diff --git a/.travis.yml b/.travis.yml index ccef4e99..0d75681d 100644 --- a/.travis.yml +++ b/.travis.yml @@ -3,3 +3,5 @@ r: - oldrel - release - devel + +warnings_are_errors: false diff --git a/R/volcano_trio.R b/R/volcano_trio.R index bc49baba..09e491fc 100644 --- a/R/volcano_trio.R +++ b/R/volcano_trio.R @@ -366,6 +366,10 @@ volcano_plot <- function(pvalues_df, #' \item h: padj > p_cutoff & fc >= fc_cutoff #' } #' } +#' @param colour_scheme How to factor the colour scheme. Colour by "none" for +#' significance group (by p and fold change cut-off), "upregulated" colour- +#' coded according to the upregulated groups, or "polar" for the significance +#' group. #' @param fc_line Logical whether to add vertical dashed line at fc_cutoff #' (default = TRUE). #' @param p_line Logical whether to add horizontal dashed line at p_cutoff diff --git a/docs/articles/Extended_Vignette.html b/docs/articles/Extended_Vignette.html index a56e1de3..0cbdaec4 100644 --- a/docs/articles/Extended_Vignette.html +++ b/docs/articles/Extended_Vignette.html @@ -1255,8 +1255,8 @@

radial_plotly(polar = syn_polar, label_rows = c("SLAMF6", "PARP16", "ITM2C"), hover=hovertext) -
-

By hovering over certain points you can also determine genes for future interrogation.

+
+

By hovering over certain points you can also determine genes for future interrogation.

Similarly we can create a static ggplot image using radial_ggplot:

 radial_ggplot(polar = syn_polar,
@@ -1307,9 +1307,9 @@ 

                       box_colours = c("pink", "gold"), 
                       plot_method='plotly') 
 
-plotly::subplot(plot1, plot2, plot3, titleY=TRUE, margin=0.05)
-
-

Or using ggplot

+plotly::subplot(plot1, plot2, plot3, titleY=TRUE, margin=0.05) +
+

Or using ggplot

 plot1 <- boxplot_trio(syn_polar,
                       value = "FAM92B",
@@ -1353,8 +1353,8 @@ 

                plot_height = 800)
 
 p
-
-

We can alter the colour code using the colours parameter. These are assigned in order group1+, group1+group2+, group2+, group2+group3+, group3+, group1+group3+.

+
+

We can alter the colour code using the colours parameter. These are assigned in order group1+, group1+group2+, group2+, group2+group3+, group3+, group1+group3+.

 p <- volcano3D(syn_polar,
                label_rows = c("SLAMF6", "PARP16", "ITM2C"),
@@ -1367,8 +1367,8 @@ 

                plot_height=800)
 
 p
-
- +
+
@@ -1380,7 +1380,7 @@

Static Images

There are a few ways to save plotly plots as static images. Firstly plotly offers a download button ( ) in the figure mode bar (appears top right). By default this saves images as png, however it is possible to convert to svg, jpeg or webp using:

-p %>% plotly::config(toImageButtonOptions = list(format = "svg"))
+p %>% plotly::config(toImageButtonOptions = list(format = "svg"))

Alternatively, if orca command-line utility is installed, this can also be used to save plotly images. To install follow the instructions here.

 orca(p, "./volcano_3d_synovium.svg", format = "svg")
@@ -1413,8 +1413,8 @@

p <- show_grid(four_grid) p$cylindrical -
-

and pass it into the plotting functions:

+
+

and pass it into the plotting functions:

 volcano3D(syn_polar,
           grid = four_grid,
@@ -1422,8 +1422,8 @@ 

           label_size = 10,
           xy_aspectratio = 1,
           z_aspectratio = 0.9)
-
-

For example to extend the radial axis and increase the number of spokes in 2D we can apply:

+
+

For example to extend the radial axis and increase the number of spokes in 2D we can apply:

 new_grid = polar_grid(r_vector=NULL,
                       z_vector=-log10(syn_polar@pvalues$LRT_pvalue),
@@ -1440,8 +1440,8 @@ 

                   label_rows = c("SLAMF6", "PARP16", "ITM2C"))
 
 p %>% config(editable = TRUE)
-
- +
+

@@ -1506,8 +1506,8 @@ 

 radial_plotly(polar = syn_mod_polar,
               label_rows = c("M156.0", "M37.2"))
-
-

Or a ggplot static image using radial_ggplot:

+
+

Or a ggplot static image using radial_ggplot:

 radial_ggplot(polar = syn_mod_polar,
               label_rows = c("M156.0", "M37.2"),
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diff --git a/docs/articles/Vignette.html b/docs/articles/Vignette.html
index 514206d4..1a3bccec 100644
--- a/docs/articles/Vignette.html
+++ b/docs/articles/Vignette.html
@@ -142,7 +142,7 @@ 

 
  • setting up the input pvalues data frame
    • 
 
  • using the volcano3D package to create and deploy a shiny app
    • 
 
-
     Lifecycle: Maturing License: GPL v2 CRAN status Downloads 2021-02-04 Build Status GitHub issues
    
+
     Lifecycle: Maturing License: GPL v2 CRAN status Downloads 2021-02-19 Build Status GitHub issues
    
 
    
 
    
 Getting Started
    
@@ -872,7 +872,7 @@ 
    
 Static Images
    
 
    There are a few ways to save plotly plots as static images. Firstly plotly offers a download button (  ) in the figure mode bar (appears top right). By default this saves images as png, however it is possible to convert to svg, jpeg or webp using:
    
 
    -p %>% plotly::config(toImageButtonOptions = list(format = "svg"))
    
+p %>% plotly::config(toImageButtonOptions = list(format = "svg"))

    Alternatively, if orca command-line utility is installed, this can also be used to save plotly images. To install follow the instructions here.

     orca(p, "./volcano_3d_synovium.svg", format = "svg")
    diff --git a/docs/articles/Vignette_files/figure-html/unnamed-chunk-13-1.png b/docs/articles/Vignette_files/figure-html/unnamed-chunk-13-1.png index 1d5666ed..582af9d3 100644 Binary files a/docs/articles/Vignette_files/figure-html/unnamed-chunk-13-1.png and b/docs/articles/Vignette_files/figure-html/unnamed-chunk-13-1.png differ diff --git a/docs/articles/Vignette_files/figure-html/unnamed-chunk-15-1.png b/docs/articles/Vignette_files/figure-html/unnamed-chunk-15-1.png index ff304c65..871d490d 100644 Binary files a/docs/articles/Vignette_files/figure-html/unnamed-chunk-15-1.png and b/docs/articles/Vignette_files/figure-html/unnamed-chunk-15-1.png differ diff --git a/docs/articles/pvalues_generator_files/figure-html/unnamed-chunk-18-1.png b/docs/articles/pvalues_generator_files/figure-html/unnamed-chunk-18-1.png index 39539c96..202b9192 100644 Binary files a/docs/articles/pvalues_generator_files/figure-html/unnamed-chunk-18-1.png and b/docs/articles/pvalues_generator_files/figure-html/unnamed-chunk-18-1.png differ diff --git a/docs/articles/pvalues_generator_files/figure-html/unnamed-chunk-20-1.png b/docs/articles/pvalues_generator_files/figure-html/unnamed-chunk-20-1.png index 13ff9908..544e6e0e 100644 Binary files a/docs/articles/pvalues_generator_files/figure-html/unnamed-chunk-20-1.png and b/docs/articles/pvalues_generator_files/figure-html/unnamed-chunk-20-1.png differ diff --git a/docs/articles/shiny_builder.html b/docs/articles/shiny_builder.html index 19da68ac..f59040ac 100644 --- a/docs/articles/shiny_builder.html +++ b/docs/articles/shiny_builder.html @@ -330,7 +330,7 @@

    # Tab 2: 3D volcano plot tabPanel("Volcano", value="v", fluidPage( - column(8, withSpinner(plotlyOutput("volcano", height=720))), + column(8, withSpinner(plotlyOutput("volcano", height=720))), column(4, fluidRow( # option for data type @@ -394,7 +394,7 @@

    updateNavbarPage(session, "mainNavbarPage", "t")}) # Volcano tab: Create the 3D volcano plot - output$volcano <- renderPlotly({ + output$volcano <- renderPlotly({ data_type <- as.numeric(input$data_type) colour_scheme <- as.numeric(input$colour_type) @@ -407,13 +407,13 @@

    fc_or_zscore = switch(data_type, "zscore", "fc"), xy_aspectratio = 1, z_aspectratio = 0.9) %>% - layout(showlegend = switch(colour_scheme, T, F)) + layout(showlegend = switch(colour_scheme, T, F)) }) # Volcano tab: Create pathotype boxplots when genes clicked output$boxplots <- renderPlot({ - s <- event_data("plotly_click") + s <- event_data("plotly_click") req(length(s) > 0) gene = s$key boxplot_trio(syn_polar, diff --git a/docs/articles/shiny_builder_files/figure-html/unnamed-chunk-7-1.png b/docs/articles/shiny_builder_files/figure-html/unnamed-chunk-7-1.png index 414bb783..d24f2a27 100644 Binary files a/docs/articles/shiny_builder_files/figure-html/unnamed-chunk-7-1.png and b/docs/articles/shiny_builder_files/figure-html/unnamed-chunk-7-1.png differ diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index dd0f06ae..82a951f5 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -6,5 +6,5 @@ articles: Vignette: Vignette.html pvalues_generator: pvalues_generator.html shiny_builder: shiny_builder.html -last_built: 2021-02-04T20:43Z +last_built: 2021-02-19T18:13Z diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png index 206e7ef5..1a44d2f2 100644 Binary files a/docs/reference/Rplot002.png and b/docs/reference/Rplot002.png differ diff --git a/docs/reference/volcano_plot-1.png b/docs/reference/volcano_plot-1.png index 7daa2306..d32c4b5a 100644 Binary files a/docs/reference/volcano_plot-1.png and b/docs/reference/volcano_plot-1.png differ diff --git a/docs/reference/volcano_plot.html b/docs/reference/volcano_plot.html index ef746ef8..56cc1f72 100644 --- a/docs/reference/volcano_plot.html +++ b/docs/reference/volcano_plot.html @@ -354,7 +354,7 @@

    Examp label_col = "Gene", label_rows=c("SLAMF6"), fc_col_suffix="log2FoldChange") -

    #> Error in grid.Call(C_convert, x, as.integer(whatfrom), as.integer(whatto), valid.units(unitTo)): Viewport has zero dimension(s)
    +