Add rmarkdowns

.gitignore

@@ -49,3 +49,9 @@ po/*~
 rsconnect/
 docs
 inst/doc
+
+# Mac things
+.DS_Store
+
+# Temporary output files
+tmp.*

NAMESPACE

@@ -21,6 +21,7 @@ export(importPhyloseq)
 export(importQIIME2)
 export(importTreeSE)
 export(importTreeSummarizedExperiment)
+export(mbiodb_html_format)
 export(rankedAbundance)
 export(selfCorrelation)
 export(updateCollectionName)

R/utils-markdown.R

@@ -0,0 +1,89 @@
+# Helper functions for creating the R Markdown files.
+
+#' Create R Markdown file from compute result
+#' This function will create an R Markdown file that from a ComputeResult object. The markdown
+#' file will describe how to access the data in the ComputeResult object and create a plot. Finally,
+#' it will render the R Markdown file to HTML. Templates for these mardown files are stored in the
+#' inst/rmarkdown/templates directory.
+#' @param result A compute result object
+#' @param rmd_file_name The name of the R Markdown file to be created. Default is 'tmp.Rmd'
+#' @return A list containing the plots created for the R markdown file.
+createRMarkdownFromComputeResult <- function(result, rmd_file_name = "tmp.Rmd"){
+
+  dt <- getComputeResult(result)
+  plot_list <- list()
+
+  if (result@name == 'betaDiv') {
+    # We'll create a pcoa scatterplot
+    axis1_name <- result@computedVariableMetadata[[1]]@displayName
+    axis2_name <- result@computedVariableMetadata[[2]]@displayName
+    p <- ggplot2::ggplot(dt) +
+      aes(x=Axis1, y=Axis2) + 
+      geom_point() +
+      labs(y= axis2_name, x =axis1_name,
+            title="PCoA plot of beta diversity results",
+            caption=paste0("produced on ", Sys.time())) +
+      theme_bw()
+
+    template <- "inst/rmarkdown/templates/beta_div_mkdn/skeleton/skeleton.Rmd"
+    plot_list[[1]] <- p
+
+  } else if (result@name == 'alphaDiv') {
+
+    # Show the distribution of alpha diversity values with a histogram
+    alpha_div_display_name <- result@computedVariableMetadata[[1]]@displayName
+    breaks <- pretty(range(dt$alphaDiversity),
+              n = nclass.Sturges(dt$alphaDiversity),
+              min.n = 1)
+    p <- ggplot2::ggplot(dt) +
+      aes(x=alphaDiversity) + 
+      geom_histogram(breaks=breaks, color=1, fill='white') +
+      labs(y= "Frequency", x =alpha_div_display_name,
+            title="Distribution of alpha diversity values",
+            caption=paste0("produced on ", Sys.time())) +
+      theme_bw()
+
+    template <- "inst/rmarkdown/templates/alpha_div_mkdn/skeleton/skeleton.Rmd"
+    plot_list[[1]] <- p
+  } else {
+    stop(paste0("This function does not support ComputeResult objects with name=", data@name))
+  }
+
+  # Create the R Markdown file
+  file.copy(template, rmd_file_name, overwrite = TRUE)
+  rmarkdown::render(rmd_file_name)
+
+  return(plot_list)
+
+}
+
+
+#' Custom HTML template, based on the custom 
+#'
+#' Loads additional style and template file
+#'
+#' @param toc should a table of contents be displayed?
+#' @param ... additional arguments provided to \@code{html_document}
+#' @export
+#'
+mbiodb_html_format <- function(toc = TRUE, ...) {
+
+  # locations of resource files in the package
+  pkg_resource <- function(...) {
+    system.file(..., package = "MicrobiomeDB")
+  }
+
+  css <- pkg_resource("rmarkdown/resources/styles.css")
+
+  # call the base html_document function
+  rmarkdown::html_document(
+    toc = toc,
+    toc_float = TRUE,
+    fig_width = 6.5,
+    fig_height = 4,
+    theme = "lumen",
+    df_print = "kable",
+    number_sections = TRUE,
+    ...
+  )
+}

inst/rmarkdown/resources/styles.css

@@ -0,0 +1,4 @@
+.kable-table {
+  overflow-x: auto;
+  text-transform: capitalize;
+}

inst/rmarkdown/templates/alpha_div_mkdn/skeleton/skeleton.Rmd

@@ -0,0 +1,45 @@
+---
+title: "Alpha Diversity Output Rmd"
+output: MicrobiomeDB:::mbiodb_html_format
+---
+
+<img src="inst/rmarkdown/resources/MicrobiomeDB_hex_final.png" width=95 height=100 style="position:absolute;top:10px;right:38px;" />
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+## Examine the ComputationResult object
+The `ComputationResult` object contains useful information about the the alpha diversity calculation.
+```{r computation_result, echo=TRUE}
+# Input parameters of the computation
+print(result@parameters)
+
+```
+
+## Inspect the returned data
+```{r example_data, echo=TRUE}
+# Extract the output of the alpha diversity computation
+dt <- getComputeResult(result, format='data.table')
+head(dt)
+```
+
+## Example plot
+```{r example_plot, echo=TRUE}
+# Grab nice names for the axes
+alpha_div_display_name <- result@computedVariableMetadata[[1]]@displayName
+
+# Create histogram
+alpha_div_display_name <- result@computedVariableMetadata[[1]]@displayName
+breaks <- pretty(range(dt$alphaDiversity),
+              n = nclass.Sturges(dt$alphaDiversity),
+              min.n = 1)
+p <- ggplot2::ggplot(dt) +
+  aes(x=alphaDiversity) + 
+  geom_histogram(breaks=breaks, color=1, fill='white') +
+  labs(y= "Frequency", x =alpha_div_display_name,
+        title="Distribution of alpha diversity values",
+        caption=paste0("produced on ", Sys.time())) +
+  theme_bw()
+p
+```

inst/rmarkdown/templates/alpha_div_mkdn/template.yaml

@@ -0,0 +1,3 @@
+name: "alpha_div_mkdn"
+description: "Alpha Diversity Output Rmd Template"
+create_dir: true

inst/rmarkdown/templates/beta_div_mkdn/skeleton/skeleton.Rmd

@@ -0,0 +1,44 @@
+---
+title: "Beta Diversity Output Rmd"
+output: MicrobiomeDB:::mbiodb_html_format
+---
+
+<img src="inst/rmarkdown/resources/MicrobiomeDB_hex_final.png" width=95 height=100 style="position:absolute;top:10px;right:38px;" />
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+## Examine the ComputationResult object
+The `ComputationResult` object contains useful information about the the beta diversity calculation.
+```{r computation_result, echo=TRUE}
+# Input parameters of the computation
+print(result@parameters)
+
+# The computed variable display names include the percent variance captured by each axis.
+print(paste0(result@computedVariableMetadata[[1]]@displayName, ', ', result@computedVariableMetadata[[2]]@displayName))
+```
+
+## Inspect the returned data
+```{r example_data, echo=TRUE}
+# Extract the output of the beta diversity computation
+dt <- getComputeResult(result, format='data.table')
+head(dt)
+```
+
+## Example plot
+```{r example_plot, echo=TRUE}
+# Grab nice names for the axes
+axis1_name <- result@computedVariableMetadata[[1]]@displayName
+axis2_name <- result@computedVariableMetadata[[2]]@displayName
+
+# Create the PCoA scatterplot
+p <- ggplot2::ggplot(dt) +
+  aes(x=Axis1, y=Axis2) + 
+  geom_point() +
+  labs(y= axis2_name, x = axis1_name,
+        title='Beta diversity PCoA plot',
+        caption=paste0('produced on ', Sys.time())) +
+  theme_bw()
+p
+```

inst/rmarkdown/templates/beta_div_mkdn/template.yaml

@@ -0,0 +1,3 @@
+name: "beta_div_mkdn"
+description: "Beta Diversity Output Rmd Template"
+create_dir: false

inst/rmarkdown/templates/rankedAbundance_mkdn/skeleton/skeleton.Rmd

@@ -0,0 +1,64 @@
+---
+title: "Ranked Abundance Output Rmd"
+output: MicrobiomeDB:::mbiodb_html_format
+---
+
+<img src="inst/rmarkdown/resources/MicrobiomeDB_hex_final.png" width=95 height=100 style="position:absolute;top:10px;right:38px;" />
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+## Examine the ComputationResult object
+The `ComputationResult` object contains useful information about the ranked Abundance calculation.
+```{r computation_result, echo=TRUE}
+# Input parameters of the computation
+print(result@parameters)
+
+# The rankedAbundance function will return only the top n (default n=10) most abundant taxa (pathways, etc.),
+# while ignoring any taxa with {method} = 0 (for example, if method = 'median', we ignore taxa with median = 0).
+# The computationDetails slot lets us know if the rankedAbundance function had to cutoff the list of taxa at n.
+print(result@computationDetails)
+```
+
+## Inspect the returned data
+```{r example_data, echo=TRUE}
+# Extract the output of the ranked abundance computation
+dt <- getComputeResult(result, format='data.table')
+ancestorIdCols <- result@ancestorIdColumns
+
+# Show the names of the top taxa (pathways, etc.) by abundance
+print(names(dt)[(length(ancestorIdCols)+2):ncol(dt)])
+
+# Finally, check out the data
+head(dt)
+```
+
+## Example plot
+```{r example_plot, echo=TRUE, fig.height=9}
+
+# Create a boxplot showing the taxa with the top abundance values.
+# Prep data
+rankedAbund_pivot <- tidyr::pivot_longer(dt, # dataframe to be pivoted
+                                    cols = (length(result@ancestorIdColumns)+2):ncol(dt), # column names to be stored as a SINGLE variable
+                                    names_to = "taxa", # name of that new variable (column)
+                                    values_to = "abundance") # name of new variable (column) storing all the values (data)
+rankedAbund_pivot$taxa <- factor(rankedAbund_pivot$taxa, levels = names(dt)[ncol(dt):(length(result@ancestorIdColumns)+2)])
+method <- gsub(".*method = ([^, ]+).*", "\\1", rabund@parameters)
+
+# Plot
+p <- ggplot2::ggplot(rankedAbund_pivot) +
+      ggplot2::aes(x=taxa, y=abundance) +
+      ggplot2::geom_boxplot() +
+      ggplot2::labs(y= "Abundance", x = "Taxa",
+            title=paste0("Ranked abundance output, decending by ", method),
+            caption=paste0("produced on ", Sys.time())) +
+      ggplot2::coord_flip() +
+      ggplot2::theme_bw()
+p
+```
+
+## Interactive plot
+```{r interactive_plot, echo=TRUE, fig.height=9}
+plotly::ggplotly(p)
+```

inst/rmarkdown/templates/rankedAbundance_mkdn/template.yaml

@@ -0,0 +1,3 @@
+name: "beta_div_mkdn"
+description: "Beta Diversity Output Rmd Template"
+create_dir: false