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Develop #180

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Oct 19, 2023
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Develop #180

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40129bd
Update the document for FeatureStatPlot
zhanghao-njmu Oct 18, 2023
1de4b5b
Removed the restriction in FeatureStatPlot that required the slot to …
zhanghao-njmu Oct 19, 2023
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7 changes: 0 additions & 7 deletions R/SCP-analysis.R
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Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,6 @@
#' @importFrom reshape2 dcast melt
#' @importFrom biomaRt listEnsemblArchives useMart listDatasets useDataset getBM listAttributes useEnsembl
#' @export
#'
GeneConvert <- function(geneID, geneID_from_IDtype = "symbol", geneID_to_IDtype = "entrez_id",
species_from = "Homo_sapiens", species_to = NULL,
Ensembl_version = 103, biomart = NULL, mirror = NULL, max_tries = 5) {
Expand Down Expand Up @@ -3400,7 +3399,6 @@ PrepareDB <- function(species = c("Homo_sapiens", "Mus_musculus"),
#' @importFrom BiocParallel bplapply bpprogressbar<- bpRNGseed<- bpworkers ipcid ipclock ipcunlock
#' @importFrom clusterProfiler enricher simplify
#' @export
#'
RunEnrichment <- function(srt = NULL, group_by = NULL, test.use = "wilcox", DE_threshold = "avg_log2FC > 0 & p_val_adj < 0.05",
geneID = NULL, geneID_groups = NULL, geneID_exclude = NULL, IDtype = "symbol", result_IDtype = "symbol", species = "Homo_sapiens",
db = "GO_BP", db_update = FALSE, db_version = "latest", db_combine = FALSE, convert_species = TRUE, Ensembl_version = 103, mirror = NULL,
Expand Down Expand Up @@ -3665,7 +3663,6 @@ RunEnrichment <- function(srt = NULL, group_by = NULL, test.use = "wilcox", DE_t
#' @importFrom BiocParallel bplapply bpprogressbar<- bpRNGseed<- bpworkers ipcid ipclock ipcunlock
#' @importFrom clusterProfiler GSEA simplify
#' @export
#'
RunGSEA <- function(srt = NULL, group_by = NULL, test.use = "wilcox", DE_threshold = "p_val_adj < 0.05", scoreType = "std",
geneID = NULL, geneScore = NULL, geneID_groups = NULL, geneID_exclude = NULL, IDtype = "symbol", result_IDtype = "symbol", species = "Homo_sapiens",
db = "GO_BP", db_update = FALSE, db_version = "latest", db_combine = FALSE, convert_species = TRUE, Ensembl_version = 103, mirror = NULL,
Expand Down Expand Up @@ -4984,7 +4981,6 @@ py_to_r_auto <- function(x) {
#' @importFrom Seurat GetAssayData
#' @importFrom Matrix t
#' @export
#'
srt_to_adata <- function(srt, features = NULL,
assay_X = "RNA", slot_X = "counts",
assay_layers = c("spliced", "unspliced"), slot_layers = "counts",
Expand Down Expand Up @@ -5418,7 +5414,6 @@ check_python_element <- function(x, depth = maxDepth(x)) {
#' CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "PAGAUMAP2D", paga = pancreas_sub@misc$paga)
#'
#' @export
#'
RunPAGA <- function(srt = NULL, assay_X = "RNA", slot_X = "counts", assay_layers = c("spliced", "unspliced"), slot_layers = "counts",
adata = NULL, group_by = NULL,
linear_reduction = NULL, nonlinear_reduction = NULL, basis = NULL,
Expand Down Expand Up @@ -5529,7 +5524,6 @@ RunPAGA <- function(srt = NULL, assay_X = "RNA", slot_X = "counts", assay_layers
#' pancreas_sub <- RunSCVELO(srt = pancreas_sub, assay_X = "SCT", group_by = "SubCellType", linear_reduction = "Standardpca", nonlinear_reduction = "StandardTSNE2D")
#'
#' @export
#'
RunSCVELO <- function(srt = NULL, assay_X = "RNA", slot_X = "counts", assay_layers = c("spliced", "unspliced"), slot_layers = "counts",
adata = NULL, group_by = NULL,
linear_reduction = NULL, nonlinear_reduction = NULL, basis = NULL,
Expand Down Expand Up @@ -5636,7 +5630,6 @@ RunSCVELO <- function(srt = NULL, assay_X = "RNA", slot_X = "counts", assay_laye
#' FeatureDimPlot(pancreas_sub, paste0(c("Alpha", "Beta", "Delta", "Epsilon"), "_diff_potential"))
#'
#' @export
#'
RunPalantir <- function(srt = NULL, assay_X = "RNA", slot_X = "counts", assay_layers = c("spliced", "unspliced"), slot_layers = "counts",
adata = NULL, group_by = NULL,
linear_reduction = NULL, nonlinear_reduction = NULL, basis = NULL,
Expand Down
28 changes: 23 additions & 5 deletions R/SCP-plot.R
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Expand Up @@ -3363,7 +3363,16 @@ FeatureDimPlot3D <- function(srt, features = NULL, reduction = NULL, dims = c(1,
#' group.by = "SubCellType", bg.by = "CellType", stack = TRUE, flip = TRUE
#' ) %>% panel_fix_overall(width = 8, height = 5) # As the plot is created by combining, we can adjust the overall height and width directly.
#'
#' FeatureStatPlot(pancreas_sub, stat.by = c("G2M_score", "Fev"), group.by = "CellType", plot.by = "feature")
#' FeatureStatPlot(pancreas_sub, stat.by = c("Neurog3", "Rbp4", "Ins1"), group.by = "CellType", plot.by = "feature")
#' FeatureStatPlot(pancreas_sub,
#' stat.by = c("Neurog3", "Rbp4", "Ins1"), group.by = "CellType", plot.by = "feature",
#' multiplegroup_comparisons = TRUE, sig_label = "p.format", sig_labelsize = 4
#' )
#' FeatureStatPlot(pancreas_sub,
#' stat.by = c("Neurog3", "Rbp4", "Ins1"), group.by = "CellType", plot.by = "feature",
#' comparisons = list(c("Neurog3", "Rbp4"), c("Rbp4", "Ins1")),
#' stack = TRUE
#' )
#' FeatureStatPlot(pancreas_sub, stat.by = c(
#' "Sox9", "Anxa2", "Bicc1", # Ductal
#' "Neurog3", "Hes6", # EPs
Expand All @@ -3372,14 +3381,21 @@ FeatureDimPlot3D <- function(srt, features = NULL, reduction = NULL, dims = c(1,
#' "Ins1", "Gcg", "Sst", "Ghrl" # Beta, Alpha, Delta, Epsilon
#' ), group.by = "SubCellType", plot.by = "feature", stack = TRUE)
#'
#' data <- pancreas_sub@assays$RNA@data
#' pancreas_sub@[email protected] <- as.matrix(data / rowMeans(data))
#' FeatureStatPlot(pancreas_sub,
#' stat.by = c("Neurog3", "Rbp4", "Ins1"), group.by = "CellType",
#' slot = "scale.data", ylab = "FoldChange", same.y.lims = TRUE, y.max = 4
#' )
#'
#' @importFrom Seurat FetchData
#' @importFrom reshape2 melt
#' @importFrom gtable gtable_add_cols gtable_add_rows gtable_add_grob gtable_add_padding
#' @importFrom grid grobHeight grobWidth
#' @importFrom patchwork wrap_plots
#' @export
FeatureStatPlot <- function(srt, stat.by, group.by = NULL, split.by = NULL, bg.by = NULL, plot.by = c("group", "feature"), fill.by = c("group", "feature", "expression"),
cells = NULL, slot = c("data", "counts"), assay = NULL, keep_empty = FALSE, individual = FALSE,
cells = NULL, slot = "data", assay = NULL, keep_empty = FALSE, individual = FALSE,
plot_type = c("violin", "box", "bar", "dot", "col"),
palette = "Paired", palcolor = NULL, alpha = 1,
bg_palette = "Paired", bg_palcolor = NULL, bg_alpha = 0.2,
Expand All @@ -3401,17 +3417,19 @@ FeatureStatPlot <- function(srt, stat.by, group.by = NULL, split.by = NULL, bg.b
meta.data <- [email protected]
meta.data[["cells"]] <- rownames(meta.data)
assay <- assay %||% DefaultAssay(srt)
slot <- match.arg(slot)
exp.data <- slot(srt@assays[[assay]], slot)
plot.by <- match.arg(plot.by)

if (plot.by == "feature") {
if (length(group.by) > 1) {
stop("The 'group.by' must have a length of 1 when 'plot.by' is set to 'feature'")
}
if (!is.null(bg.by)) {
message("'bg.by' is invalid when plot.by is set to 'feature'")
}
message("Setting 'group.by' to 'Features' as 'plot.by' is set to 'feature'")
srt@assays[setdiff(names(srt@assays), assay)] <- NULL
meta.reshape <- FetchData(srt, vars = c(stat.by, group.by, split.by, bg.by), cells = cells %||% rownames(meta.data), slot = slot)
meta.reshape <- FetchData(srt, vars = c(stat.by, group.by, split.by), cells = cells %||% rownames(meta.data), slot = slot)
meta.reshape[["cells"]] <- rownames(meta.reshape)
meta.reshape <- melt(meta.reshape, measure.vars = stat.by, variable.name = "Features", value.name = "Stat.by")
rownames(meta.reshape) <- paste0(meta.reshape[["cells"]], "-", meta.reshape[["Features"]])
Expand All @@ -3421,7 +3439,7 @@ FeatureStatPlot <- function(srt, stat.by, group.by = NULL, split.by = NULL, bg.b
if (length(rownames(meta.reshape)[meta.reshape[[group.by]] == g]) > 0) {
meta.reshape[[g]] <- meta.reshape[["Stat.by"]]
p <- ExpressionStatPlot(
exp.data = exp.data, meta.data = meta.reshape, stat.by = g, group.by = "Features", split.by = split.by, bg.by = bg.by, plot.by = "group", fill.by = fill.by,
exp.data = exp.data, meta.data = meta.reshape, stat.by = g, group.by = "Features", split.by = split.by, bg.by = NULL, plot.by = "group", fill.by = fill.by,
cells = rownames(meta.reshape)[meta.reshape[[group.by]] == g], keep_empty = keep_empty, individual = individual,
plot_type = plot_type,
palette = palette, palcolor = palcolor, alpha = alpha,
Expand Down
20 changes: 18 additions & 2 deletions man/FeatureStatPlot.Rd
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