Merge pull request #161 from rstudio/v0.5.1

Release candidate v0.5.1

Author: Barbara Borges Ribeiro

.Rbuildignore

@@ -5,6 +5,5 @@ README.R?md
 ^inst/examples/.+\.html
 ^inst/examples/.+_files
 ^inst/examples/.+\.Rnb\.cached
-
-
+^examples/*
 

DESCRIPTION

@@ -1,12 +1,13 @@
 Package: flexdashboard
 Type: Package
 Title: R Markdown Format for Flexible Dashboards
-Version: 0.5
+Version: 0.5.1
 Description: Format for converting an R Markdown document to a grid oriented
   dashboard. The dashboard flexibly adapts the size of it's components to the
   containing web page.
 Authors@R: c(
-  person("JJ", "Allaire", role = c("aut", "cre"), email = "[email protected]"),
+  person("Barbara", "Borges", role = c("aut", "cre"), email = "[email protected]"),
+  person("JJ", "Allaire", role = "aut", email = "[email protected]"),
   person(family = "RStudio", role = "cph"),
   person(family = "Keen IO", role = c("ctb", "cph"), comment = "Dashboard CSS"),
   person("Abdullah", "Almsaeed", role = c("ctb", "cph"), comment = "Dashboard CSS"),

NEWS.md

@@ -0,0 +1,59 @@
+flexdashboard 0.5.1
+===========
+
+* Fixed [#149](https://github.com/rstudio/flexdashboard/issues/149): a compatability issue when using Pandoc 2.0. ([#150](https://github.com/rstudio/flexdashboard/pull/150))
+
+* Fixed [#139](https://github.com/rstudio/flexdashboard/issues/139): remove previous valueBox handlers when rebinding.
+
+* Update to roxygen2 6.0.
+
+flexdashboard 0.5.0
+===========
+
+(tagged @ commit [#d99dd62](https://github.com/rstudio/flexdashboard/commit/d99dd62d49375d414336386e11da8d1807c01fae))
+
+* Don't hook graphics device option for `fig_mobile` if it's a data chunk (this broke knitr caching for `shiny_prerendered` data chunks).
+
+
+flexdashboard 0.4.0
+===========
+(tagged @ commit [#0a88a91](https://github.com/rstudio/flexdashboard/commit/0a88a91654a1a18b30b23b60097f6fb16ad2c317))
+
+* Add support for `target` field in navbar links (e.g. target: "_blank").
+
+* Fixed [#100](https://github.com/rstudio/flexdashboard/issues/100): problem w/ embedding source code for Rmd w/ spaces in path.
+
+* Fixed [#106](https://github.com/rstudio/flexdashboard/issues/106): ensure that previous bg class on valueBox is cleared.
+
+
+flexdashboard 0.3.0
+===========
+(tagged @ commit [#2b6eb71](https://github.com/rstudio/flexdashboard/commit/2b6eb71b1f75078ea36b33d5aa3c9f8d4ace639b))
+
+* Support `.hidden` attribute for pages to hide them from the navbar.
+
+* Scroll sidebar when content overflows vertically.
+
+* Correct handling for storyboard notes in mobile layout.
+
+* Handle titles with extended characters (auto-assign id if pandoc doesn't).
+
+* Handle page titles with punctuation (sanitize id for bootstrap tabs).
+
+* Use `pre_knit` hook to get access to the source file path.
+
+* Restore original DT options after rendering.
+
+
+flexdashboard 0.2.0
+===========
+(tagged @ commit [#64d975f](https://github.com/rstudio/flexdashboard/commit/64d975f962dd3eca8ab2067f55a35ec05d72d4ac))
+
+* Initial release to CRAN.
+
+
+flexdashboard 0.1.0
+===========
+(tagged @ commit [#990d10c](https://github.com/rstudio/flexdashboard/commit/990d10c2b3c4a8fa2029a7723f7e1a4ce86d3717))
+
+* init commit!

examples/00_pandoc-version-test-layout/dashboard-pandoc2.0.3.html

@@ -0,0 +1,40 @@
+---
+title: "Pandoc 1.x -> 2.x test"
+output: 
+  flexdashboard::flex_dashboard:
+    orientation: columns
+    source_code: embed
+---
+
+```{r, include = FALSE}
+library(ggplot2)
+library(dplyr)
+```
+
+```{r}
+paste("Pandoc version:", rmarkdown::pandoc_version())
+```
+
+Column
+-------------------------------------
+    
+### Chart 1
+    
+```{r}
+DT::datatable(mtcars)
+```
+   
+Column
+-------------------------------------
+    
+### Chart 2
+    
+```{r}
+ggplot(mtcars, aes(mpg, wt)) + geom_boxplot()
+```
+    
+### Chart 3
+
+```{r}
+ggplot(mtcars, aes(mpg, wt)) + geom_point()
+```

examples/00_pandoc-version-test-layout/dashboard.Rmd

@@ -0,0 +1,30 @@
+---
+title: "NBA Scoring (2008)"
+output: 
+  flexdashboard::flex_dashboard:
+    orientation: rows
+    social: menu
+    source_code: embed
+---
+
+```{r setup, include=FALSE}
+library(knitr)
+library(d3heatmap)
+library(flexdashboard)
+
+url <- "http://datasets.flowingdata.com/ppg2008.csv"
+nba_players <- read.csv(url, row.names = 1)
+```
+
+### Stats by Player {data-width=650}
+
+```{r}
+d3heatmap(nba_players, scale = "column")
+```
+
+### Top Scorers {data-width=350}
+
+```{r}
+knitr::kable(nba_players[1:20,c("G", "MIN", "PTS")])
+```
+

examples/01_NBA-scoring-with-d3heatmap/dashboard-pandoc2.0.3.html

@@ -0,0 +1,163 @@
+---
+title: "ggplotly geoms"
+author: "Carson Sievert"
+output: 
+  flexdashboard::flex_dashboard:
+    orientation: rows
+    social: menu
+    source_code: embed
+---
+
+```{r setup, include=FALSE}
+library(ggplot2)
+library(plotly)
+library(plyr)
+library(flexdashboard)
+
+# Make some noisily increasing data
+set.seed(955)
+dat <- data.frame(cond = rep(c("A", "B"), each=10),
+                  xvar = 1:20 + rnorm(20,sd=3),
+                  yvar = 1:20 + rnorm(20,sd=3))
+```
+
+geom_point
+=======================================================================
+
+Row
+-----------------------------------------------------------------------
+
+### Scatter Chart with geom_point
+
+```{r}
+p <- ggplot(dat, aes(x=xvar, y=yvar)) +
+            geom_point(shape=1)      # Use hollow circles
+ggplotly(p)
+```
+
+
+### geom_smooth Linear Regression
+
+```{r}
+p <- ggplot(dat, aes(x=xvar, y=yvar)) +
+            geom_point(shape=1) +    # Use hollow circles
+            geom_smooth(method=lm)   # Add linear regression line
+ggplotly(p)
+```
+
+Row
+-----------------------------------------------------------------------
+
+### geom_smooth with Loess Smoothed Fit
+
+```{r}
+p <- ggplot(dat, aes(x=xvar, y=yvar)) +
+            geom_point(shape=1) +    # Use hollow circles
+            geom_smooth()            # Add a loess smoothed fit curve with confidence region
+ggplotly(p)
+```
+
+### Constraining Slope with stat_smooth
+
+```{r}
+n <- 20
+x1 <- rnorm(n); x2 <- rnorm(n)
+y1 <- 2 * x1 + rnorm(n)
+y2 <- 3 * x2 + (2 + rnorm(n))
+A <- as.factor(rep(c(1, 2), each = n))
+df <- data.frame(x = c(x1, x2), y = c(y1, y2), A = A)
+fm <- lm(y ~ x + A, data = df)
+
+p <- ggplot(data = cbind(df, pred = predict(fm)), aes(x = x, y = y, color = A))
+p <- p + geom_point() + geom_line(aes(y = pred))
+ggplotly(p)
+```
+
+geom_density
+=======================================================================
+
+Row
+-----------------------------------------------------------------------
+
+### stat_density Example
+
+```{r}
+dfGamma = data.frame(nu75 = rgamma(100, 0.75),
+           nu1 = rgamma(100, 1),
+           nu2 = rgamma(100, 2))
+
+dfGamma = stack(dfGamma)
+
+p <- ggplot(dfGamma, aes(x = values)) +
+            stat_density(aes(group = ind, color = ind),position="identity",geom="line")
+ggplotly(p)
+```
+
+### Add Conditional Density Curves to Plot
+
+```{r}
+dim1 <- c(rnorm(100, mean=1), rnorm(100, mean=4))
+dim2 <- rnorm(200, mean=1)
+cat <- factor(c(rep("a", 100), rep("b", 100)))
+mydf <- data.frame(cbind(dim2, dim1, cat))
+p <- ggplot(data=mydf, aes(x=dim1, y=dim2, colour=as.factor(cat))) +
+  geom_point() +
+  stat_density(aes(x=dim1, y=(-2+(..scaled..))),
+               position="identity", geom="line")
+
+# extract the x range to make the new densities align with y-axis
+xrange <- ggplot_build(p)$layout$panel_ranges[[1]]$x.range
+
+## Get densities of dim2
+ds <- do.call(rbind, lapply(unique(mydf$cat), function(lev) {
+    dens <- with(mydf, density(dim2[cat==lev]))
+    data.frame(x=dens$y+xrange[1], y=dens$x, cat=lev)
+}))
+
+p <- p + geom_path(data=ds, aes(x=x, y=y, color=factor(cat)))
+
+ggplotly(p)
+```
+
+Row
+-----------------------------------------------------------------------
+
+### geom_density and facet_wrap Together
+
+```{r}
+dd<-data.frame(matrix(rnorm(144, mean=2, sd=2),72,2),c(rep("A",24),rep("B",24),rep("C",24)))
+colnames(dd) <- c("x_value", "Predicted_value",  "State_CD")
+
+dd <- data.frame(
+  predicted = rnorm(72, mean = 2, sd = 2),
+  state = rep(c("A", "B", "C"), each = 24)
+)
+
+grid <- with(dd, seq(min(predicted), max(predicted), length = 100))
+normaldens <- ddply(dd, "state", function(df) {
+  data.frame(
+    predicted = grid,
+    density = dnorm(grid, mean(df$predicted), sd(df$predicted))
+  )
+})
+
+p <- ggplot(dd, aes(predicted))  +
+            geom_density() +
+            geom_line(aes(y = density), data = normaldens, colour = "red") +
+            facet_wrap(~ state)
+ggplotly(p)
+```
+
+### Density and Scatterplot Overlay Using geom_density
+
+```{r}
+df <- data.frame(x <- rchisq(1000, 10, 10),
+                 y <- rnorm(1000))
+
+p <- ggplot(df, aes(x, y)) + 
+     geom_point(alpha = 0.5) + 
+     geom_density_2d() + 
+     theme(panel.background = element_rect(fill = '#ffffff'))
+
+ggplotly(p)
+```

examples/01_NBA-scoring-with-d3heatmap/dashboard.Rmd

@@ -0,0 +1,74 @@
+---
+title: "Gene Expression Biclustering"
+author: "Bryan Lewis"
+output: 
+  flexdashboard::flex_dashboard:
+    orientation: rows
+    social: menu
+    source_code: embed
+runtime: shiny
+---
+
+```{r global, include=FALSE}
+# load data in 'global' chunk so it can be shared by all users of the dashboard
+library(biclust)
+data(BicatYeast)
+set.seed(1)
+res <- biclust(BicatYeast, method=BCPlaid(), verbose=FALSE)
+```
+
+Inputs {.sidebar}
+-----------------------------------------------------------------------
+
+```{r}
+ selectInput("clusterNum", label = h3("Cluster number"), 
+    choices = list("1" = 1, "2" = 2, "3" = 3, "4" = 4, "5" = 5), 
+    selected = 1)
+```
+
+Microarray data matrix for 80 experiments with Saccharomyces Cerevisiae
+organism extracted from R's `biclust` package.
+
+Sebastian Kaiser, Rodrigo Santamaria, Tatsiana Khamiakova, Martin Sill, Roberto
+  Theron, Luis Quintales, Friedrich Leisch and Ewoud De Troyer. (2015). biclust:
+  BiCluster Algorithms. R package version 1.2.0.
+  http://CRAN.R-project.org/package=biclust
+
+Row
+-----------------------------------------------------------------------
+
+### Heatmap
+    
+```{r}
+
+num <- reactive(as.integer(input$clusterNum))
+
+col = colorRampPalette(c("red", "white", "darkblue"), space="Lab")(10)
+renderPlot({
+    p = par(mai=c(0,0,0,0))
+    heatmapBC(BicatYeast, res, number=num(), xlab="", ylab="",
+      order=TRUE, useRaster=TRUE, col=col)
+    par(p)
+})
+```
+
+
+Row {.tabset}
+-----------------------------------------------------------------------
+
+### Parallel Coordinates
+    
+```{r}
+renderPlot(
+  parallelCoordinates(BicatYeast, res, number=num())
+)
+```
+   
+### Data for Selected Cluster
+
+```{r}
+# only display table for values in cluster 4
+renderTable(
+  BicatYeast[which(res@RowxNumber[, num()]), which(res@NumberxCol[num(), ])]
+)
+```