Update the FeatureStatPlot function

zhanghao-njmu · Oct 18, 2023 · b445576 · b445576
1 parent b08f526
commit b445576
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Showing 16 changed files with 314 additions and 182 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -138,7 +138,6 @@ export(download)
 export(drop_data)
 export(exist_Python_pkgs)
 export(fastMNN_integrate)
-export(filter)
 export(find_conda)
 export(geom_alluvial)
 export(geom_alluvial_label)
@@ -148,15 +147,14 @@ export(geom_sankey_bump)
 export(geom_sankey_label)
 export(geom_sankey_text)
 export(get_vars)
-export(group_by)
 export(installed_Python_pkgs)
 export(invoke)
 export(isOutlier)
 export(iterchunks)
 export(make_long)
 export(palette_scp)
 export(panel_fix)
-export(panel_fix_single)
+export(panel_fix_overall)
 export(scVI_integrate)
 export(segementsDf)
 export(show_palettes)
@@ -168,7 +166,6 @@ export(theme_sankey)
 export(theme_sankey_bump)
 export(theme_scp)
 export(tochunks)
-export(top_n)
 export(try_get)
 export(unnest)
 importFrom(AnnotationDbi,columns)
@@ -330,7 +327,6 @@ importFrom(dplyr,reframe)
 importFrom(dplyr,slice_head)
 importFrom(dplyr,summarise)
 importFrom(dplyr,summarise_at)
-importFrom(dplyr,top_n)
 importFrom(ggforce,geom_mark_ellipse)
 importFrom(ggforce,geom_mark_hull)
 importFrom(ggnewscale,new_scale)

diff --git a/R/SCP-analysis.R b/R/SCP-analysis.R
@@ -1244,6 +1244,7 @@ FindConservedMarkers2 <- function(object, grouping.var, ident.1, ident.2 = NULL,
 #'
 #' @seealso \code{\link{RunEnrichment}} \code{\link{RunGSEA}} \code{\link{GroupHeatmap}}
 #' @examples
+#' library(dplyr)
 #' data("pancreas_sub")
 #' pancreas_sub <- RunDEtest(pancreas_sub, group_by = "SubCellType")
 #' AllMarkers <- filter(pancreas_sub@tools$DEtest_SubCellType$AllMarkers_wilcox, p_val_adj < 0.05 & avg_log2FC > 1)
@@ -4051,7 +4052,7 @@ RunMonocle2 <- function(srt, assay = NULL, slot = "counts", expressionFamily = "
                         root_state = NULL, seed = 11) {
   set.seed(seed)
   check_R(c("monocle", "DDRTree", "BiocGenerics", "Biobase", "VGAM"))
-  library(monocle)
+  attachNamespace("DDRTree")
 
   assay <- assay %||% DefaultAssay(srt)
   expr_matrix <- as.sparse(GetAssayData(srt, assay = assay, slot = slot))

diff --git a/R/SCP-app.R b/R/SCP-app.R
@@ -538,7 +538,8 @@ CreateSeuratObject2 <- function(counts, project = "SeuratProject", assay = "RNA"
 #'   initial_dataset = "mouse_pancreas",
 #'   initial_group = "CellType",
 #'   initial_feature = "Neurog3",
-#'   workers = 2, overwrite = TRUE
+#'   session_workers = 2,
+#'   overwrite = TRUE
 #' )
 #' list.files("./SCExplorer") # This directory can be used as site directory for Shiny Server.
 #'
@@ -1274,6 +1275,28 @@ ui <- fluidPage(
             height = "100px",
             placeholder = paste(sample(all_features, 4), collapse = "\\n")
           ),
+          fluidRow(
+            column(
+              width = 6, align = "center",
+              radioButtons(
+                inputId = "plotby4",
+                label = "Plot by",
+                choices = c("group", "feature"),
+                selected = "group",
+                inline = TRUE
+              )
+            ),
+            column(
+              width = 6, align = "center",
+              radioButtons(
+                inputId = "fillby4",
+                label = "Fill by",
+                choices = c("group", "feature", "expression"),
+                selected = "group",
+                inline = TRUE
+              )
+            )
+          ),
           fluidRow(
             column(
               width = 4, align = "center",
@@ -1338,12 +1361,6 @@ ui <- fluidPage(
               )
             )
           ),
-          selectInput(
-            inputId = "fillby4",
-            label = "Fill by",
-            choices = c("group", "feature", "expression"),
-            selected = "group"
-          ),
           selectInput(
             inputId = "palette4",
             label = "Select a palette",
@@ -2038,13 +2055,14 @@ server <- function(input, output, session) {
     plottype4 <- input$plottype4
     features4 <- input$features4
     feature_area4 <- input$feature_area4
+    plotby4 <- input$plotby4
+    fillby4 <- input$fillby4
     coExp4 <- input$coExp4 == "Yes"
     stack4 <- input$stack4 == "Yes"
     flip4 <- input$flip4 == "Yes"
     addbox4 <- input$addbox4 == "Yes"
     addpoint4 <- input$addpoint4 == "Yes"
     addtrend4 <- input$addtrend4 == "Yes"
-    fillby4 <- input$fillby4
     palette4 <- input$palette4
     theme4 <- input$theme4
     sameylims4 <- input$sameylims4 == "Yes"
@@ -2104,7 +2122,7 @@ server <- function(input, output, session) {
           srt = srt_tmp, stat.by = features4, group.by = group4, split.by = split4, cells = cells, slot = "data", plot_type = plottype4,
           calculate_coexp = coExp4, stack = stack4, flip = flip4,
           add_box = addbox4, add_point = addpoint4, add_trend = addtrend4,
-          fill.by = fillby4, palette = palette4, theme_use = theme4, same.y.lims = sameylims4,
+          plot.by = plotby4, fill.by = fillby4, palette = palette4, theme_use = theme4, same.y.lims = sameylims4,
           aspect.ratio = as.numeric(aspect.ratio), # must be class of numeric instead of integer
           ncol = ncol4, byrow = byrow4, force = TRUE
         )