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fix bugs
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zhanghao-njmu committed Jan 24, 2024
1 parent b0e49c8 commit aa0fa48
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Showing 7 changed files with 169 additions and 103 deletions.
3 changes: 2 additions & 1 deletion .gitignore
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Expand Up @@ -11,4 +11,5 @@ tmaps
src/*.so
src/*.o
test.R
test.cpp
test.cpp
test
4 changes: 4 additions & 0 deletions R/SCP-analysis.R
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Expand Up @@ -3996,6 +3996,8 @@ RunEnrichment <- function(srt = NULL, group_by = NULL, test.use = "wilcox", DE_t
results <- results[!sapply(results, is.null)]
results <- results[intersect(c(nm, paste0(nm, "_sim")), names(results))]
enrichment <- do.call(rbind, lapply(results, function(x) x@result))
enrichment[["Groups"]] <- factor(enrichment[["Groups"]], levels = levels(geneID_groups))
enrichment[["Database"]] <- factor(enrichment[["Database"]], levels = unique(enrichment[["Database"]]))
rownames(enrichment) <- NULL

time_end <- Sys.time()
Expand Down Expand Up @@ -4293,6 +4295,8 @@ RunGSEA <- function(srt = NULL, group_by = NULL, test.use = "wilcox", DE_thresho
results <- results[!sapply(results, is.null)]
results <- results[intersect(c(nm, paste0(nm, "_sim")), names(results))]
enrichment <- do.call(rbind, lapply(results, function(x) x@result))
enrichment[["Groups"]] <- factor(enrichment[["Groups"]], levels = levels(geneID_groups))
enrichment[["Database"]] <- factor(enrichment[["Database"]], levels = unique(enrichment[["Database"]]))
rownames(enrichment) <- NULL

time_end <- Sys.time()
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2 changes: 1 addition & 1 deletion R/SCP-app.R
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Expand Up @@ -595,7 +595,7 @@ RunSCExplorer <- function(base_dir = "SCExplorer",
initial_raster = NULL,
session_workers = 2,
plotting_workers = 8,
create_script = FALSE,
create_script = TRUE,
style_script = require("styler", quietly = TRUE),
overwrite = FALSE) {
check_R(c("rhdf5", "HDF5Array", "[email protected]", "ggplot2", "ragg", "htmlwidgets", "plotly", "bslib", "future", "promises", "BiocParallel"))
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224 changes: 123 additions & 101 deletions R/SCP-plot.R

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5 changes: 5 additions & 0 deletions man/CellDimPlot.Rd

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3 changes: 3 additions & 0 deletions man/FeatureStatPlot.Rd

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31 changes: 31 additions & 0 deletions man/MergeRows.Rd

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