## ----message = FALSE, warning = FALSE----------------------------------------- library(myTAI); library(S7); library(ggplot2); library(patchwork) data("example_phyex_set") ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=4, fig.width=6, fig.alt="plot_signature function output with stat_flatline_test", dev.args = list(bg = 'transparent'), fig.align='center'---- myTAI::plot_signature(example_phyex_set, show_p_val = TRUE, conservation_test = stat_flatline_test, colour = "lavender") + # as the plots are ggplot2 objects, we can simply modify them using ggplot2 ggplot2::labs(title = "Developmental stages of A. thaliana") ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=4, fig.width=6, fig.alt="plot_signature function output with stat_reductive_hourglass_test", dev.args = list(bg = 'transparent'), fig.align='center'---- module_info <- list(early = 1:3, mid = 4:6, late = 7:8) myTAI::plot_signature(example_phyex_set, show_p_val = TRUE, conservation_test = stat_reductive_hourglass_test, modules = module_info, colour = "lavender") ## ----message = FALSE, fig.height=5, fig.width=8, fig.alt="plot_signature_transformed function output", dev.args = list(bg = 'transparent'), fig.align='center'---- myTAI::plot_signature_transformed( example_phyex_set) ## ----message = FALSE, fig.height=5, fig.width=8, fig.alt="plot_signature_gene_quantiles function output", dev.args = list(bg = 'transparent'), fig.align='center'---- myTAI::plot_signature_gene_quantiles( example_phyex_set) ## ----message = FALSE, warning = FALSE, fig.height=3, fig.width=5, fig.alt="stat_flatline_test function output", dev.args = list(bg = 'transparent'), fig.align='center'---- myTAI::stat_flatline_test( example_phyex_set, plot_result = TRUE) ## ----message = FALSE, warning = FALSE----------------------------------------- res_flt <- myTAI::stat_flatline_test(example_phyex_set, plot_result = FALSE) ## ----message = FALSE, warning = FALSE, fig.height=5, fig.width=5, fig.alt="plot_cullen_frey function output for stat_flatline_test", dev.args = list(bg = 'transparent'), fig.align='center'---- myTAI::plot_cullen_frey(res_flt) ## ----message = FALSE, warning = FALSE, fig.height=5, fig.width=5, fig.alt="plot_null_txi_sample function output for stat_flatline_test", dev.args = list(bg = 'transparent'), fig.align='center'---- myTAI::plot_null_txi_sample(res_flt) + ggplot2::guides(x = guide_axis(angle = 90)) ## ----message = FALSE, warning = FALSE, fig.height=3, fig.width=5, fig.alt="stat_reductive_hourglass_test function output", dev.args = list(bg = 'transparent'), fig.align='center'---- module_info <- list(early = 1:3, mid = 4:6, late = 7:8) myTAI::stat_reductive_hourglass_test( example_phyex_set, plot_result = TRUE, modules = module_info) ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=4, fig.width=6, fig.alt="plot_strata_expression function output", dev.args = list(bg = 'transparent'), fig.align='center'---- myTAI::plot_strata_expression(example_phyex_set) ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=4, fig.width=6, fig.alt="plot_strata_expression function output ggplot2", dev.args = list(bg = 'transparent'), fig.align='center'---- myTAI::plot_strata_expression(example_phyex_set) + ggplot2::scale_y_log10() + ggplot2::labs(x = "Expression aggregated by mean (log-scaled)") ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=4, fig.width=8, fig.alt="plot_strata_expression function output", dev.args = list(bg = 'transparent'), fig.align='center'---- library(patchwork) p1 <- myTAI::plot_strata_expression(example_phyex_set |> myTAI::tf(log1p)) # equivalent to p2 <- example_phyex_set |> myTAI::tf(log1p) |> myTAI::plot_strata_expression() p1+p2 ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=4, fig.width=6, fig.alt="plot_contribution function output", dev.args = list(bg = 'transparent'), fig.align='center'---- myTAI::plot_contribution(example_phyex_set) ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=4, fig.width=8, fig.alt="plot_distribution_expression function output", dev.args = list(bg = 'transparent'), fig.align='center'---- myTAI::plot_distribution_expression(example_phyex_set) ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=6, fig.width=9, fig.alt="plot_distribution_pTAI_qqplot function output", dev.args = list(bg = 'transparent'), fig.align='center'---- myTAI::plot_distribution_pTAI_qqplot(example_phyex_set) ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=4, fig.width=6, fig.alt="plot_distribution_strata function output", dev.args = list(bg = 'transparent'), fig.align='center'---- myTAI::plot_distribution_strata(example_phyex_set@strata) / myTAI::plot_distribution_strata( example_phyex_set@strata, selected_gene_ids = myTAI::genes_top_variance(example_phyex_set, top_p = 0.95), as_log_obs_exp = TRUE ) + plot_annotation(title = "Distribution of gene ages (top), Observed vs Expected plot of top 5% variance genes (bottom)") ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=12, fig.width=12, fig.alt="plot_gene_heatmap function output default", dev.args = list(bg = 'transparent'), fig.align='center'---- myTAI::plot_gene_heatmap(example_phyex_set) ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=12, fig.width=12, fig.alt="plot_gene_heatmap function output clustered", dev.args = list(bg = 'transparent'), fig.align='center'---- myTAI::plot_gene_heatmap(example_phyex_set, cluster_rows = TRUE, show_reps=TRUE, show_gene_ids=TRUE, top_p=0.005) ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=12, fig.width=10, fig.alt="plot_gene_heatmap function output nonstd", dev.args = list(bg = 'transparent'), fig.align='center'---- myTAI::plot_gene_heatmap(example_phyex_set, cluster_rows = TRUE, show_reps=TRUE, top_p=0.005, std=FALSE, show_gene_ids=TRUE) ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=4, fig.width=6, fig.alt="plot_gene_space function output", dev.args = list(bg = 'transparent'), fig.align='center'---- myTAI::plot_gene_space(example_phyex_set) ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=4, fig.width=6, fig.alt="plot_gene_space function output by strata", dev.args = list(bg = 'transparent'), fig.align='center'---- myTAI::plot_gene_space(example_phyex_set,colour_by = "strata") ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=4, fig.width=12, fig.alt="plot_sample_space function output by TXI", dev.args = list(bg = 'transparent'), fig.align='center'---- myTAI::plot_sample_space(example_phyex_set) | myTAI::plot_sample_space(example_phyex_set, colour_by = "TXI") ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=4, fig.width=6, fig.alt="plot_sample_space function output by TXI", dev.args = list(bg = 'transparent'), fig.align='center', eval = requireNamespace("uwot", quietly = TRUE)---- # we can even do a UMAP myTAI::plot_sample_space(example_phyex_set, method = "UMAP") ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=3, fig.width=8, fig.alt="plot_mean_var function output simple vs highlighted", dev.args = list(bg = 'transparent'), fig.align='center'---- # highlighting top variance genes top_var_genes <- myTAI::genes_top_variance(example_phyex_set, top_p = 0.9995) p1 <- myTAI::plot_mean_var(example_phyex_set) p2 <- myTAI::plot_mean_var(example_phyex_set, highlight_genes = top_var_genes) p1 + p2 + plot_annotation(title = "Mean-variance: simple vs. highlighted top variance genes") ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=3, fig.width=6, fig.alt="plot_gene_space function output log transform coloured by strata", dev.args = list(bg = 'transparent'), fig.align='center'---- # with log transform and colouring by phylostratum myTAI::plot_mean_var(example_phyex_set |> myTAI::tf(log1p), colour_by = "strata") + ggplot2::guides(colour = guide_legend(ncol=2)) ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=4, fig.width=12, fig.alt="plot_gene_profiles function output manual vs strata coloring", dev.args = list(bg = 'transparent'), fig.align='center'---- # side by side: manual coloring vs strata coloring p1 <- myTAI::plot_gene_profiles(example_phyex_set, max_genes = 10, colour_by = "manual") p2 <- myTAI::plot_gene_profiles(example_phyex_set, max_genes = 10, colour_by = "strata") p1 + p2 + plot_annotation(title = "Gene profiles: manual vs. strata coloring") ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=4, fig.width=6, fig.alt="plot_gene_profiles function output stage std_log transformation", dev.args = list(bg = 'transparent'), fig.align='center'---- # stage colouring with standardized log transformation myTAI::plot_gene_profiles(example_phyex_set, max_genes = 10, transformation = "std_log", colour_by = "stage") ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=8, fig.width=12, fig.alt="plot_gene_profiles function output faceted by strata", dev.args = list(bg = 'transparent'), fig.align='center'---- # faceted by phylostratum myTAI::plot_gene_profiles(example_phyex_set, max_genes = 1000, colour_by = "strata", facet_by_strata = TRUE, show_set_mean = TRUE, show_labels = FALSE) ## ----message = FALSE, warning = FALSE----------------------------------------- # Load example single-cell data data(example_phyex_set_sc) ## ----message = FALSE, warning = FALSE----------------------------------------- example_phyex_set_sc ## ----message = FALSE, warning = FALSE----------------------------------------- # Check available identities cat("Available identities for plotting:\n") print(example_phyex_set_sc@available_idents) ## ----message = FALSE, warning = FALSE----------------------------------------- # Set up custom color schemes for better visualization day_colors <- c("Day1" = "#3498db", "Day3" = "#2980b9", "Day5" = "#1f4e79", "Day7" = "#0d2a42") condition_colors <- c("Control" = "#27ae60", "Treatment" = "#e74c3c") group_colors <- c("TypeA" = "#e74c3c", "TypeB" = "#f39c12", "TypeC" = "#9b59b6") example_phyex_set_sc@idents_colours[["day"]] <- day_colors example_phyex_set_sc@idents_colours[["condition"]] <- condition_colors example_phyex_set_sc@idents_colours[["groups"]] <- group_colors ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=4, fig.width=6, fig.alt="plot_signature single-cell basic", dev.args = list(bg = 'transparent'), fig.align='center'---- # Basic signature plot showing TXI distribution across cell types myTAI::plot_signature(example_phyex_set_sc) ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=4, fig.width=6, fig.alt="plot_signature single-cell without individual cells", dev.args = list(bg = 'transparent'), fig.align='center'---- # Plot without showing individual cells (just means) myTAI::plot_signature(example_phyex_set_sc, show_reps = FALSE) ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=4, fig.width=6, fig.alt="plot_signature single-cell by day", dev.args = list(bg = 'transparent'), fig.align='center'---- # Plot TXI distribution by developmental day instead of cell type myTAI::plot_signature(example_phyex_set_sc, primary_identity = "day", show_p_val = FALSE) ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=4, fig.width=6, fig.alt="plot_signature single-cell by condition", dev.args = list(bg = 'transparent'), fig.align='center'---- # Plot TXI distribution by experimental condition myTAI::plot_signature(example_phyex_set_sc, primary_identity = "condition", show_p_val=FALSE) ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=4, fig.width=8, fig.alt="plot_signature single-cell with secondary coloring", dev.args = list(bg = 'transparent'), fig.align='center'---- # Plot by day, colored by condition myTAI::plot_signature(example_phyex_set_sc, primary_identity = "day", secondary_identity = "condition", show_p_val=FALSE) ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=6, fig.width=10, fig.alt="plot_signature single-cell with faceting", dev.args = list(bg = 'transparent'), fig.align='center'---- # Plot by day, faceted by condition myTAI::plot_signature(example_phyex_set_sc, primary_identity = "day", secondary_identity = "batch", facet_by_secondary = TRUE, show_p_val = FALSE) ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=8, fig.width=10, fig.alt="plot_gene_heatmap single-cell", dev.args = list(bg = 'transparent'), fig.align='center'---- # Gene heatmap for single-cell data (aggregated by cell type) myTAI::plot_gene_heatmap(example_phyex_set_sc, top_p = 0.1, cluster_rows=TRUE) ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=8, fig.width=12, fig.alt="plot_gene_heatmap single-cell with individual cells", dev.args = list(bg = 'transparent'), fig.align='center'---- # Gene heatmap showing individual cells (subsampled) myTAI::plot_gene_heatmap(example_phyex_set_sc, show_reps = TRUE, max_cells_per_type = 10, top_p = 0.05, cluster_rows=TRUE) ## ----message = FALSE, warning = FALSE, results = FALSE, fig.height=8, fig.width=12, fig.alt="plot_gene_heatmap single-cell grouped by day", dev.args = list(bg = 'transparent'), fig.align='center'---- # Change identity to "day" and plot heatmap grouped by developmental time example_sc_by_day <- example_phyex_set_sc example_sc_by_day@selected_idents <- "day" myTAI::plot_gene_heatmap(example_sc_by_day, show_reps = TRUE, max_cells_per_type = 8, top_p = 0.05, cluster_rows=TRUE, show_gene_ids=TRUE, std=FALSE)