Merge pull request #1020 from jiajic/suite_dev

chore: move some deps to suggests

DESCRIPTION

@@ -44,14 +44,11 @@ Imports:
     GiottoVisuals (>= 0.2.4),
     igraph (>= 1.2.4.1),
     jsonlite,
-    limma,
     Matrix (>= 1.6-2),
     MatrixGenerics,
-    plotly,
     progressr,
     reshape2,
     reticulate (>= 1.25),
-    Rtsne (>= 0.15),
     scales (>= 1.0.0),
     sparseMatrixStats,
     stats,
@@ -86,11 +83,13 @@ Suggests:
     jackstraw,
     kableExtra,
     knitr,
+    limma,
     MAST,
     miniUI,
     multinet (>= 3.0.2),
     networkD3,
     pheatmap,
+    plotly,
     quadprog,
     harmony,
     R.utils,
@@ -99,6 +98,7 @@ Suggests:
     rlang,
     rhdf5,
     RTriangle (>= 1.6-0.10),
+    Rtsne (>= 0.15),
     Rvision,
     scater,
     scran (>= 1.10.1),

R/auxiliary_giotto.R

@@ -756,33 +756,33 @@ filterGiotto <- function(
   if(!inherits(dbMatrix, 'dbMatrix')) {
     stop('dbMatrix must be of class dbMatrix')
   }
-  
+
   if(!is.character(name)) {
     stop('name must be a character')
   }
-  
+
   # TODO: update with dbData generic
   con = dbMatrix:::get_con(dbMatrix)
-  
+
   # overwrite table by default
   if(name %in% DBI::dbListTables(con)) {
     DBI::dbRemoveTable(con, name)
   }
-  
+
   if(verbose){
     msg <- glue::glue('Computing {name} expression matrix on disk...')
-    cat(msg)   
+    cat(msg)
   }
-  
+
   dbMatrix[] |>
     dplyr::compute(temporary=F, name = name)
-    
+
   # TODO: update below with proper setters from dbMatrix
   dbMatrix[] <- dplyr::tbl(con, name) # reassign to computed mat
   dbMatrix@name <- name
-  
+
   if(verbose) cat('done \n')
-  
+
   return(dbMatrix)
 }
 
@@ -902,7 +902,7 @@ filterGiotto <- function(
             dbMatrix = norm_expr,
             name = 'normalized',
             verbose = verbose
-        ) 
+        )
     }
 
     norm_expr <- create_expr_obj(
@@ -913,14 +913,14 @@ filterGiotto <- function(
         provenance = provenance,
         misc = NULL
     )
-  
+
     # Save dbMatrix to db
     if(compute_mat && !is.null(norm_scaled_expr)){
         norm_scaled_expr = .compute_dbMatrix(
             dbMatrix = norm_scaled_expr,
             name = 'scaled',
             verbose = verbose
-        ) 
+        )
     }
 
     norm_scaled_expr <- create_expr_obj(
@@ -1297,6 +1297,8 @@ adjustGiottoMatrix <- function(
             provided.")
     }
 
+    package_check("limma")
+
     # Set feat_type and spat_unit
     spat_unit <- set_default_spat_unit(
         gobject = gobject,

R/cross_section.R

@@ -1119,6 +1119,9 @@ insertCrossSectionSpatPlot3D <- function(
         custom_ratio = NULL,
         default_save_name = "spat3D_with_cross_section",
         ...) {
+
+    package_check("plotly", repository = "CRAN:plotly")
+
     spat_unit <- set_default_spat_unit(
         gobject = gobject, spat_unit = spat_unit
     )
@@ -1253,6 +1256,9 @@ insertCrossSectionFeatPlot3D <- function(gobject,
     save_param = list(),
     default_save_name = "spatGenePlot3D_with_cross_section",
     ...) {
+
+    package_check("plotly", repository = "CRAN:plotly")
+
     spat_unit <- set_default_spat_unit(
         gobject = gobject, spat_unit = spat_unit
     )

R/dimension_reduction.R

@@ -2634,6 +2634,9 @@ runtSNE <- function(
         seed_number = 1234,
         verbose = TRUE,
         ...) {
+
+    package_check("Rtsne")
+
     # Set feat_type and spat_unit
     spat_unit <- set_default_spat_unit(
         gobject = gobject,

R/interactivity.R

@@ -96,7 +96,7 @@ plotInteractivePolygons <- function(
                         geom_polygon(
                             data = clicklist(),
                             aes(x, y, color = name),
-                            alpha = 0, 
+                            alpha = 0,
                             show.legend = FALSE,
                             ...
                         ) +
@@ -649,6 +649,12 @@ plotInteractive3D <- function(
         cell_color = "leiden_clus",
         cell_color_code = NULL, point_size = 0.5,
         width = "100%", height = "400px") {
+
+    package_check(
+        c("plotly", "miniUI", "shiny"),
+        repository = c("CRAN:plotly", "CRAN:miniUI", "CRAN:shiny")
+    )
+
     # NSE vars
     sdimx <- sdimy <- sdimz <- cell_ID <- NULL
 

R/spatial_genes.R

@@ -2924,6 +2924,9 @@ showPattern3D <- function(
         save_plot = NULL,
         save_param = list(),
         default_save_name = "showPattern3D") {
+
+    package_check("plotly", repository = "CRAN:plotly")
+
     # data.table variables
     center_x <- x_start <- x_end <- center_y <- y_start <- y_end <-
         center_z <- z_start <- z_end <- NULL

R/spatial_interaction.R

@@ -512,6 +512,8 @@ NULL
     offset = 0.1) {
     vmsg(.is_debug = TRUE, ".do_limmatest")
 
+    package_check("limma")
+
     # data.table variables
     sel <- other <- feats <- P.Value <- adj.P.Val <- p.adj <- NULL
 

R/spatial_interaction_visuals.R

@@ -720,6 +720,9 @@ NULL
         x_ticks = NULL,
         y_ticks = NULL,
         ...) {
+
+    package_check("plotly")
+
     # data.table variables
     cell_ID <- unified_int <- NULL
 
@@ -984,6 +987,9 @@ NULL
         y_ticks = NULL,
         z_ticks = NULL,
         ...) {
+
+    package_check("plotly")
+
     # data.table variables
     cell_ID <- unified_int <- NULL
 
@@ -3677,6 +3683,7 @@ cellProximitySpatPlot3D <- function(
         save_param = list(),
         default_save_name = "cellProximitySpatPlot3D",
         ...) {
+
     if (is.null(sdimz)) {
         pl <- .cellProximityVisPlot_2D_plotly(
             gobject = gobject,