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Devel #32

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Merged
mingl1997 merged 4 commits into from
Jan 7, 2025
Merged

Devel #32

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45a8204
Fixes notes about DataFrame
Ashastry2 Oct 28, 2024
c77ca3b
Merge branch 'compbiomed:devel' into devel
Ashastry2 Oct 28, 2024
0d1d468
Fixes NAMESPACE error
Ashastry2 Oct 28, 2024
6557272
Merge pull request #772 from Ashastry2/devel
joshua-d-campbell Oct 28, 2024
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1 change: 1 addition & 0 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -273,6 +273,7 @@ import(eds)
importFrom(BiocParallel,SerialParam)
importFrom(ComplexHeatmap,anno_barplot)
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,metadata)
importFrom(SingleCellExperiment,"counts<-")
importFrom(SingleCellExperiment,"reducedDim<-")
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7 changes: 6 additions & 1 deletion R/plotSCEHeatmap.R
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Expand Up @@ -113,6 +113,8 @@
#' @importFrom grid gpar
#' @importFrom ComplexHeatmap anno_barplot
#' @importFrom rlang .data
#' @importFrom S4Vectors DataFrame
#'
#'
plotSCEHeatmap <- function(inSCE, useAssay = 'logcounts', useReducedDim = NULL,
doLog = FALSE, featureIndex = NULL, cellIndex = NULL,
Expand Down Expand Up @@ -288,7 +290,7 @@ plotSCEHeatmap <- function(inSCE, useAssay = 'logcounts', useReducedDim = NULL,
#colData(SCE) <- colData(SCE)[,c(aggregateCol),drop=FALSE] ##change

temp_df<-as.data.frame(colData(SCE)[,c(aggregateCol),drop=FALSE]) %>%
unite("new_colnames",1:ncol(.),sep = "_",remove = FALSE) %>%
unite("new_colnames",1:ncol(.data),sep = "_",remove = FALSE) %>%
remove_rownames() %>%
# mutate(aggregated_column = new_colnames) %>%
# dplyr::select(new_colnames, aggregated_column) %>%
Expand Down Expand Up @@ -380,6 +382,9 @@ plotSCEHeatmap <- function(inSCE, useAssay = 'logcounts', useReducedDim = NULL,
stop('Breaks of `colorScheme` do not match with `trim`.')
}

# Avoid documentation error by setting these values to NULL
# removed NOTE about namespaces.
n<-value<-NULL

### Generate HeatmapAnnotation object
ca <- NULL
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