Fix@missing imports (#151)

* added missing imports

* Increment version number to 0.2.20.9000

* additional minor fixes

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MCView
 Title: A Shiny App for Metacell Analysis
-Version: 0.2.23
+Version: 0.2.23.9000
 Authors@R: 
     person(given = "Aviezer",
            family = "Lifshitz",
@@ -20,11 +20,11 @@ BugReports: https://github.com/tanaylab/MCView/issues
 Depends: 
     R (>= 3.5)
 Imports: 
-    anndata,    
+    anndata,
     chameleon,
     cli,
     colourpicker,
-    circlize,    
+    circlize,
     cowplot,
     cachem,
     dplyr,
@@ -43,8 +43,9 @@ Imports:
     htmltools,
     markdown (>= 1.3.0),
     matrixStats,
+    methods,
     pkgload,
-    plotly (>= 4.9.3),    
+    plotly (>= 4.9.3),
     promises,
     purrr,
     qs,
@@ -58,7 +59,7 @@ Imports:
     shinyjqui,
     shinycssloaders,
     shinydashboard,
-    shinydashboardPlus (>= 2.0.0),    
+    shinydashboardPlus (>= 2.0.0),
     shinyWidgets (>= 0.7.0),
     shinybusy,
     tglkmeans,
@@ -71,17 +72,23 @@ Imports:
     zip,
     Matrix,
     ggtext (>= 0.1.0),
-    waiter
+    waiter,
+    stats,
+    utils,
+    umap,
+    graphics
 Suggests: 
     knitr,
     R.utils,
     processx,
     testthat,
-    withr
+    withr,
+    metacell
 VignetteBuilder: 
     knitr
 Remotes: 
-    tanaylab/tgutil
+    tanaylab/tgutil,
+    tanaylab/metacell
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.2.3

NAMESPACE

@@ -35,6 +35,17 @@ importFrom(golem,add_resource_path)
 importFrom(golem,bundle_resources)
 importFrom(golem,favicon)
 importFrom(golem,with_golem_options)
+importFrom(grDevices,col2rgb)
+importFrom(grDevices,rgb)
+importFrom(graphics,axis)
+importFrom(graphics,layout)
+importFrom(graphics,par)
+importFrom(graphics,plot.new)
+importFrom(graphics,plot.window)
+importFrom(graphics,polygon)
+importFrom(graphics,rect)
+importFrom(graphics,segments)
+importFrom(graphics,text)
 importFrom(htmltools,HTML)
 importFrom(htmltools,tagAppendAttributes)
 importFrom(htmltools,tagList)
@@ -49,3 +60,25 @@ importFrom(shiny,NS)
 importFrom(shiny,column)
 importFrom(shiny,shinyApp)
 importFrom(shiny,tagList)
+importFrom(stats,approx)
+importFrom(stats,as.dendrogram)
+importFrom(stats,as.dist)
+importFrom(stats,as.hclust)
+importFrom(stats,chisq.test)
+importFrom(stats,cor)
+importFrom(stats,df)
+importFrom(stats,ecdf)
+importFrom(stats,hclust)
+importFrom(stats,loess)
+importFrom(stats,median)
+importFrom(stats,plogis)
+importFrom(stats,quantile)
+importFrom(stats,reorder)
+importFrom(stats,runif)
+importFrom(stats,setNames)
+importFrom(stats,time)
+importFrom(stats,weighted.mean)
+importFrom(utils,head)
+importFrom(utils,packageVersion)
+importFrom(utils,str)
+importFrom(utils,tail)

NEWS.md

@@ -1,3 +1,7 @@
+# MCView (development version)
+
+* Added some missing package imports.
+
 # MCView 0.2.23
 
 * Fix: plot limits were sometimes too low in differential expression plots.

R/MCView-package.R

@@ -22,5 +22,38 @@
 # The following block is used by usethis to automatically manage
 # roxygen namespace tags. Modify with care!
 ## usethis namespace: start
+#' @importFrom graphics axis
+#' @importFrom graphics layout
+#' @importFrom graphics par
+#' @importFrom graphics plot.new
+#' @importFrom graphics plot.window
+#' @importFrom graphics polygon
+#' @importFrom graphics rect
+#' @importFrom graphics segments
+#' @importFrom graphics text
+#' @importFrom grDevices col2rgb
+#' @importFrom grDevices rgb
+#' @importFrom stats approx
+#' @importFrom stats as.dendrogram
+#' @importFrom stats as.dist
+#' @importFrom stats as.hclust
+#' @importFrom stats chisq.test
+#' @importFrom stats cor
+#' @importFrom stats df
+#' @importFrom stats ecdf
+#' @importFrom stats hclust
+#' @importFrom stats loess
+#' @importFrom stats median
+#' @importFrom stats plogis
+#' @importFrom stats quantile
+#' @importFrom stats reorder
+#' @importFrom stats runif
+#' @importFrom stats setNames
+#' @importFrom stats time
+#' @importFrom stats weighted.mean
+#' @importFrom utils head
+#' @importFrom utils packageVersion
+#' @importFrom utils str
+#' @importFrom utils tail
 ## usethis namespace: end
 NULL

R/app_ui.R

@@ -99,11 +99,11 @@ app_ui <- function(request) {
             app_title <- dataset_ls(project)[1]
             config$title <- app_title
         } else {
-            app_title <- glue("MCView {version}", version = packageVersion("MCView"))
+            app_title <- glue("MCView {version}", version = utils::packageVersion("MCView"))
         }
     }
 
-    app_footer <- glue("MCView {version}", version = packageVersion("MCView"))
+    app_footer <- glue("MCView {version}", version = utils::packageVersion("MCView"))
     if (!is.null(config$metacells_version)) {
         app_footer <- glue("{app_footer} | {config$metacells_version}")
     }

R/atlas_projection.R

@@ -21,7 +21,7 @@ import_atlas <- function(query, atlas_project, atlas_dataset, projection_weights
         )
     } else {
         if (fs::file_exists(atlas_new_path)) {
-            fs::file_remove(atlas_new_path)
+            fs::file_delete(atlas_new_path)
         }
 
         fs::link_create(

R/import.R

@@ -607,7 +607,7 @@ import_dataset <- function(project,
 
     # write the version of the package
     writeLines(
-        as.character(packageVersion("MCView")),
+        as.character(utils::packageVersion("MCView")),
         project_version_file(project)
     )
 

R/import_metacell1.R

@@ -82,6 +82,10 @@ import_dataset_metacell1 <- function(project,
                                      metadata_fields = NULL,
                                      categorical = c(),
                                      ...) {
+    if (!requireNamespace("metacell", quietly = TRUE)) {
+        stop("Please install metacell R package in order to use this function")
+    }
+
     verbose <- !is.null(getOption("MCView.verbose")) && getOption("MCView.verbose")
     verify_project_dir(project, create = TRUE, ...)
 

R/metadata.R

@@ -24,7 +24,6 @@ update_metadata <- function(project,
             }
 
             cli_alert_info("Reading {.file {anndata_file}}")
-            library(anndata)
             adata <- anndata::read_h5ad(anndata_file)
         }
     } else {
@@ -107,6 +106,8 @@ update_metadata_colors <- function(project,
 #' Import cell metadata to an MCView dataset
 #'
 #'
+#' @param project path to the project
+#' @param dataset name for the dataset, e.g. "PBMC". The name of the dataset can only contain alphanumeric characters, dots, dashes and underscores.
 #' @param cell_metadata data frame with a column named "cell_id" with
 #' the cell id and other metadata columns, or a name of a delimited file which
 #' contains such data frame. For activating the "Samples" tab, the data frame should have an additional
@@ -261,15 +262,15 @@ add_tab <- function(tab, project) {
 #' @examples
 #' set.seed(60427)
 #' n_cells <- 5e6
-#' cell_metadata <- tibble(
+#' cell_metadata <- tibble::tibble(
 #'     cell_id = 1:n_cells,
 #'     md1 = sample(1:5, size = n_cells, replace = TRUE),
 #'     md2 = rnorm(n = n_cells),
 #'     md_categorical1 = sample(paste0("batch", 1:5), size = n_cells, replace = TRUE),
 #'     md_categorical2 = sample(1:5, size = n_cells, replace = TRUE)
 #' )
 #'
-#' cell_to_metacell <- tibble(
+#' cell_to_metacell <- tibble::tibble(
 #'     cell_id = 1:n_cells,
 #'     metacell = sample(0:1535, size = n_cells, replace = TRUE)
 #' )
@@ -280,7 +281,7 @@ add_tab <- function(tab, project) {
 #' head(metadata)
 #'
 #' metadata1 <- cell_metadata_to_metacell(
-#'     cell_metadata[, 11:3], cell_to_metacell,
+#'     cell_metadata[, 1:3], cell_to_metacell,
 #'     func = function(x) x * 2
 #' )
 #' head(metadata1)
@@ -416,7 +417,6 @@ cell_metadata_to_metacell_from_h5ad <- function(anndata_file, metadata_fields, f
     }
 
     cli_alert_info("Reading {.file {anndata_file}}")
-    library(anndata)
     adata <- anndata::read_h5ad(anndata_file)
 
     if (!("metacell_name" %in% colnames(adata$obs))) {

R/mod_annotate.R

@@ -570,7 +570,7 @@ mod_annotate_server <- function(id, dataset, metacell_types, cell_type_colors, g
 
             observe({
                 req(input$cell_type_table_rows_selected)
-                row <- tail(input$cell_type_table_rows_selected, n = 1)
+                row <- utils::tail(input$cell_type_table_rows_selected, n = 1)
                 colourpicker::updateColourInput(session, "selected_new_color", value = cell_type_colors()$color[row])
             })
 

R/mod_flow.R

@@ -221,7 +221,7 @@ mod_flow_server <- function(id, dataset, metacell_types, cell_type_colors, gene_
                 req(has_network(dataset()))
                 req(input$selected_metacell)
 
-                plotly::ggplotly(plot_gene_trajectory(dataset(), input$traj_genes, input$selected_metacell, anchor_gene = NULL) + theme(axis.title.y = element_text(color = "darkblue")), source = "traj_plot", tooltip = "tooltip_text") %>% sanitize_plotly_buttons()
+                plotly::ggplotly(plot_gene_trajectory(dataset(), input$traj_genes, input$selected_metacell, anchor_genes = NULL) + theme(axis.title.y = element_text(color = "darkblue")), source = "traj_plot", tooltip = "tooltip_text") %>% sanitize_plotly_buttons()
             })
         }
     )

R/plot_vein.R

@@ -18,10 +18,10 @@ mctnetwork_g_t_types <- function(net, min_time, max_time, g, mc_egc, mc_colors)
 
 
         src_flow <- as.data.frame(summarize(group_by(net_t, mc_t1, mc_t2),
-            g_src = weighted.mean(src_g, flow)
+            g_src = stats::weighted.mean(src_g, flow)
         ))
         targ_flow <- as.data.frame(summarize(group_by(net_t, mc_t1, mc_t2),
-            g_targ = weighted.mean(targ_g, flow)
+            g_targ = stats::weighted.mean(targ_g, flow)
         ))
 
 
@@ -58,7 +58,7 @@ mctnetwork_g_t_types <- function(net, min_time, max_time, g, mc_egc, mc_colors)
 
 
 add_alpha <- function(col, alpha) {
-    return(rgb(t(col2rgb(col)) / 256, alpha = alpha))
+    return(grDevices::rgb(t(grDevices::col2rgb(col)) / 256, alpha = alpha))
 }
 
 
@@ -72,18 +72,18 @@ get_sig_edge <- function(x1, x2, x2t, y1, y2, y2t, flow, col1, col2, col_alpha =
     dxt <- x2 - x1
     dyt <- y2 - y1t
 
-    col1 <- col2rgb(col1)[, 1]
+    col1 <- grDevices::col2rgb(col1)[, 1]
     names(col1) <- c("red", "green", "blue")
-    col2 <- col2rgb(col2)[, 1]
+    col2 <- grDevices::col2rgb(col2)[, 1]
     names(col2) <- c("red", "green", "blue")
     res <- 0.05
 
-    beta0 <- plogis(0, loc = 0.5, scale = 0.2)
-    beta_f <- plogis(1, loc = 0.5, scale = 0.2) - plogis(0, loc = 0.5, scale = 0.2)
+    beta0 <- stats::plogis(0, loc = 0.5, scale = 0.2)
+    beta_f <- stats::plogis(1, loc = 0.5, scale = 0.2) - stats::plogis(0, loc = 0.5, scale = 0.2)
     polygons <- list()
     for (r in seq(0, 0.98, res)) {
-        beta <- (plogis(r, loc = 0.5, scale = 0.2) - beta0) / beta_f
-        beta5 <- (plogis(r + res, loc = 0.5, scale = 0.2) - beta0) / beta_f
+        beta <- (stats::plogis(r, loc = 0.5, scale = 0.2) - beta0) / beta_f
+        beta5 <- (stats::plogis(r + res, loc = 0.5, scale = 0.2) - beta0) / beta_f
 
         sx1 <- x1 + r * dx
         sy1 <- y1 + beta * dy
@@ -99,7 +99,7 @@ get_sig_edge <- function(x1, x2, x2t, y1, y2, y2t, flow, col1, col2, col_alpha =
         rgb_r <- col2["red"] * r_col + col1["red"] * (1 - r_col)
         rgb_g <- col2["green"] * r_col + col1["green"] * (1 - r_col)
         rgb_b <- col2["blue"] * r_col + col1["blue"] * (1 - r_col)
-        col <- rgb(rgb_r / 256, rgb_g / 256, rgb_b / 256, col_alpha)
+        col <- grDevices::rgb(rgb_r / 256, rgb_g / 256, rgb_b / 256, col_alpha)
         poly_list <- list(
             mat = matrix(c(sx1, sx2, sx2t, sx1t, sy1, sy2, sy2t, sy1t), nrow = 2, byrow = TRUE),
             col = col,
@@ -226,15 +226,15 @@ plot_vein <- function(dataset,
                         col1 <- egc_to_col((targ_g_tt[[t - 1]][c, c] + src_g_tt[[t]][c, c]) / 2)
                     }
                     col2 <- egc_to_col((targ_g_tt[[t]][c, c] + src_g_tt[[t + 1]][c, c]) / 2)
-                    col1 <- col2rgb(col1)[, 1]
+                    col1 <- grDevices::col2rgb(col1)[, 1]
                     names(col1) <- c("red", "green", "blue")
-                    col2 <- col2rgb(col2)[, 1]
+                    col2 <- grDevices::col2rgb(col2)[, 1]
                     names(col2) <- c("red", "green", "blue")
                     for (lamda in seq(0, 0.99, l = 100)) {
                         rgb_r <- col2["red"] * lamda + col1["red"] * (1 - lamda)
                         rgb_g <- col2["green"] * lamda + col1["green"] * (1 - lamda)
                         rgb_b <- col2["blue"] * lamda + col1["blue"] * (1 - lamda)
-                        col <- rgb(rgb_r / 256, rgb_g / 256, rgb_b / 256, col_alpha)
+                        col <- grDevices::rgb(rgb_r / 256, rgb_g / 256, rgb_b / 256, col_alpha)
 
                         poly_list <- list(
                             mat = matrix(c(ys$x[i], ys$x[i + 1], ys$x[i + 1], ys$x[i], base + lo[i], base + lo[i + 1], base - lo[i + 1], base - lo[i]), nrow = 2, byrow = TRUE),
@@ -382,7 +382,7 @@ plot_vein <- function(dataset,
         cols <- purrr::map_chr(polygons, ~ .x$col)
         lwds <- purrr::map_dbl(polygons, ~ .x$lwd)
         borders <- purrr::map_chr(polygons, ~ .x$border)
-        polygon(xs, ys, col = cols, border = borders, lwd = lwds)
+        graphics::polygon(xs, ys, col = cols, border = borders, lwd = lwds)
     }
 
     future_promise({