Added shiny

jespermaag · Oct 24, 2018 · 90b8451 · 90b8451
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -6,4 +6,6 @@
 ^README\.Rmd$
 ^figure$
 ^data-raw$
+^shiny$
+^cell$
 
diff --git a/README.md b/README.md
@@ -13,7 +13,7 @@ Create anatogram images for different organisms. <br/> This package uses the tis
 Citation
 --------
 
-#### Maag JLV. gganatogram: An R package for modular visualisation of anatograms and tissues based on ggplot2 \[version 1; referees: awaiting peer review\]. F1000Research 2018, 7:1576 (doi: 10.12688/f1000research.16409.1)
+#### Maag JLV. gganatogram: An R package for modular visualisation of anatograms and tissues based on ggplot2 \[version 1; referees: 1 approved\]. F1000Research 2018, 7:1576 (doi: 10.12688/f1000research.16409.1)
 
 <https://f1000research.com/articles/7-1576/v1>
 
@@ -51,6 +51,16 @@ Install from github using devtools.
 devtools::install_github("jespermaag/gganatogram")
 ```
 
+shiny
+-----
+
+I have now included a shiny app for gganatogram. <br/> An online version can be found at shinapps.io. <br/> <https://jespermaag.shinyapps.io/gganatogram/> <br/> Unfortunately, there is a limit of 25h per month of app activity, so if you know R/Rstudio, please run it locally. <br/> To run it locally, use the following command.
+
+``` r
+library(shiny)
+runGitHub( "gganatogram", "jespermaag",  subdir = "shiny") 
+```
+
 Usage
 -----
 
@@ -421,15 +431,15 @@ To plot the whole cell with colours or values, use the following command. If you
 gganatogram(data=cell_key[['cell']], outline = T, fillOutline='steelblue', organism="cell", fill="colour")  +theme_void()   + coord_fixed()
 ```
 
-![](figure/unnamed-chunk-9-1.svg)
+![](figure/unnamed-chunk-10-1.svg)
 
 ``` r
 
 
 gganatogram(data=cell_key[['cell']], outline = T, fillOutline='lightgray', organism="cell", fill="value")  +theme_void() +  coord_fixed() +  scale_fill_viridis()
 ```
 
-![](figure/unnamed-chunk-9-2.svg)
+![](figure/unnamed-chunk-10-2.svg)
 
 To see all the subsstructures individually, you can plot the data one at a time
 
@@ -442,42 +452,42 @@ for (i in 1:nrow(cell_key[['cell']])) {
 do.call(grid.arrange,  c(figureList[1:4], ncol=2))
 ```
 
-![](figure/unnamed-chunk-10-1.svg)
+![](figure/unnamed-chunk-11-1.svg)
 
 ``` r
 
 do.call(grid.arrange,  c(figureList[5:8], ncol=2))
 ```
 
-![](figure/unnamed-chunk-10-2.svg)
+![](figure/unnamed-chunk-11-2.svg)
 
 ``` r
 
 do.call(grid.arrange,  c(figureList[9:12], ncol=2))
 ```
 
-![](figure/unnamed-chunk-10-3.svg)
+![](figure/unnamed-chunk-11-3.svg)
 
 ``` r
 
 do.call(grid.arrange,  c(figureList[13:16], ncol=2))
 ```
 
-![](figure/unnamed-chunk-10-4.svg)
+![](figure/unnamed-chunk-11-4.svg)
 
 ``` r
 
 do.call(grid.arrange,  c(figureList[17:20], ncol=2))
 ```
 
-![](figure/unnamed-chunk-10-5.svg)
+![](figure/unnamed-chunk-11-5.svg)
 
 ``` r
 
 do.call(grid.arrange,  c(figureList[21:24], ncol=2))
 ```
 
-![](figure/unnamed-chunk-10-6.svg)
+![](figure/unnamed-chunk-11-6.svg)
 
 Other organisms i.e. tier 2 organisms
 -------------------------------------

diff --git a/README.rmd b/README.rmd
@@ -39,6 +39,7 @@ This package uses the tissue coordinates from the figure in Expression Atlas. [h
 [https://github.com/ebi-gene-expression-group/anatomogram](https://github.com/ebi-gene-expression-group/anatomogram)  <br/>
 
 ```{r, eval=TRUE, echo=FALSE, AllSpeciesCellPlotValueTop, fig.width = 8, fig.height = 8, dpi = 300}
+
 hgMale <- gganatogram(data=hgMale_key, fillOutline='#440154FF', organism='human', sex='male', fill="value") + theme_void() +  scale_fill_viridis()
 hgFemale <- gganatogram(data=hgFemale_key, fillOutline='#440154FF', organism='human', sex='female', fill="value") + theme_void() +  scale_fill_viridis()
 mmMale <- gganatogram(data=mmMale_key, fillOutline='#440154FF', organism='mouse', sex='male', fill="value") + theme_void() +  scale_fill_viridis()
@@ -59,7 +60,7 @@ grid.arrange(p1, p2, ncol=2)
 
 
 ## Citation
-#### Maag JLV. gganatogram: An R package for modular visualisation of anatograms and tissues based on ggplot2 [version 1; referees: awaiting peer review]. F1000Research 2018, 7:1576 (doi: 10.12688/f1000research.16409.1)
+#### Maag JLV. gganatogram: An R package for modular visualisation of anatograms and tissues based on ggplot2 [version 1; referees: 1 approved]. F1000Research 2018, 7:1576 (doi: 10.12688/f1000research.16409.1)
 https://f1000research.com/articles/7-1576/v1
 
 ```{r}
@@ -85,6 +86,18 @@ Install from github using devtools.
 devtools::install_github("jespermaag/gganatogram")
 ```
 
+## shiny 
+I have now included a shiny app for gganatogram.  <br/>
+An online version can be found at shinapps.io.   <br/>
+[https://jespermaag.shinyapps.io/gganatogram/](https://jespermaag.shinyapps.io/gganatogram/)  <br/>
+Unfortunately, there is a limit of 25h per month of app activity, so if you know R/Rstudio, please run it locally.  <br/>
+To run it locally, use the following command.
+
+```{r, eval=FALSE}
+library(shiny)
+runGitHub( "gganatogram", "jespermaag",  subdir = "shiny") 
+```
+
 ## Usage
 
 This package requires `ggplot2` and `ggpolypath` which loads when loading the package

diff --git a/data-raw/createAnatograms.R b/data-raw/createAnatograms.R
@@ -411,19 +411,20 @@ library(roxygen2)
 #create("gganatogram")
 #hgMale_key <- allAnatomy
 #hgMale_key$value <- runif(46, 0, 20)
-devtools::use_data(pkg = "gganatogram", hgMale_key, overwrite=TRUE)
-devtools::use_data(pkg = "gganatogram", hgFemale_key, overwrite=TRUE)
-devtools::use_data(pkg = "gganatogram", mmMale_key, overwrite=TRUE)
-devtools::use_data(pkg = "gganatogram", mmFemale_key, overwrite=TRUE)
+hgFemale_key <- hgFemale_key[c(60:70,1:59),]
+devtools::use_data(pkg = "../gganatogram", hgMale_key, overwrite=TRUE)
+devtools::use_data(pkg = "../gganatogram", hgFemale_key, overwrite=TRUE)
+devtools::use_data(pkg = "../gganatogram", mmMale_key, overwrite=TRUE)
+devtools::use_data(pkg = "../gganatogram", mmFemale_key, overwrite=TRUE)
 #hgMale_list <- humanList
-devtools::use_data(pkg = "gganatogram", hgMale_list, overwrite= TRUE)
-devtools::use_data(pkg = "gganatogram", hgFemale_list, overwrite= TRUE)
-devtools::use_data(pkg = "gganatogram", mmMale_list, overwrite=TRUE)
-devtools::use_data(pkg = "gganatogram", mmFemale_list, overwrite=TRUE)
+devtools::use_data(pkg = "../gganatogram", hgMale_list, overwrite= TRUE)
+devtools::use_data(pkg = "../gganatogram", hgFemale_list, overwrite= TRUE)
+devtools::use_data(pkg = "../gganatogram", mmMale_list, overwrite=TRUE)
+devtools::use_data(pkg = "../gganatogram", mmFemale_list, overwrite=TRUE)
 
 
-document('gganatogram')
-install('gganatogram')
+document('../gganatogram')
+install('../gganatogram')
 
 #gganatogram(data=hgFemale_key[hgFemale_key$type=='nervous_system',], outline = T, fillOutline='#a6bddb', organism='human', sex='female', fill="colour") +facet_wrap(~type, ncol=4) +theme_classic()
 
@@ -434,6 +435,17 @@ gganatogram(data=mmMale_key, outline = T, fillOutline='#a6bddb', organism='mouse
 gganatogram(data=mmFemale_key, outline = T, fillOutline='#a6bddb', organism='mouse', sex='female', fill="colour") +facet_wrap(~type, ncol=4) +theme_classic()
 
 
+hgFemale_key$value[c(54,49,69:70)] <- c(18,18,0, 5)
+
+hgMale <- gganatogram(data=hgMale_key, fillOutline='#440154FF', organism='human', sex='male', fill="value") + theme_void() +  scale_fill_viridis()
+hgFemale <- gganatogram(data=hgFemale_key, fillOutline='#440154FF', organism='human', sex='female', fill="value") + theme_void() +  scale_fill_viridis()
+mmMale <- gganatogram(data=mmMale_key, fillOutline='#440154FF', organism='mouse', sex='male', fill="value") + theme_void() +  scale_fill_viridis()
+mmFemale <- gganatogram(data=mmFemale_key, outline = T, fillOutline='#440154FF', organism='mouse', sex='female', fill="value")  +theme_void()   +  scale_fill_viridis()
+
+png('figure/HsMm_val.png', res=300, units='in', width=10, height=10)
+grid.arrange(hgMale, hgFemale, mmMale, mmFemale, ncol=2)
+dev.off()
+
 hgMale_key %>%
     dplyr::filter(type =='other') %>%
     dplyr::filter(!organ =='path9') %>%