From cb0f3a8405f847506d49252c2fa00bd4715bc242 Mon Sep 17 00:00:00 2001
From: Miles Smith <miles-smith@omrf.org>
Date: Thu, 12 Aug 2021 11:58:27 -0500
Subject: [PATCH] Fix: more of the same

---
 CHANGELOG.md   |  5 ++++-
 DESCRIPTION    |  2 +-
 NAMESPACE      |  1 +
 R/paga.R       | 46 +++++++++++++++++++++++++---------------------
 pyproject.toml |  2 +-
 5 files changed, 32 insertions(+), 24 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d7a248e..22daacc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,11 +3,14 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+## [2.5.3] - 2021-08-12
+### Fixed
+  - More missing imports and namespace specification
+
 ## [2.5.2] - 2021-08-12
 ### Fixed
   - Missing imports and namespace specification
 
-
 ## [2.5.1] - 2021-08-12
 ### Fixed
   - Fixed a typo
diff --git a/DESCRIPTION b/DESCRIPTION
index 6465372..3649728 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ReductionWrappers
 Title: Wrapper exposing several Python dimensional reduction tools
-Version: 2.5.2
+Version: 2.5.3
 Authors@R: 
     person(given = "Miles",
            family = "Smith",
diff --git a/NAMESPACE b/NAMESPACE
index 77a533b..bee2110 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -30,6 +30,7 @@ importFrom(SingleCellExperiment,reducedDimNames)
 importFrom(SummarizedExperiment,"colData<-")
 importFrom(SummarizedExperiment,colData)
 importFrom(dplyr,across)
+importFrom(dplyr,filter)
 importFrom(dplyr,mutate)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,geom_point)
diff --git a/R/paga.R b/R/paga.R
index 1da444d..64266f1 100644
--- a/R/paga.R
+++ b/R/paga.R
@@ -61,7 +61,7 @@
 #' @importFrom Seurat DietSeurat Idents<- DefaultAssay CreateDimReducObject
 #' @importFrom magrittr set_rownames set_colnames
 #' @importFrom rlang %||%
-#' @importFrom dplyr mutate across
+#' @importFrom dplyr mutate across filter
 #' @importFrom tibble as_tibble tibble
 #'
 #' @examples
@@ -247,8 +247,8 @@ PAGA <-
     )
 
     paga <- list(
-      connectivities           = converted_object$uns[["paga"]]$connectivities$todense() |>
-        magrittr::set_rownames(levels(converted_object$obs[[converted_object$uns[["paga"]]$groups]])) |>
+      connectivities           = converted_object$uns[["paga"]]$connectivities$todense() %>%
+        magrittr::set_rownames(levels(converted_object$obs[[converted_object$uns[["paga"]]$groups]])) %>%
         magrittr::set_colnames(levels(converted_object$obs[[converted_object$uns[["paga"]]$groups]])),
       connectivities_tree      = converted_object$uns[["paga"]]$connectivities_tree$todense(),
       group_name               = converted_object$uns[["paga"]]$groups,
@@ -261,7 +261,7 @@ PAGA <-
           converted_object$uns[["paga"]]$pos
           ),
         .name_repair = ~make.names(c("group","x", "y"))
-      ) |>
+      ) %>%
       dplyr::mutate(
         dplyr::across(
           x:y,
@@ -283,19 +283,19 @@ PAGA <-
     paga$edges <- tibble::tibble(
       group1 = paga$groups[row(paga$connectivities)[upper.tri(paga$connectivities)]],
       group2 = paga$groups[col(paga$connectivities)[upper.tri(paga$connectivities)]],
-      weight = paga$connectivities[upper.tri(paga$connectivities)] |> as.numeric()
-    ) |>
-      dplyr::mutate(
-        x1 = paga$position$x[match(.$group1, rownames(paga$position))] |> as.numeric(),
-        y1 = paga$position$y[match(.$group1, rownames(paga$position))] |> as.numeric(),
-        x2 = paga$position$x[match(.$group2, rownames(paga$position))] |> as.numeric(),
-        y2 = paga$position$y[match(.$group2, rownames(paga$position))] |> as.numeric()
-      ) |>
-      filter(weight >= edge_filter_weight)
+      weight = paga$connectivities[upper.tri(paga$connectivities)] %>% as.numeric()
+      ) %>%
+    dplyr::mutate(
+      x1 = paga$position$x[match(.$group1, rownames(paga$position))] %>% as.numeric(),
+      y1 = paga$position$y[match(.$group1, rownames(paga$position))] %>% as.numeric(),
+      x2 = paga$position$x[match(.$group2, rownames(paga$position))] %>% as.numeric(),
+      y2 = paga$position$y[match(.$group2, rownames(paga$position))] %>% as.numeric()
+      ) %>%
+    dplyr::filter(weight >= edge_filter_weight)
 
     paga_umap <- Seurat::CreateDimReducObject(
-      embeddings = converted_object$obsm[['X_umap']] |>
-        magrittr::set_rownames(colnames(object[[assay]])) |>
+      embeddings = converted_object$obsm[['X_umap']] %>%
+        magrittr::set_rownames(colnames(object[[assay]])) %>%
         magrittr::set_colnames(
           paste0(
             "UMAP_",
@@ -337,7 +337,7 @@ PAGAplot <-
     object,
     edge_scale_weight = 0.2
   ){
-    object@misc$paga$position |>
+    object@misc$paga$position %>%
       ggplot2::ggplot(aes(x, y)) +
       ggplot2::geom_segment(
         data = object@misc$paga$edges,
@@ -357,10 +357,14 @@ PAGAplot <-
         alpha       = 1,
         show.legend = FALSE) +
       ggplot2::scale_color_brewer() +
-      ggplot2::geom_text(ggplot2::aes(label = group),
-                color = "black",
-                fontface = "bold") +
-      ggplot2::labs(x = "UMAP_1",
-           y = "UMAP_2") +
+      ggplot2::geom_text(
+        ggplot2::aes(label = group),
+        color = "black",
+        fontface = "bold"
+        ) +
+      ggplot2::labs(
+        x = "UMAP_1",
+        y = "UMAP_2"
+        ) +
       ggpubr::theme_pubr()
   }
diff --git a/pyproject.toml b/pyproject.toml
index a524ab6..80c5221 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "reductionwrappers"
-version = "2.5.2"
+version = "2.5.3"
 description = "companion Python installer for R package {ReductionWrappers}"
 authors = ["Miles Smith <miles-smith@omrf.org>"]
 license = "BSD-3"