Adding titles to the UMAP plots

[sevdarafatov]

• At the visualization part the UMAP plots don`t have any title. It hard to understand what is what.
• Suggestion: Add titles to the UMAP plots --> 02_process_pipeline.Rmd

[sevdarafatov]

plotDimensionsWithTitle <- function(SO, scenario) { Idents(SO) <- SO$seurat_clusters

# Create the UMAP plot
umap_plot <- DimPlot(SO)

# Add a title to the plot
umap_plot <- umap_plot + ggtitle(paste("UMAP Plot - Scenario", scenario))

# Print the plot
print(umap_plot)

if (goodQ & scenario != "1") {
    # Load cell cycle scores and phase table
    phaseTable <- read.table(paste0("../05_additionalControls/cellCycleScoresAssignation_", DATASET, "_scenario_", scenario, ".csv"), sep = ",", header = TRUE)
    phaseTable <- column_to_rownames(phaseTable, var = "cellIDs")

    # merge phase column of cell cycle scores to the SO metadata table according to the cellnames
    SO@meta.data <- merge(SO@meta.data, phaseTable["Phase"], by = "row.names", all.y = FALSE)
    SO@meta.data <- column_to_rownames(SO@meta.data, var = "Row.names")

    Idents(SO) <- SO@meta.data$Phase

    # Create the UMAP plot with a title
    umap_plot_with_title <- DimPlot(SO, shuffle = TRUE) + ggtitle(paste("UMAP Plot (Cell Cycle) - Scenario", scenario))

    # Print the plot with the title
    print(umap_plot_with_title)
}

}

invisible(mapply(plotDimensionsWithTitle, SO.list, names(SO.list)))