From 7ba931a098f04636ea994feab34a326d9addcce4 Mon Sep 17 00:00:00 2001 From: Nuno Agostinho Date: Sat, 22 Apr 2017 13:14:40 +0100 Subject: [PATCH] Fix non-portable file names and documentation issues --- R/analysis_information.R | 1 - R/globalAccess.R | 2 +- man/noinfo.Rd | 2 -- man/setDifferentialAnalysesZoom.Rd | 4 ++-- vignettes/GUI_tutorial.Rmd | 14 +++++++------- .../img/{1. load data.png => 1_load_data.png} | Bin ...ntify splicing.png => 2_quantify_splicing.png} | Bin vignettes/img/{3. survival.png => 3_survival.png} | Bin vignettes/img/{4. pca.png => 4_pca.png} | Bin .../{5. psi cutoff 2.png => 5_psi_cutoff_2.png} | Bin .../{6. diff splicing.png => 6_diff_splicing.png} | Bin .../img/{7. psi cutoff.png => 7_psi_cutoff.png} | Bin 12 files changed, 10 insertions(+), 13 deletions(-) rename vignettes/img/{1. load data.png => 1_load_data.png} (100%) rename vignettes/img/{2. quantify splicing.png => 2_quantify_splicing.png} (100%) rename vignettes/img/{3. survival.png => 3_survival.png} (100%) rename vignettes/img/{4. pca.png => 4_pca.png} (100%) rename vignettes/img/{5. psi cutoff 2.png => 5_psi_cutoff_2.png} (100%) rename vignettes/img/{6. diff splicing.png => 6_diff_splicing.png} (100%) rename vignettes/img/{7. psi cutoff.png => 7_psi_cutoff.png} (100%) diff --git a/R/analysis_information.R b/R/analysis_information.R index ee065e31..be60d4ca 100644 --- a/R/analysis_information.R +++ b/R/analysis_information.R @@ -137,7 +137,6 @@ infoUI <- function(id) { #' Interface when no information could be retrieved #' @param output Shiny output -#' @param title Character: title of the message to show to the user #' @param description Character: description of the message to show to the user #' @inheritDotParams errorDialog -description #' diff --git a/R/globalAccess.R b/R/globalAccess.R index 3bed6d31..f2ac5250 100644 --- a/R/globalAccess.R +++ b/R/globalAccess.R @@ -390,7 +390,7 @@ setDifferentialAnalysesHighlightedEvents <- function(events, #' category #' @note Needs to be called inside a reactive function #' -#' @param brush Integer: X and Y coordinates +#' @param zoom Integer: X and Y coordinates #' @param category Character: data category (e.g. "Carcinoma 2016"); by default, #' it uses the selected data category #' diff --git a/man/noinfo.Rd b/man/noinfo.Rd index 461b36d6..515cc016 100644 --- a/man/noinfo.Rd +++ b/man/noinfo.Rd @@ -20,8 +20,6 @@ noinfo(output, \item{buttonLabel}{Character: button label (NULL by default)} \item{buttonIcon}{Character: button icon (NULL by default)} }} - -\item{title}{Character: title of the message to show to the user} } \value{ NULL (this function is used to modify the Shiny session's state) diff --git a/man/setDifferentialAnalysesZoom.Rd b/man/setDifferentialAnalysesZoom.Rd index 19a14064..e19a882d 100644 --- a/man/setDifferentialAnalysesZoom.Rd +++ b/man/setDifferentialAnalysesZoom.Rd @@ -8,10 +8,10 @@ category} setDifferentialAnalysesZoom(zoom, category = getCategory()) } \arguments{ +\item{zoom}{Integer: X and Y coordinates} + \item{category}{Character: data category (e.g. "Carcinoma 2016"); by default, it uses the selected data category} - -\item{brush}{Integer: X and Y coordinates} } \value{ NULL (this function is used to modify the Shiny session's state) diff --git a/vignettes/GUI_tutorial.Rmd b/vignettes/GUI_tutorial.Rmd index cab4f6d7..d3ae277f 100644 --- a/vignettes/GUI_tutorial.Rmd +++ b/vignettes/GUI_tutorial.Rmd @@ -77,7 +77,7 @@ field below the column name. Filtering and sorting of loaded data have **no** impact on the subsequent analyses available in the application. ```{r, echo=FALSE, fig.retina=NULL, out.width='400pt'} -knitr::include_graphics("img/1. load data.png") +knitr::include_graphics("img/1_load_data.png") ``` **Figure 1:** Available options for TCGA data loading. @@ -103,7 +103,7 @@ by parsing the annotation from programs like [VAST-TOOLS][4], [MISO][3], Click on **Quantify events** to start quantifying alternative splicing. ```{r, echo=FALSE, fig.retina=NULL, out.width='400pt'} -knitr::include_graphics("img/2. quantify splicing.png") +knitr::include_graphics("img/2_quantify_splicing.png") ``` **Figure 2:** Available options for alternative splicing quantification. @@ -172,7 +172,7 @@ over a survival curve in the plot. The plot also allows zooming in by clicking and dragging and to omit data series by clicking on their name in the legend. ```{r, echo=FALSE, fig.retina=NULL, out.width='400pt'} -knitr::include_graphics("img/3. survival.png") +knitr::include_graphics("img/3_survival.png") ``` **Figure 3:** Available options for patient survival. @@ -213,7 +213,7 @@ in the PCA plot. 4. Click on **Plot PCA**. ```{r, echo=FALSE, fig.retina=NULL, out.width='700pt'} -knitr::include_graphics("img/4. pca.png") +knitr::include_graphics("img/4_pca.png") ``` **Figure 4:** Available options for PCA performance and plotting. @@ -281,7 +281,7 @@ Click the buttons *Plot survival curves* and/or *Fit Cox PH model* whenever this slider is changed to update the Kaplan-Meier plot and/or the Cox model. ```{r, echo=FALSE, fig.retina=NULL, out.width='350pt'} -knitr::include_graphics("img/5. psi cutoff 2.png") +knitr::include_graphics("img/5_psi_cutoff_2.png") ``` **Figure 5:** Options to adjust the alternative splicing quantification cut-off @@ -332,7 +332,7 @@ When the analyses complete, the results are shown in a plot and in a filtrable and sortable table. ```{r, echo=FALSE, fig.retina=NULL, out.width='350pt'} -knitr::include_graphics("img/6. diff splicing.png") +knitr::include_graphics("img/6_diff_splicing.png") ``` **Figure 6:** Options for differential splicing analysis. @@ -399,7 +399,7 @@ the screen**. 6. Click on **Plot survival curves**. ```{r, echo=FALSE, fig.retina=NULL, out.width='400pt'} -knitr::include_graphics("img/7. psi cutoff.png") +knitr::include_graphics("img/7_psi_cutoff.png") ``` **Figure 7:** Available options for survival analysis. diff --git a/vignettes/img/1. load data.png b/vignettes/img/1_load_data.png similarity index 100% rename from vignettes/img/1. load data.png rename to vignettes/img/1_load_data.png diff --git a/vignettes/img/2. quantify splicing.png b/vignettes/img/2_quantify_splicing.png similarity index 100% rename from vignettes/img/2. quantify splicing.png rename to vignettes/img/2_quantify_splicing.png diff --git a/vignettes/img/3. survival.png b/vignettes/img/3_survival.png similarity index 100% rename from vignettes/img/3. survival.png rename to vignettes/img/3_survival.png diff --git a/vignettes/img/4. pca.png b/vignettes/img/4_pca.png similarity index 100% rename from vignettes/img/4. pca.png rename to vignettes/img/4_pca.png diff --git a/vignettes/img/5. psi cutoff 2.png b/vignettes/img/5_psi_cutoff_2.png similarity index 100% rename from vignettes/img/5. psi cutoff 2.png rename to vignettes/img/5_psi_cutoff_2.png diff --git a/vignettes/img/6. diff splicing.png b/vignettes/img/6_diff_splicing.png similarity index 100% rename from vignettes/img/6. diff splicing.png rename to vignettes/img/6_diff_splicing.png diff --git a/vignettes/img/7. psi cutoff.png b/vignettes/img/7_psi_cutoff.png similarity index 100% rename from vignettes/img/7. psi cutoff.png rename to vignettes/img/7_psi_cutoff.png