From 406c9f0bac401ac49719c8f3c51793a1b1a0ea8c Mon Sep 17 00:00:00 2001
From: theHumanBorch <ncborch@gmail.com>
Date: Fri, 3 May 2024 14:00:10 -0500
Subject: [PATCH] working on final issues of dplyr|igraph conflict

---
 NAMESPACE             |  4 ++++
 R/clonalCluster.R     | 13 +++++++------
 R/clonalNetwork.R     |  4 +---
 R/combineExpression.R |  9 ++++++---
 man/clonalNetwork.Rd  |  6 ++----
 5 files changed, 20 insertions(+), 16 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 276286ad..682a158c 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -47,9 +47,13 @@ importFrom(SummarizedExperiment,colData)
 importFrom(VGAM,dpareto)
 importFrom(cubature,adaptIntegrate)
 importFrom(dplyr,"%>%")
+importFrom(dplyr,across)
+importFrom(dplyr,all_of)
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_rows)
+importFrom(dplyr,coalesce)
 importFrom(dplyr,count)
+importFrom(dplyr,desc)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
 importFrom(dplyr,left_join)
diff --git a/R/clonalCluster.R b/R/clonalCluster.R
index 3a445bc7..2b4af6f7 100644
--- a/R/clonalCluster.R
+++ b/R/clonalCluster.R
@@ -42,6 +42,8 @@
 #' @importFrom rlang %||%
 #' @importFrom SummarizedExperiment colData<- colData
 #' @importFrom stats na.omit
+#' @importFrom S4Vectors DataFrame
+#' 
 #' @export
 #' @concept Visualizing_Clones
 #' @return Either amended input with edit-distanced clusters added 
@@ -177,12 +179,11 @@ clonalCluster <- function(input.data,
       col.name <- names(PreMeta) %||% colnames(PreMeta)
       input.data[[col.name]] <- PreMeta
     } else {
-      rownames <- rownames(colData(input.data))
-      combined_col_names <- unique(c(colnames(colData(input.data)), colnames(PreMeta)))
-      full_data <- merge(colData(input.data), PreMeta[rownames, , drop = FALSE], by = "row.names", all = TRUE)
-      colData(input.data) <- full_data[, combined_col_names]
-      
-      rownames(colData(input.data)) <- rownames 
+      combined_col_names <- unique(c(colnames(colData(sc.data)), colnames(PreMeta)))
+      full_data <- merge(colData(sc.data), PreMeta[rownames, , drop = FALSE], by = "row.names", all.x = TRUE)
+      rownames(full_data) <- full_data[, 1]
+      full_data  <- full_data[, -1]
+      colData(sc.data) <- DataFrame(full_data[, combined_col_names])
     }
   } else {
     #Reorder columns
diff --git a/R/clonalNetwork.R b/R/clonalNetwork.R
index 8bd1d4d7..4f9d921c 100644
--- a/R/clonalNetwork.R
+++ b/R/clonalNetwork.R
@@ -45,7 +45,6 @@
 #' @param chain indicate if both or a specific chain should be used - 
 #' e.g. "both", "TRA", "TRG", "IGH", "IGL".
 #' @param exportTable Exports a table of the data into the global 
-#' environment in addition to the visualization.
 #' @param exportClones Exports a table of clones that are shared
 #' across multiple identity groups and ordered by the total number
 #' of clone copies.
@@ -55,7 +54,7 @@
 #' @import ggplot2
 #' @importFrom stringr str_sort
 #' @importFrom igraph graph_from_data_frame V `V<-`
-#' @importFrom dplyr %>% group_by select summarize_all count n
+#' @importFrom dplyr %>% group_by select summarize_all count n across all_of desc
 #' @importFrom tidygraph as_tbl_graph activate
 #' @importFrom ggraph ggraph geom_edge_bend  geom_node_point scale_edge_colour_gradientn circle guide_edge_colourbar
 #' @importFrom stats setNames
@@ -72,7 +71,6 @@ clonalNetwork <- function(sc.data,
                           filter.graph = FALSE,
                           cloneCall = "strict", 
                           chain = "both", 
-                          exportTable = FALSE, 
                           exportClones = FALSE,
                           palette = "inferno") {
     to <- from <- weight <- y <- NULL
diff --git a/R/combineExpression.R b/R/combineExpression.R
index 5d1890e5..afcfebe4 100644
--- a/R/combineExpression.R
+++ b/R/combineExpression.R
@@ -45,9 +45,10 @@
 #' @param addLabel This will add a label to the frequency header, allowing
 #' the user to try multiple group.by variables or recalculate frequencies after 
 #' subsetting the data.
-#' @importFrom dplyr bind_rows %>% summarise left_join mutate select n
+#' @importFrom dplyr bind_rows %>% summarise left_join mutate select n all_of coalesce
 #' @importFrom  rlang %||% sym :=
 #' @importFrom SummarizedExperiment colData<- colData
+#' @importFrom S4Vectors DataFrame
 #' @export
 #' @concept SC_Functions
 #' @return Single-cell object with clone information added to meta data
@@ -205,8 +206,10 @@ combineExpression <- function(input.data,
         warning(.warn_str) }
       
       combined_col_names <- unique(c(colnames(colData(sc.data)), colnames(PreMeta)))
-      full_data <- merge(colData(sc.data), PreMeta[rownames, , drop = FALSE], by = "row.names", all = TRUE)
-      colData(sc.data) <- full_data[, combined_col_names]
+      full_data <- merge(colData(sc.data), PreMeta[rownames, , drop = FALSE], by = "row.names", all.x = TRUE)
+      rownames(full_data) <- full_data[, 1]
+      full_data  <- full_data[, -1]
+      colData(sc.data) <- DataFrame(full_data[, combined_col_names])
       
       rownames(colData(sc.data)) <- rownames  
     }
diff --git a/man/clonalNetwork.Rd b/man/clonalNetwork.Rd
index 95d0d950..7b7e9bbe 100644
--- a/man/clonalNetwork.Rd
+++ b/man/clonalNetwork.Rd
@@ -14,7 +14,6 @@ clonalNetwork(
   filter.graph = FALSE,
   cloneCall = "strict",
   chain = "both",
-  exportTable = FALSE,
   exportClones = FALSE,
   palette = "inferno"
 )
@@ -48,15 +47,14 @@ in the data.}
 \item{chain}{indicate if both or a specific chain should be used - 
 e.g. "both", "TRA", "TRG", "IGH", "IGL".}
 
-\item{exportTable}{Exports a table of the data into the global 
-environment in addition to the visualization.}
-
 \item{exportClones}{Exports a table of clones that are shared
 across multiple identity groups and ordered by the total number
 of clone copies.}
 
 \item{palette}{Colors to use in visualization - input any 
 \link[grDevices]{hcl.pals}.}
+
+\item{exportTable}{Exports a table of the data into the global}
 }
 \value{
 ggplot object