Merge pull request #100 from databio/dev

1.3.0 release

Author: vpnagraj

.gitignore

@@ -14,3 +14,4 @@ apps/LOLAweb/shinylog
 apps/LOLAweb/results
 apps/LOLAweb/userSets
 apps/LOLAweb/scratch.R
+*.rdb

apps/LOLAweb/about.md

@@ -97,7 +97,13 @@ The columns in the results table are:
 <a name="how-to-cite"> </a>
 ### How do I cite LOLAweb?
 
-LOLAweb is pending publication. In the interim, please cite the LOLA R package:
+LOLAweb is published in *Nucleic Acids Research*:
+
+V. P. Nagraj, N. E. Magee and N. C. Sheffield, "LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis," Nucleic Acids Research, vol. 46, no. w1, pp. w194-w199, Jul. 2018.
+
+[https://doi.org/10.1093/nar/gky464](https://doi.org/10.1093/nar/gky464)
+
+The LOLA R package is published in *Bioinformatics*:
 
 N. C. Sheffield and C. Bock, “LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor,” Bioinformatics, vol. 32, no. 4, pp. 587–589, Oct. 2016.
 

apps/LOLAweb/app.R

@@ -133,7 +133,11 @@ ui <- list(
                     uiOutput("slider_pvalue"),
                     uiOutput("select_collection"),
                     uiOutput("select_sort"),
-                    uiOutput("select_userset")),
+                    uiOutput("select_userset"),
+                    shinyjs::hidden(
+                      downloadButton("all_plots_dl",
+                                     label = "Download all plots",
+                                     class = "dt-button"))),
                     column(10,
                            shinyjs::hidden(
                              div(
@@ -210,7 +214,8 @@ ui <- list(
                ),
       tabPanel("Run summary",
                                 h4("Run summary"),
-                                tableOutput("run_sum"), style = "font-size:18px;")
+                                tableOutput("run_sum"),
+               style = "font-size:18px;")
            ),
       id = "result-tabs")))
   )
@@ -740,7 +745,6 @@ server <- function(input, output, session) {
     shinyjs::show("gear2")
     shinyjs::show("result-tabs")
 
-    
     # show help text for results sliders and plots
     shinyjs::show("infoplot_div")
     shinyjs::show("infodisplay_div")
@@ -770,6 +774,8 @@ server <- function(input, output, session) {
 
       shinyjs::hide("gear2")
       shinyjs::show("scatterhead")
+      shinyjs::show("all_plots_dl")
+      
 
     }
 
@@ -1064,7 +1070,7 @@ server <- function(input, output, session) {
                                   ".pdf", 
                                   sep="") },
     content = function(file) {
-      ggsave(file, plot = scatterplot_input()
+      ggsave(file, plot = scatterplot_input() + theme(axis.text = element_text(size = 9), text = element_text(size = 9))
              , device = "pdf")
     }
   )
@@ -1084,7 +1090,7 @@ server <- function(input, output, session) {
                                   ".pdf", 
                                   sep="") },
     content = function(file) {
-      ggsave(file, plot = plot_input(dat(), "oddsRatio", "Odds ratio", input$select_sort_i)
+      ggsave(file, plot = plot_input(dat(), "oddsRatio", "Odds ratio", input$select_sort_i) + theme(axis.text = element_text(size = 9), text = element_text(size = 9))
 , device = "pdf")
     }
   )
@@ -1118,7 +1124,7 @@ server <- function(input, output, session) {
                                   ".pdf", 
                                   sep="") },
     content = function(file) {
-      ggsave(file, plot = plot_input(dat(), "support", "Support", input$select_sort_i)
+      ggsave(file, plot = plot_input(dat(), "support", "Support", input$select_sort_i) + theme(axis.text = element_text(size = 9), text = element_text(size = 9))
 , device = "pdf")
     }
   )
@@ -1154,7 +1160,7 @@ server <- function(input, output, session) {
                                   ".pdf", 
                                   sep="") },
     content = function(file) {
-      ggsave(file, plot = plot_input(dat(), "pValueLog", "log(p value)", input$select_sort_i)
+      ggsave(file, plot = plot_input(dat(), "pValueLog", "log(p value)", input$select_sort_i) + theme(axis.text = element_text(size = 9), text = element_text(size = 9))
 , device = "pdf")
     }
   )
@@ -1167,7 +1173,7 @@ server <- function(input, output, session) {
 
     if (is.null(genDist)) {
 
-      NULL
+      missing_plot()
 
     } else {
 
@@ -1195,7 +1201,7 @@ server <- function(input, output, session) {
 
     if (is.null(TSSDist)) {
 
-      NULL 
+      missing_plot()
 
     } else {
 
@@ -1222,7 +1228,7 @@ server <- function(input, output, session) {
 
     if(is.null(gp)) {
 
-      NULL
+      missing_plot()
 
     } else {
 
@@ -1247,7 +1253,7 @@ server <- function(input, output, session) {
                                   ".pdf", 
                                   sep="") },
     content = function(file) {
-      ggsave(file, plot = distrib_plot_input(), device = "pdf")
+      ggsave(file, plot = distrib_plot_input() + theme(axis.text = element_text(size = 9), text = element_text(size = 9)), device = "pdf", width = 11, height = 5)
     }
   )
 
@@ -1256,19 +1262,74 @@ server <- function(input, output, session) {
                                   ".pdf", 
                                   sep="") },
     content = function(file) {
-      ggsave(file, plot = dist_plot_input(), device = "pdf")
+      ggsave(file, plot = dist_plot_input() + theme(axis.text = element_text(size = 9), text = element_text(size = 9)), device = "pdf")
     }
   )
 
   output$part_plot_dl <- downloadHandler(
-    filename = function() { paste("paritions",
+    filename = function() { paste("partitions",
                                   ".pdf", 
                                   sep="") },
     content = function(file) {
-      ggsave(file, plot = part_plot_input(), device = "pdf")
+      ggsave(file, plot = part_plot_input() + theme(axis.text = element_text(size = 9), text = element_text(size = 9)), device = "pdf")
     }
   )
 
+  # to zip all plots and save individually ...
+  
+  output$all_plots_dl <- downloadHandler(
+    filename = function() {
+      paste("lolawebplots", "zip", sep=".")
+    },
+    content = function(fname) {
+
+      ggsave(filename = "scatter.pdf",
+             plot = scatterplot_input() + theme(axis.text = element_text(size = 9), text = element_text(size = 9)),
+             device = "pdf",
+             path = "plots")
+
+      ggsave(filename = "oddsratio.pdf",
+             plot = plot_input(dat(), "oddsRatio", "Odds ratio", input$select_sort_i) + theme(axis.text = element_text(size = 9), text = element_text(size = 9)),
+             device = "pdf",
+             path = "plots")
+
+      ggsave(filename = "support.pdf",
+             plot = plot_input(dat(), "support", "Support", input$select_sort_i) + theme(axis.text = element_text(size = 9), text = element_text(size = 9)),
+             device = "pdf",
+             path = "plots")
+
+      ggsave(filename = "pvalue.pdf",
+             plot = plot_input(dat(), "pValueLog", "log(p value)", input$select_sort_i) + theme(axis.text = element_text(size = 9), text = element_text(size = 9)),
+             device = "pdf",
+             path = "plots")
+      
+      # using pdf() device here bc custom aspect ratio not working with ggsave() in this case
+      pdf("plots/gendist.pdf", width = 11, height = 5)
+      print(distrib_plot_input() + theme(axis.text = element_text(size = 9), text = element_text(size = 9)))
+      dev.off()
+
+      ggsave(filename = "tssdist.pdf",
+             plot = dist_plot_input() + theme(axis.text = element_text(size = 9), text = element_text(size = 9)),
+             device = "pdf",
+             path = "plots")
+
+      ggsave(filename = "partitions.pdf",
+             plot = part_plot_input() + theme(axis.text = element_text(size = 9), text = element_text(size = 9)),
+             device = "pdf",
+             path = "plots")
+      
+      # identify files to be zipped and zip them
+      fs <- list.files("plots", full.names = TRUE)
+      zip(zipfile=fname, files=fs)
+      
+      # delete tmp plot files after zip is done
+      unlink(fs)
+
+    },
+    contentType = "application/zip"
+
+  )
+  
 
 
   # data table

apps/LOLAweb/misc.R

@@ -60,6 +60,22 @@ plot_input <- function(res, metric, ylabel, sortcol) {
 
 }
 
+# missing_plot() creates 
+missing_plot <- function() {
+  
+  ggplot(data.frame(x=1:5, y = 1:5), aes(x, y)) +
+  geom_blank() +
+  annotate("text", x = 3, y = 4, label = "Unable to render plot", size = 10, col = "red") +
+  xlab("") +
+  ylab("") +
+  theme(line = element_blank(), 
+        rect = element_blank(), 
+        axis.ticks.length = unit(0,"cm"),
+        axis.text = element_blank(),
+        legend.position = "none", 
+        panel.spacing = unit(0,"lines"), 
+        plot.margin = unit(c(0, 0, 0, 0), "lines"))
+}
 
 # This function just wraps the base Sys.gentenv function to provide a default
 # value for the case that the environment variable is not specified.

docker/Dockerfile

@@ -13,6 +13,10 @@ RUN git clone https://github.com/databio/LOLAweb.git
 # add dir for cache
 RUN mkdir LOLAweb/cache
 RUN chown -R shiny:shiny LOLAweb/cache
+ 
+# add plots dir for zipping up all figures to download with one button
+RUN mkdir LOLAweb/apps/LOLAweb/plots
+RUN chown -R shiny:shiny LOLAweb/apps/LOLAweb/plots
 
 # run the server setup script
 CMD ["/usr/bin/shiny-server.sh"]

docker/README.md

@@ -2,6 +2,8 @@
 
 # Shiny LOLAweb for Docker
 
+The `databio/lolaweb` container is based on the `databio/shinybase` container, which you can find in its [github repository](https://github.com/databio/shinyBase) or [on dockerhub](https://hub.docker.com/r/databio/shinybase/).
+
 ## `build` the container image yourself
 
 1. Clone this repository

docker/dev/Dockerfile

@@ -14,5 +14,9 @@ RUN git clone -b dev https://github.com/databio/LOLAweb.git
 RUN mkdir LOLAweb/cache
 RUN chown -R shiny:shiny LOLAweb/cache
 
+# add plots dir for zipping up all figures to download with one button
+RUN mkdir LOLAweb/apps/LOLAweb/plots
+RUN chown -R shiny:shiny LOLAweb/apps/LOLAweb/plots
+
 # run the server setup script
 CMD ["/usr/bin/shiny-server.sh"]

docker/dev/shiny-server.sh

@@ -5,6 +5,10 @@
 mkdir -p /var/log/shiny-server
 chown shiny.shiny /var/log/shiny-server
 
+# make sure relevant environment variables are visible to shiny server .Renviron
+env | grep "LWLOCAL\|LWREF" > /home/shiny/.Renviron
+chown shiny.shiny /home/shiny/.Renviron
+
 exec shiny-server 2>&1
 
 # done

docker/shiny-server.sh

@@ -5,6 +5,10 @@
 mkdir -p /var/log/shiny-server
 chown shiny.shiny /var/log/shiny-server
 
+# make sure relevant environment variables are visible to shiny server .Renviron
+env | grep "LWLOCAL\|LWREF" > /home/shiny/.Renviron
+chown shiny.shiny /home/shiny/.Renviron
+
 exec shiny-server 2>&1
 
 # done