v-0.99.10

rikenbit · Nov 6, 2018 · 73e671a · 73e671a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: scTensor
 Type: Package
 Title: Detection of cell-cell interaction within single-cell RNA-Seq data
-Version: 0.99.9
+Version: 0.99.10
 Date: 2018-09-25
 Authors@R: person("Koki", "Tsuyuzaki", role = c("aut", "cre"), email = "k.t.the-answer@hotmail.co.jp")
 Depends: R (>= 3.5.0)

diff --git a/inst/NEWS b/inst/NEWS
@@ -1,3 +1,7 @@
+VERSION 0.99.10
+------------------------
+   o Revised and modified some parts
+
 VERSION 0.99.9
 ------------------------
    o Revised and modified some parts

diff --git a/man/cellCellReport.Rd b/man/cellCellReport.Rd
@@ -59,7 +59,24 @@ The result is saved as HTML report which contains with multiple files.
 \author{Koki Tsuyuzaki}
 
 \examples{
-showMethods("cellCellReport")
+	if(interactive()){
+	library("SingleCellExperiment")
+	library("LRBase.Hsa.eg.db")
+	library("MeSH.Hsa.eg.db")
+	source("scTensor/R/scTensor-internal.R")
+
+	data(GermMale)
+	data(labelGermMale)
+	data(tsneGermMale)
+	sce <- SingleCellExperiment(assays=list(counts = GermMale))
+	reducedDims(sce) <- SimpleList(TSNE=tsneGermMale$Y)
+	cellCellSetting(sce, LRBase.Hsa.eg.db, labelGermMale, names(labelGermMale))
+	rks <- cellCellRanks(sce)
+	cellCellDecomp(sce, ranks=rks$selected)
+	cellCellReport(sce, reducedDimNames="TSNE",
+	    title="Cell-cell interaction within Germline_Male, GSE86146",
+	    author="Koki Tsuyuzaki", thr=15, html.open=TRUE)
+    }
 }
 
 \keyword{methods}
diff --git a/vignettes/scTensor.Rmd b/vignettes/scTensor.Rmd
@@ -321,14 +321,9 @@ rks$selected
 ### HTML Report : cellCellReport
 
 If `cellCellDecomp` is properly finished, we can perform `cellCellReport`
-function to output the HTML report like belows.
-
-```{r cellCellReport, echo=TRUE}
-cellCellReport(sce, reducedDimNames="TSNE",
-    title="Cell-cell interaction within Germline_Male, GSE86146",
-    author="Koki Tsuyuzaki", thr=5, top=2, html.open=FALSE)
-```
-
+function to output the HTML report like belows. Please type
+`example(cellCellReport)` and the report will be generated in the temporary
+directory (it costs 5 to 10 minutes).
 After `cellCellReport`, multiple R markdown files, compiled HTML files,
 figures, and R binary file containing the result of analysis are saved to
 `out.dir` (Figure 2). For more details, open the `index.html` by your web