Minor changes to seurat report

R/htmlReports.R

@@ -291,7 +291,7 @@ reportFindMarker <- function(inSCE, output_file = NULL, output_dir = NULL) {
 #'  each figure in the report. Default is \code{FALSE}.
 #' @param forceRun A logical value indicating if all computations previously
 #'  computed should be re-calculated regardless if these computations are
-#'  available in the input object. Default is \code{FALSE}.
+#'  available in the input object. Default is \code{TRUE}.
 #'
 #' @return A \code{\link[SingleCellExperiment]{SingleCellExperiment}} object
 #'  with computations stored.
@@ -318,7 +318,7 @@ reportSeuratRun <- function(inSCE,
                             authors =  NULL,
                             showSession = FALSE,
                             pdf = FALSE,
-                            forceRun = FALSE){
+                            forceRun = TRUE){
 
   if(is.null(biological.group)){
     stop("Must specify atleast one biological.group that is present in the colData of input object.")
@@ -431,7 +431,7 @@ reportSeuratRun <- function(inSCE,
 #'  each figure in the report. Default is \code{FALSE}.
 #' @param forceRun A logical value indicating if all computations previously
 #'  computed should be re-calculated regardless if these computations are
-#'  available in the input object. Default is \code{FALSE}.
+#'  available in the input object. Default is \code{TRUE}.
 #'
 #' @return A \code{\link[SingleCellExperiment]{SingleCellExperiment}} object
 #'  with computations stored.
@@ -454,7 +454,7 @@ reportSeuratResults <- function(inSCE,
                                 authors =  NULL,
                                 showSession = FALSE,
                                 pdf = FALSE,
-                                forceRun = FALSE){
+                                forceRun = TRUE){
 
   if(is.null(biological.group)){
     stop("Must specify atleast one biological.group that is present in the colData of input object.")
@@ -544,7 +544,7 @@ reportSeuratResults <- function(inSCE,
 #'  each figure in the report. Default is \code{FALSE}.
 #' @param forceRun A logical value indicating if all computations previously
 #'  computed should be re-calculated regardless if these computations are
-#'  available in the input object. Default is \code{FALSE}.
+#'  available in the input object. Default is \code{TRUE}.
 #'
 #' @return A \code{\link[SingleCellExperiment]{SingleCellExperiment}} object
 #'  with computations stored.
@@ -561,7 +561,7 @@ reportSeuratDimRed <- function(inSCE,
                                authors =  NULL,
                                showSession = FALSE,
                                pdf = FALSE,
-                               forceRun = FALSE){
+                               forceRun = TRUE){
 
   if(is.null(outputPath)){
     outputPath <- getwd()
@@ -621,7 +621,7 @@ reportSeuratDimRed <- function(inSCE,
 #'  each figure in the report. Default is \code{FALSE}.
 #' @param forceRun A logical value indicating if all computations previously
 #'  computed should be re-calculated regardless if these computations are
-#'  available in the input object. Default is \code{FALSE}.
+#'  available in the input object. Default is \code{TRUE}.
 #'
 #' @return A \code{\link[SingleCellExperiment]{SingleCellExperiment}} object
 #'  with computations stored.
@@ -633,7 +633,7 @@ reportSeuratNormalization <- function(inSCE,
                                authors =  NULL,
                                showSession = FALSE,
                                pdf = FALSE,
-                               forceRun = FALSE){
+                               forceRun = TRUE){
 
   if(is.null(outputPath)){
     outputPath <- getwd()
@@ -693,7 +693,7 @@ reportSeuratNormalization <- function(inSCE,
 #'  each figure in the report. Default is \code{FALSE}.
 #' @param forceRun A logical value indicating if all computations previously
 #'  computed should be re-calculated regardless if these computations are
-#'  available in the input object. Default is \code{FALSE}.
+#'  available in the input object. Default is \code{TRUE}.
 #'
 #' @return A \code{\link[SingleCellExperiment]{SingleCellExperiment}} object
 #'  with computations stored.
@@ -708,7 +708,7 @@ reportSeuratFeatureSelection <- function(inSCE,
                                          authors =  NULL,
                                          showSession = FALSE,
                                          pdf = FALSE,
-                                         forceRun = FALSE){
+                                         forceRun = TRUE){
   if(is.null(outputPath)){
     outputPath <- getwd()
     message("No output directory defined, using current working directory ", outputPath, " instead.")
@@ -763,7 +763,7 @@ reportSeuratFeatureSelection <- function(inSCE,
 #'  each figure in the report. Default is \code{FALSE}.
 #' @param forceRun A logical value indicating if all computations previously
 #'  computed should be re-calculated regardless if these computations are
-#'  available in the input object. Default is \code{FALSE}.
+#'  available in the input object. Default is \code{TRUE}.
 #'
 #' @return A \code{\link[SingleCellExperiment]{SingleCellExperiment}} object
 #'  with computations stored.
@@ -775,7 +775,7 @@ reportSeuratScaling <- function(inSCE,
                            authors =  NULL,
                            showSession = FALSE,
                            pdf = FALSE,
-                           forceRun = FALSE){
+                           forceRun = TRUE){
 
   if(is.null(outputPath)){
     outputPath <- getwd()
@@ -848,7 +848,7 @@ reportSeuratScaling <- function(inSCE,
 #'  each figure in the report. Default is \code{FALSE}.
 #' @param forceRun A logical value indicating if all computations previously
 #'  computed should be re-calculated regardless if these computations are
-#'  available in the input object. Default is \code{FALSE}.
+#'  available in the input object. Default is \code{TRUE}.
 #'
 #' @return A \code{\link[SingleCellExperiment]{SingleCellExperiment}} object
 #'  with computations stored.
@@ -869,7 +869,7 @@ reportSeuratClustering <- function(inSCE,
                                    authors =  NULL,
                                    showSession = FALSE,
                                    pdf = FALSE,
-                                   forceRun = FALSE){
+                                   forceRun = TRUE){
 
   if(is.null(biological.group)){
     stop("Must specify atleast one biological.group that is present in the colData of input object.")
@@ -1090,7 +1090,7 @@ reportSeuratMarkerSelection <- function(inSCE,
 #'  to visualize in each group. Default \code{10}.
 #' @param forceRun A logical value indicating if all algorithms should be
 #'  re-run regardless if they have been computed previously in the input object.
-#'  Default is \code{FALSE}.
+#'  Default is \code{TRUE}.
 #'
 #' @return A \code{\link[SingleCellExperiment]{SingleCellExperiment}} object
 #'  with computations stored.
@@ -1123,7 +1123,7 @@ reportSeurat <- function(
   runMSClusters = TRUE,
   runMSBioGroup = TRUE,
   numTopFeatures = 10,
-  forceRun = FALSE){
+  forceRun = TRUE){
 
   if(is.null(biological.group)){
     stop("Must specify atleast one biological.group that is present in the colData of input object.")

inst/rmarkdown/seurat/reportSeurat.Rmd

@@ -58,14 +58,14 @@ sampleNames <- unique(colData(data)[[biological.group]])
 
 ```{r, echo=FALSE, results='asis', warning=FALSE, message=FALSE}
 showSession <- FALSE
-seuratRun <- knitr::knit_child('reportSeuratRun.Rmd', quiet = TRUE, envir = environment())
+seuratRun <- knitr::knit_child(system.file("rmarkdown/seurat", "reportSeuratRun.Rmd", package = "singleCellTK"), quiet = TRUE, envir = environment())
 ```
 
 <!-- Seurat Results -->
 
 ```{r, echo=FALSE, results='asis', warning=FALSE, message=FALSE}
 showSession <- FALSE
-seuratResults <- knitr::knit_child('reportSeuratResults.Rmd', quiet = TRUE, envir = environment())
+seuratResults <- knitr::knit_child(system.file("rmarkdown/seurat", "reportSeuratResults.Rmd", package = "singleCellTK"), quiet = TRUE, envir = environment())
 ```
 
 # Summary {-}

inst/rmarkdown/seurat/reportSeuratResults.Rmd

@@ -72,7 +72,7 @@ maxResolution <- clustering.resolution
 numClusters <- 10 #remove this later
 showClusterDesc <- FALSE
 
-resClustering <- knitr::knit_child('reportSeuratClustering.Rmd', quiet = TRUE, envir = environment())
+resClustering <- knitr::knit_child(system.file("rmarkdown/seurat", "reportSeuratClustering.Rmd", package = "singleCellTK"), quiet = TRUE, envir = environment())
 ```
 
 ```{r, echo=FALSE, results='asis', warning=FALSE, message=FALSE}
@@ -88,7 +88,7 @@ selectedOption <- paste0("Seurat_louvain_Resolution", clustering.resolution)
 groupTitle <- "Clusters"
 titleMarkerPlots <- "Gene Plots of Top Markers by Clusters"
 headingMS <- "##"
-resMSC <- knitr::knit_child('reportSeuratMarkerSelection.Rmd', quiet = TRUE, envir = environment())
+resMSC <- knitr::knit_child(system.file("rmarkdown/seurat", "reportSeuratMarkerSelection.Rmd", package = "singleCellTK"), quiet = TRUE, envir = environment())
 numMarkerGenesCluster <- nrow(data.markers[data.markers$p_val_adj < 0.05, ])
 ```
 
@@ -101,7 +101,7 @@ selectedOption <- biological.group
 groupTitle <- biological.group
 titleMarkerPlots <- paste0("Gene Plots of Top Markers by Group: ", biological.group)
 headingMS <- "##"
-resMSB <- knitr::knit_child('reportSeuratMarkerSelection.Rmd', quiet = TRUE)
+resMSB <- knitr::knit_child(system.file("rmarkdown/seurat", "reportSeuratMarkerSelection.Rmd", package = "singleCellTK"), quiet = TRUE)
 numMarkerGenesBio <- nrow(data.markers[data.markers$p_val_adj < 0.05, ])
 ```
 
@@ -116,7 +116,7 @@ titleMarkerPlots <- "Plot Selected Features"
 numTopFeatures <- length(selected.markers)
 headingMS <- "#"
 
-resPSM <- knitr::knit_child('reportSeuratMarkerSelection.Rmd', quiet = TRUE)
+resPSM <- knitr::knit_child(system.file("rmarkdown/seurat", "reportSeuratMarkerSelection.Rmd", package = "singleCellTK"), quiet = TRUE)
 ```
 
 ```{r, echo=FALSE, results='asis', warning=FALSE, message=FALSE, eval=!is.null(selected.markers)}

inst/rmarkdown/seurat/reportSeuratRun.Rmd

@@ -85,19 +85,19 @@ numSamples <- length(sampleNames)
 <!-- Normalization -->
 ```{r, echo=FALSE, results='asis', message=FALSE}
 headingNorm <- "##"
-resNormalization <- knitr::knit_child('reportSeuratNormalizeData.Rmd', quiet = TRUE, envir = environment())
+resNormalization <- knitr::knit_child(system.file("rmarkdown/seurat", "reportSeuratNormalizeData.Rmd", package = "singleCellTK"), quiet = TRUE, envir = environment())
 ```
 
 <!-- Feature Selection -->
 ```{r, echo=FALSE, results='asis'}
 headingFS <- "##"
-resFeatureSelection <- knitr::knit_child('reportSeuratFeatureSelection.Rmd', quiet = TRUE)
+resFeatureSelection <- knitr::knit_child(system.file("rmarkdown/seurat", "reportSeuratFeatureSelection.Rmd", package = "singleCellTK"), quiet = TRUE)
 ```
 
 <!-- Scale Data -->
 ```{r, echo=FALSE, results='asis', warning=FALSE, message=FALSE}
 headingSD <- "##"
-resScaleData <- knitr::knit_child('reportSeuratScaleData.Rmd', quiet = TRUE)
+resScaleData <- knitr::knit_child(system.file("rmarkdown/seurat", "reportSeuratScaleData.Rmd", package = "singleCellTK"), quiet = TRUE)
 ```
 
 <!-- Dimensionality Reduction -->
@@ -106,7 +106,7 @@ headingDR <- "##"
 headingDR2 <- "###"
 significant_PC <- 10
 
-resDimRed <- knitr::knit_child('reportSeuratDimRed.Rmd', quiet = TRUE, envir = environment())
+resDimRed <- knitr::knit_child(system.file("rmarkdown/seurat", "reportSeuratDimRed.Rmd", package = "singleCellTK"), quiet = TRUE, envir = environment())
 ```
 
 <!-- Clustering -->
@@ -115,7 +115,7 @@ numClusters <- 10 # this should be computed by the code itself (do later)
 showClusterDesc <- TRUE
 headingClust <- "##"
 
-resClustering <- knitr::knit_child('reportSeuratClustering.Rmd', quiet = TRUE, envir = environment())
+resClustering <- knitr::knit_child(system.file("rmarkdown/seurat", "reportSeuratClustering.Rmd", package = "singleCellTK"), quiet = TRUE, envir = environment())
 ```
 
 # Seurat Run