From 9aee64e55c96be6b1e1588ac20a24fa1e3537fce Mon Sep 17 00:00:00 2001
From: mischko <mhem@mailbox.org>
Date: Thu, 14 Nov 2024 23:25:10 +0100
Subject: [PATCH] fix problem with plotPropeller example

---
 R/visualization.R       |  3 +--
 man/dotplotPropeller.Rd |  2 +-
 man/plotSlingshot.Rd    | 15 +++++++++++++--
 3 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/R/visualization.R b/R/visualization.R
index dee890c..251c0ff 100644
--- a/R/visualization.R
+++ b/R/visualization.R
@@ -845,8 +845,7 @@ plotPropeller <- function(data, color, filename, width = 5, height = 5, FDR, dir
 #' @return create and save propeller abundance barplot
 #' @examples
 #' propeller_data <- data.frame(
-
-#' #'     cluster = c("Cluster1", "Cluster2", "Cluster3"),
+#'      cluster = c("Cluster1", "Cluster2", "Cluster3"),
 #'     log2ratio = c(1.5, -2.0, 0.5)
 #' )
 #' color <- c("Cluster1" = "blue", "Cluster2" = "red", "Cluster3" = "green")
diff --git a/man/dotplotPropeller.Rd b/man/dotplotPropeller.Rd
index fec131c..fd6e44b 100644
--- a/man/dotplotPropeller.Rd
+++ b/man/dotplotPropeller.Rd
@@ -34,7 +34,7 @@ The function creates a barplot of the propeller results and saves the plot
 }
 \examples{
 propeller_data <- data.frame(
-#'     cluster = c("Cluster1", "Cluster2", "Cluster3"),
+     cluster = c("Cluster1", "Cluster2", "Cluster3"),
     log2ratio = c(1.5, -2.0, 0.5)
 )
 color <- c("Cluster1" = "blue", "Cluster2" = "red", "Cluster3" = "green")
diff --git a/man/plotSlingshot.Rd b/man/plotSlingshot.Rd
index 34e0b71..882526b 100644
--- a/man/plotSlingshot.Rd
+++ b/man/plotSlingshot.Rd
@@ -4,7 +4,7 @@
 \alias{plotSlingshot}
 \title{plot slingshot results}
 \usage{
-plotSlingshot(object, lineage, pt)
+plotSlingshot(object, lineage, pt, curves)
 }
 \arguments{
 \item{object}{A Seurat object}
@@ -12,6 +12,8 @@ plotSlingshot(object, lineage, pt)
 \item{lineage}{A character string indicating the lineage of interest.}
 
 \item{pt}{A numeric vector of pseudotime values.}
+
+\item{curves}{A dataframe containing the curves.}
 }
 \value{
 A ggplot object.
@@ -23,7 +25,16 @@ The function creates a colored UMAP plot and curves split by lineage
 library(Seurat)
 set.seed(123)
 pbmc_small$lineage <- sample(c("Lineage1", "Lineage2"), ncol(pbmc_small), replace = TRUE)
-pbmc_small$umap <- CreateDimReducObject(embeddings = Embeddings(pbmc_small, reduction = "tsne"), key = "UMAP_", assay = "RNA")
+pbmc_small$umap <-
+CreateDimReducObject(
+ embeddings =
+   Embeddings(
+     pbmc_small,
+     reduction = "tsne"
+   ),
+ key = "UMAP_",
+ assay = "RNA"
+)
 curves <- data.frame(
     UMAP_1 = runif(ncol(pbmc_small), min = -10, max = 10),
     UMAP_2 = runif(ncol(pbmc_small), min = -10, max = 10),