update vignettes

satijalab · Jun 24, 2018 · 3e90f5e · 3e90f5e
1 parent 529a860
commit 3e90f5e
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Showing 13 changed files with 19 additions and 16 deletions.
diff --git a/inst/doc/batch_correction.R b/inst/doc/batch_correction.R
@@ -3,7 +3,7 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
   digits = 2,
-  fig.width=5, fig.height=3, dpi=150, out.width = '70%'
+  fig.width=5, fig.height=3, dpi=100, out.width = '70%'
 )
 
 ## ----load_packages, include=FALSE----------------------------------------

diff --git a/inst/doc/batch_correction.Rmd b/inst/doc/batch_correction.Rmd
@@ -14,7 +14,7 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
   digits = 2,
-  fig.width=5, fig.height=3, dpi=150, out.width = '70%'
+  fig.width=5, fig.height=3, dpi=100, out.width = '70%'
 )
 ```
 

diff --git a/inst/doc/denoising.R b/inst/doc/denoising.R
@@ -3,7 +3,7 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
   digits = 2,
-  fig.width=6, fig.height=4, dpi=150, out.width = '70%'
+  fig.width=6, fig.height=4, dpi=100, out.width = '70%'
 )
 
 ## ----load_packages, include=FALSE----------------------------------------
@@ -28,7 +28,7 @@ pricu <- princurve::principal.curve(pca$x, smoother='lowess', f=0.5, stretch=333
 # cell projection onto curve is maturation score
 maturation_score <- pricu$lambda/max(pricu$lambda)
 
-## ------------------------------------------------------------------------
+## ---- fig.width=8, fig.height=4, out.width = '100%'----------------------
 y_smooth <- sctransform::smooth_via_pca(vst_out$y, do_plot = TRUE)
 
 ## ------------------------------------------------------------------------

diff --git a/inst/doc/denoising.Rmd b/inst/doc/denoising.Rmd
@@ -14,7 +14,7 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
   digits = 2,
-  fig.width=6, fig.height=4, dpi=150, out.width = '70%'
+  fig.width=6, fig.height=4, dpi=100, out.width = '70%'
 )
 ```
 
@@ -53,7 +53,7 @@ maturation_score <- pricu$lambda/max(pricu$lambda)
 
 We will now smooth the Pearson residual by PCA. Internally `smooth_via_pca` performs PCA, then keeps only significant dimensions and back-rotates to the original data space. The number of significant dimensions is determined using the 'elbow' method. To speed things up we could also use only a subset of the genes for this operation (e.g. variable genes).
 
-```{r}
+```{r, fig.width=8, fig.height=4, out.width = '100%'}
 y_smooth <- sctransform::smooth_via_pca(vst_out$y, do_plot = TRUE)
 ```
 

diff --git a/inst/doc/differential_expression.R b/inst/doc/differential_expression.R
@@ -3,7 +3,7 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
   digits = 2,
-  fig.width=4, fig.height=2.5, dpi=300, out.width = '70%'
+  fig.width=4, fig.height=2.5, dpi=100, out.width = '70%'
 )
 
 ## ----load_packages, include=FALSE----------------------------------------

diff --git a/inst/doc/differential_expression.Rmd b/inst/doc/differential_expression.Rmd
@@ -14,7 +14,7 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
   digits = 2,
-  fig.width=4, fig.height=2.5, dpi=300, out.width = '70%'
+  fig.width=4, fig.height=2.5, dpi=100, out.width = '70%'
 )
 ```
 

diff --git a/inst/doc/variance_stabilizing_transformation.R b/inst/doc/variance_stabilizing_transformation.R
@@ -3,7 +3,7 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
   digits = 2,
-  fig.width=4, fig.height=2.5, dpi=150, out.width = '70%'
+  fig.width=4, fig.height=2.5, dpi=100, out.width = '70%'
 )
 
 ## ----load_packages, include=FALSE----------------------------------------

diff --git a/inst/doc/variance_stabilizing_transformation.Rmd b/inst/doc/variance_stabilizing_transformation.Rmd
@@ -14,7 +14,7 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
   digits = 2,
-  fig.width=4, fig.height=2.5, dpi=150, out.width = '70%'
+  fig.width=4, fig.height=2.5, dpi=100, out.width = '70%'
 )
 ```
 

diff --git a/sctransform.Rproj b/sctransform.Rproj
@@ -17,5 +17,8 @@ StripTrailingWhitespace: Yes
 
 BuildType: Package
 PackageUseDevtools: Yes
-PackageInstallArgs: --no-multiarch --with-keep.source
-PackageCheckArgs: --as-cran --no-vignettes --no-build-vignettes
+PackageInstallArgs: --no-multiarch --with-keep.source --no-build-vignettes
+PackageBuildArgs: --no-build-vignettes
+PackageBuildBinaryArgs: --no-build-vignettes
+PackageCheckArgs: --as-cran --no-build-vignettes
+PackageRoxygenize: rd,collate,namespace
diff --git a/vignettes/batch_correction.Rmd b/vignettes/batch_correction.Rmd
@@ -14,7 +14,7 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
   digits = 2,
-  fig.width=5, fig.height=3, dpi=150, out.width = '70%'
+  fig.width=5, fig.height=3, dpi=100, out.width = '70%'
 )
 ```
 

diff --git a/vignettes/denoising.Rmd b/vignettes/denoising.Rmd
@@ -14,7 +14,7 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
   digits = 2,
-  fig.width=6, fig.height=4, dpi=150, out.width = '70%'
+  fig.width=6, fig.height=4, dpi=100, out.width = '70%'
 )
 ```
 

diff --git a/vignettes/differential_expression.Rmd b/vignettes/differential_expression.Rmd
@@ -14,7 +14,7 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
   digits = 2,
-  fig.width=4, fig.height=2.5, dpi=300, out.width = '70%'
+  fig.width=4, fig.height=2.5, dpi=100, out.width = '70%'
 )
 ```
 

diff --git a/vignettes/variance_stabilizing_transformation.Rmd b/vignettes/variance_stabilizing_transformation.Rmd
@@ -14,7 +14,7 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
   digits = 2,
-  fig.width=4, fig.height=2.5, dpi=150, out.width = '70%'
+  fig.width=4, fig.height=2.5, dpi=100, out.width = '70%'
 )
 ```