Bcollado%252Bweber%252Bhicks%252Bmartinowich%252Bjaffe)
+for more details about this project.
+
+## Study design
+
+As a quick overview, the data presented here is from portion of the
+DLPFC that spans six neuronal layers plus white matter (**A**) for a
+total of three subjects with two pairs of spatially adjacent replicates
+(**B**). Each dissection of DLPFC was designed to span all six layers
+plus white matter (**C**). Using this web application you can explore
+the expression of known genes such as *SNAP25* (**D**, a neuronal gene),
+*MOBP* (**E**, an oligodendrocyte gene), and known layer markers from
+mouse studies such as *PCP4* (**F**, a known layer 5 marker gene).
+
+<img src="man/figures/paper_figure1.jpg" align="center" width="800px" />
+
+This web application was built such that we could annotate the spots to
+layers as you can see under the **spot-level data** tab. Once we
+annotated each spot to a layer, we compressed the information by a
+pseudo-bulking approach into **layer-level data**. We then analyzed the
+expression through a set of models whose results you can also explore
+through this web application. Finally, you can upload your own gene sets
+of interest as well as layer enrichment statistics and compare them with
+our LIBD Human DLPFC Visium dataset.
+
+If you are interested in running this web application locally, you can
+do so thanks to the `spatialLIBD` R/Bioconductor package that powers
+this web application as shown below.
+
+``` r
+## Run this web application locally
+spatialLIBD::run_app()
+
+## You will have more control about the length of the
+## session and memory usage.
+
+## You could also use this function to visualize your
+## own data given some requirements described
+## in detail in the package vignette documentation
+## at http://research.libd.org/spatialLIBD/.
+```
+
+## R/Bioconductor package
+
 The `spatialLIBD` package contains functions for:
 
   - Accessing the spatial transcriptomics data from the LIBD Human Pilot
@@ -109,7 +168,7 @@ citation('spatialLIBD')
 #> 10.18129/B9.bioc.spatialLIBD (URL:
 #> https://doi.org/10.18129/B9.bioc.spatialLIBD),
 #> https://github.com/LieberInstitute/spatialLIBD - R package version
-#> 0.99.1, <URL: http://www.bioconductor.org/packages/spatialLIBD>.
+#> 0.99.2, <URL: http://www.bioconductor.org/packages/spatialLIBD>.
 #> 
 #> Maynard KR, Collado-Torres L, Weber LM, Uytingco C, Williams SR, II
 #> JLC, Barry BK, Tran MN, Besich Z, Tippani M, Chew J, Yin Y, Hyde TM,