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Develop #194

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Oct 30, 2023
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Develop #194

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fa33ee3
Update the SCP workflow
zhanghao-njmu Oct 30, 2023
e743249
Increment version number to 0.5.4
zhanghao-njmu Oct 30, 2023
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Package: SCP
Type: Package
Title: Single Cell Pipeline
Version: 0.5.3
Version: 0.5.4
Author: Hao Zhang
Maintainer: Hao Zhang <[email protected]>
Description: An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
Expand Down
118 changes: 81 additions & 37 deletions R/SCP-workflow.R
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Original file line number Diff line number Diff line change
Expand Up @@ -1373,7 +1373,7 @@ Seurat_integrate <- function(srtMerge = NULL, batch = NULL, append = TRUE, srtLi
cat(paste0("[", Sys.time(), "]", " Perform integration(Seurat) on the data...\n"))
params2 <- list(
anchorset = srt_anchors,
new.assay.name = "Seurat",
new.assay.name = "Seuratcorrected",
normalization.method = normalization_method,
features.to.integrate = HVF,
verbose = FALSE
Expand All @@ -1383,8 +1383,8 @@ Seurat_integrate <- function(srtMerge = NULL, batch = NULL, append = TRUE, srtLi
}
srtIntegrated <- invoke(.fn = IntegrateData, .args = params2)

DefaultAssay(srtIntegrated) <- "Seurat"
VariableFeatures(srtIntegrated[["Seurat"]]) <- HVF
DefaultAssay(srtIntegrated) <- "Seuratcorrected"
VariableFeatures(srtIntegrated[["Seuratcorrected"]]) <- HVF

if (isTRUE(do_scaling) || (is.null(do_scaling) && any(!HVF %in% rownames(GetAssayData(srtIntegrated, slot = "scale.data", assay = DefaultAssay(srtIntegrated)))))) {
cat(paste0("[", Sys.time(), "]", " Perform ScaleData on the data...\n"))
Expand Down Expand Up @@ -1446,7 +1446,6 @@ Seurat_integrate <- function(srtMerge = NULL, batch = NULL, append = TRUE, srtLi
srtIntegrated <- SrtReorder(srtIntegrated, features = HVF, reorder_by = "seurat_clusters", slot = "data")
srtIntegrated[["seurat_clusters"]] <- NULL
srtIntegrated[["Seuratclusters"]] <- Idents(srtIntegrated)

srtIntegrated
},
error = function(error) {
Expand Down Expand Up @@ -1620,8 +1619,8 @@ scVI_integrate <- function(srtMerge = NULL, batch = NULL, append = TRUE, srtList

latent <- as.matrix(model$get_latent_representation())
rownames(latent) <- colnames(srtIntegrated)
colnames(latent) <- paste0("scvi_", seq_len(ncol(latent)))
srtIntegrated[["scVI"]] <- CreateDimReducObject(embeddings = latent, key = "scvi_", assay = DefaultAssay(srtIntegrated))
colnames(latent) <- paste0("scVI_", seq_len(ncol(latent)))
srtIntegrated[["scVI"]] <- CreateDimReducObject(embeddings = latent, key = "scVI_", assay = DefaultAssay(srtIntegrated))
if (is.null(scVI_dims_use)) {
scVI_dims_use <- 1:ncol(srtIntegrated[["scVI"]]@cell.embeddings)
}
Expand All @@ -1640,7 +1639,6 @@ scVI_integrate <- function(srtMerge = NULL, batch = NULL, append = TRUE, srtList
srtIntegrated <- SrtReorder(srtIntegrated, features = HVF, reorder_by = "seurat_clusters", slot = "data")
srtIntegrated[["seurat_clusters"]] <- NULL
srtIntegrated[["scVIclusters"]] <- Idents(srtIntegrated)

srtIntegrated
},
error = function(error) {
Expand Down Expand Up @@ -1844,7 +1842,6 @@ MNN_integrate <- function(srtMerge = NULL, batch = NULL, append = TRUE, srtList
srtIntegrated <- SrtReorder(srtIntegrated, features = HVF, reorder_by = "seurat_clusters", slot = "data")
srtIntegrated[["seurat_clusters"]] <- NULL
srtIntegrated[["MNNclusters"]] <- Idents(srtIntegrated)

srtIntegrated
},
error = function(error) {
Expand Down Expand Up @@ -2016,7 +2013,6 @@ fastMNN_integrate <- function(srtMerge = NULL, batch = NULL, append = TRUE, srtL
srtIntegrated <- SrtReorder(srtIntegrated, features = HVF, reorder_by = "seurat_clusters", slot = "data")
srtIntegrated[["seurat_clusters"]] <- NULL
srtIntegrated[["fastMNNclusters"]] <- Idents(srtIntegrated)

srtIntegrated
},
error = function(error) {
Expand Down Expand Up @@ -2066,7 +2062,7 @@ fastMNN_integrate <- function(srtMerge = NULL, batch = NULL, append = TRUE, srtL
#'
#' @inheritParams Integration_SCP
#' @param Harmony_dims_use A vector specifying the dimensions returned by RunHarmony that will be utilized for downstream cell cluster finding and non-linear reduction. If set to NULL, all the returned dimensions will be used by default.
#' @param RunHarmony_params A list of parameters for the RunHarmony function, default is an empty list.
#' @param RunHarmony_params A list of parameters for the harmony::RunHarmony function, default is an empty list.
#'
#' @importFrom Seurat GetAssayData ScaleData SetAssayData DefaultAssay DefaultAssay<- Embeddings FindNeighbors FindClusters Idents VariableFeatures VariableFeatures<-
#' @export
Expand Down Expand Up @@ -2219,7 +2215,6 @@ Harmony_integrate <- function(srtMerge = NULL, batch = NULL, append = TRUE, srtL
srtIntegrated <- SrtReorder(srtIntegrated, features = HVF, reorder_by = "seurat_clusters", slot = "data")
srtIntegrated[["seurat_clusters"]] <- NULL
srtIntegrated[["Harmonyclusters"]] <- Idents(srtIntegrated)

srtIntegrated
},
error = function(error) {
Expand Down Expand Up @@ -2415,7 +2410,6 @@ Scanorama_integrate <- function(srtMerge = NULL, batch = NULL, append = TRUE, sr
srtIntegrated <- SrtReorder(srtIntegrated, features = HVF, reorder_by = "seurat_clusters", slot = "data")
srtIntegrated[["seurat_clusters"]] <- NULL
srtIntegrated[["Scanoramaclusters"]] <- Idents(srtIntegrated)

srtIntegrated
},
error = function(error) {
Expand Down Expand Up @@ -2464,7 +2458,7 @@ Scanorama_integrate <- function(srtMerge = NULL, batch = NULL, append = TRUE, sr
#' BBKNN_integrate
#'
#' @inheritParams Integration_SCP
#' @param bbknn_params A list of parameters for the bbknn.bbknn_matrix function, default is an empty list.
#' @param bbknn_params A list of parameters for the bbknn.matrix.bbknn function, default is an empty list.
#'
#' @importFrom Seurat GetAssayData ScaleData SetAssayData DefaultAssay DefaultAssay<- as.Graph Embeddings FindClusters Idents VariableFeatures VariableFeatures<- as.sparse
#' @importFrom Matrix t
Expand Down Expand Up @@ -2508,7 +2502,7 @@ BBKNN_integrate <- function(srtMerge = NULL, batch = NULL, append = TRUE, srtLis
"leiden" = 4
)

check_Python("bbknn==1.5.1")
check_Python("bbknn")
bbknn <- import("bbknn")
set.seed(seed)

Expand Down Expand Up @@ -2592,7 +2586,7 @@ BBKNN_integrate <- function(srtMerge = NULL, batch = NULL, append = TRUE, srtLis
for (nm in names(bbknn_params)) {
params[[nm]] <- bbknn_params[[nm]]
}
bem <- invoke(.fn = bbknn$bbknn_matrix, .args = params)
bem <- invoke(.fn = bbknn$matrix$bbknn, .args = params)
n.neighbors <- bem[[3]]$n_neighbors
srtIntegrated <- srtMerge

Expand Down Expand Up @@ -2635,7 +2629,6 @@ BBKNN_integrate <- function(srtMerge = NULL, batch = NULL, append = TRUE, srtLis
srtIntegrated <- SrtReorder(srtIntegrated, features = HVF, reorder_by = "seurat_clusters", slot = "data")
srtIntegrated[["seurat_clusters"]] <- NULL
srtIntegrated[["BBKNNclusters"]] <- Idents(srtIntegrated)

srtIntegrated
},
error = function(error) {
Expand Down Expand Up @@ -2843,7 +2836,6 @@ CSS_integrate <- function(srtMerge = NULL, batch = NULL, append = TRUE, srtList
srtIntegrated <- SrtReorder(srtIntegrated, features = HVF, reorder_by = "seurat_clusters", slot = "data")
srtIntegrated[["seurat_clusters"]] <- NULL
srtIntegrated[["CSSclusters"]] <- Idents(srtIntegrated)

srtIntegrated
},
error = function(error) {
Expand Down Expand Up @@ -3047,7 +3039,6 @@ LIGER_integrate <- function(srtMerge = NULL, batch = NULL, append = TRUE, srtLis
srtIntegrated <- SrtReorder(srtIntegrated, features = HVF, reorder_by = "seurat_clusters", slot = "data")
srtIntegrated[["seurat_clusters"]] <- NULL
srtIntegrated[["LIGERclusters"]] <- Idents(srtIntegrated)

srtIntegrated
},
error = function(error) {
Expand Down Expand Up @@ -3248,7 +3239,6 @@ Conos_integrate <- function(srtMerge = NULL, batch = NULL, append = TRUE, srtLis
srtIntegrated <- SrtReorder(srtIntegrated, features = HVF, reorder_by = "seurat_clusters", slot = "data")
srtIntegrated[["seurat_clusters"]] <- NULL
srtIntegrated[["Conosclusters"]] <- Idents(srtIntegrated)

srtIntegrated
},
error = function(error) {
Expand Down Expand Up @@ -3447,7 +3437,6 @@ ComBat_integrate <- function(srtMerge = NULL, batch = NULL, append = TRUE, srtLi
srtIntegrated <- SrtReorder(srtIntegrated, features = HVF, reorder_by = "seurat_clusters", slot = "data")
srtIntegrated[["seurat_clusters"]] <- NULL
srtIntegrated[["ComBatclusters"]] <- Idents(srtIntegrated)

srtIntegrated
},
error = function(error) {
Expand Down Expand Up @@ -3540,7 +3529,15 @@ ComBat_integrate <- function(srtMerge = NULL, batch = NULL, append = TRUE, srtLi
#' linear_reduction = linear_reductions,
#' nonlinear_reduction = "umap"
#' )
#' plist1 <- lapply(linear_reductions, function(lr) CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = paste0("Standard", lr, "UMAP2D"), theme_use = "theme_blank"))
#' plist1 <- lapply(linear_reductions, function(lr) {
#' CellDimPlot(pancreas_sub,
#' group.by = "SubCellType",
#' reduction = paste0("Standard", lr, "UMAP2D"),
#' xlab = "", ylab = "", title = lr,
#' legend.position = "none",
#' theme_use = "theme_blank"
#' )
#' })
#' patchwork::wrap_plots(plotlist = plist1)
#'
#' nonlinear_reductions <- c("umap", "tsne", "dm", "phate", "pacmap", "trimap", "largevis", "fr")
Expand All @@ -3549,7 +3546,15 @@ ComBat_integrate <- function(srtMerge = NULL, batch = NULL, append = TRUE, srtLi
#' linear_reduction = "pca",
#' nonlinear_reduction = nonlinear_reductions
#' )
#' plist2 <- lapply(nonlinear_reductions, function(nr) CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = paste0("Standardpca", toupper(nr), "2D"), theme_use = "theme_blank"))
#' plist2 <- lapply(nonlinear_reductions, function(nr) {
#' CellDimPlot(pancreas_sub,
#' group.by = "SubCellType",
#' reduction = paste0("Standardpca", toupper(nr), "2D"),
#' xlab = "", ylab = "", title = nr,
#' legend.position = "none",
#' theme_use = "theme_blank"
#' )
#' })
#' patchwork::wrap_plots(plotlist = plist2)
#'
#' @importFrom Seurat Assays GetAssayData NormalizeData SCTransform SCTResults ScaleData SetAssayData DefaultAssay DefaultAssay<- FindNeighbors FindClusters Idents VariableFeatures VariableFeatures<-
Expand Down Expand Up @@ -3648,7 +3653,6 @@ Standard_SCP <- function(srt, prefix = "Standard", assay = NULL,
srt <- SrtReorder(srt, features = HVF, reorder_by = "seurat_clusters", slot = "data")
srt[["seurat_clusters"]] <- NULL
srt[[paste0(prefix, lr, "clusters")]] <- Idents(srt)

srt
},
error = function(error) {
Expand Down Expand Up @@ -3727,25 +3731,42 @@ Standard_SCP <- function(srt, prefix = "Standard", assay = NULL,
#' @examples
#' data("panc8_sub")
#' panc8_sub <- Integration_SCP(
#' srtMerge = panc8_sub, batch = "tech", integration_method = "Uncorrected"
#' srtMerge = panc8_sub, batch = "tech",
#' integration_method = "Uncorrected"
#' )
#' CellDimPlot(panc8_sub, group.by = c("tech", "celltype"))
#'
#' panc8_sub <- Integration_SCP(
#' srtMerge = panc8_sub, batch = "tech",
#' integration_method = "Uncorrected",
#' HVF_min_intersection = 5
#' )
#' CellDimPlot(panc8_sub, group.by = c("tech", "celltype"))
#'
#' panc8_sub <- Integration_SCP(
#' srtMerge = panc8_sub, batch = "tech", integration_method = "Seurat"
#' srtMerge = panc8_sub, batch = "tech",
#' integration_method = "Seurat"
#' )
#' CellDimPlot(panc8_sub, group.by = c("tech", "celltype"))
#'
#' \dontrun{
#' integration_methods <- c("Uncorrected", "Seurat", "scVI", "MNN", "fastMNN", "Harmony", "Scanorama", "BBKNN", "CSS", "LIGER", "Conos", "ComBat")
#' integration_methods <- c(
#' "Uncorrected", "Seurat", "scVI", "MNN", "fastMNN", "Harmony",
#' "Scanorama", "BBKNN", "CSS", "LIGER", "Conos", "ComBat"
#' )
#' for (method in integration_methods) {
#' panc8_sub <- Integration_SCP(
#' srtMerge = panc8_sub, batch = "tech",
#' integration_method = method,
#' linear_reduction_dims_use = 1:50,
#' nonlinear_reduction = "umap"
#' )
#' print(CellDimPlot(panc8_sub, group.by = c("tech", "celltype"), reduction = paste0(method, "UMAP2D"), theme_use = "theme_blank"))
#' print(CellDimPlot(panc8_sub,
#' group.by = c("tech", "celltype"),
#' reduction = paste0(method, "UMAP2D"),
#' xlab = "", ylab = "", title = method,
#' legend.position = "none", theme_use = "theme_blank"
#' ))
#' }
#'
#' nonlinear_reductions <- c("umap", "tsne", "dm", "phate", "pacmap", "trimap", "largevis", "fr")
Expand All @@ -3756,7 +3777,12 @@ Standard_SCP <- function(srt, prefix = "Standard", assay = NULL,
#' nonlinear_reduction = nonlinear_reductions
#' )
#' for (nr in nonlinear_reductions) {
#' print(CellDimPlot(panc8_sub, group.by = c("tech", "celltype"), reduction = paste0("Seurat", nr, "2D"), theme_use = "theme_blank"))
#' print(CellDimPlot(panc8_sub,
#' group.by = c("tech", "celltype"),
#' reduction = paste0("Seurat", nr, "2D"),
#' xlab = "", ylab = "", title = nr,
#' legend.position = "none", theme_use = "theme_blank"
#' ))
#' }
#' }
#'
Expand All @@ -3774,18 +3800,36 @@ Integration_SCP <- function(srtMerge = NULL, batch, append = TRUE, srtList = NUL
stop("Neither 'srtList' nor 'srtMerge' was found.")
}
if (length(integration_method) == 1 && integration_method %in% c("Uncorrected", "Seurat", "scVI", "MNN", "fastMNN", "Harmony", "Scanorama", "BBKNN", "CSS", "LIGER", "Conos", "ComBat")) {
args1 <- mget(names(formals()))
args2 <- as.list(match.call())
for (n in names(args2)) {
args1[[n]] <- args2[[n]]
}
args1 <- args1[!names(args1) %in% c("integration_method", "...")]
# Convert the arguments of the function call to a list and remove the function itself
args <- as.list(match.call())[-1]

# Create a new environment, the parent of which is the environment that called the foo function
new_env <- new.env(parent = parent.frame())

# Evaluate the arguments in the new environment to get the correct values
args <- lapply(args, function(x) eval(x, envir = new_env))

# Keep srtMerge and srtList as type of 'symbol' when use `do.call` function
# args[!names(args) %in% c("srtMerge", "srtList")] <- lapply(args[!names(args) %in% c("srtMerge", "srtList")], function(x) eval(x, envir = new_env))

# print("================ args ================ ")
# print(args)

# Get the function's formal arguments and their default values
formals <- mget(names(formals()))
formals <- formals[names(formals) != "..."]

# print("================ formals ================ ")
# print(formals)

# Merge the formal arguments with the actual arguments, so that all arguments are included
args <- modifyList(formals, args)

time_start <- Sys.time()
cat(paste0("[", time_start, "] ", paste0("Start ", integration_method, "_integrate"), "\n"))
srtIntegrated <- do.call(
what = paste0(integration_method, "_integrate"),
args = args1[names(args1) %in% formalArgs(paste0(integration_method, "_integrate"))]
srtIntegrated <- invoke(
.fn = paste0(integration_method, "_integrate"),
.args = args[names(args) %in% formalArgs(paste0(integration_method, "_integrate"))]
)
time_end <- Sys.time()
cat(paste0("[", time_end, "] ", paste0(integration_method, "_integrate done\n")))
Expand Down
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