From 204e58afc445a66988a1df5228974e5c322792d3 Mon Sep 17 00:00:00 2001 From: Michael Geuenich Date: Sat, 21 Oct 2023 17:46:30 -0400 Subject: [PATCH] update fig 1 with final datasets --- pipeline/figures/figure1.R | 66 ++++++++++++++++---------------- pipeline/whatsthatcell-helpers.R | 41 +++++++++++--------- 2 files changed, 55 insertions(+), 52 deletions(-) diff --git a/pipeline/figures/figure1.R b/pipeline/figures/figure1.R index 49047f3..42622f8 100644 --- a/pipeline/figures/figure1.R +++ b/pipeline/figures/figure1.R @@ -27,10 +27,8 @@ snRNA <- runTSNE(snRNA) scRNALung <- readRDS(snakemake@input$scRNALung) scRNALung <- runTSNE(scRNALung) - -tabulaLiver <- readRDS(snakemake@input$tabulaLiver) -tabulaLiver <- runTSNE(tabulaLiver) - +liverAtlas <- readRDS(snakemake@input$liverAtlas) +liverAtlas <- runTSNE(liverAtlas) tabulaVasc <- readRDS(snakemake@input@tabulaVasc) tabulaVasc <- runTSNE(tabulaVasc) @@ -69,11 +67,10 @@ plot_dim_red <- function(sce, mod, include_axis = FALSE, } - ### CYTOF cytof_tsne <- plot_dim_red(CyTOF, "CyTOF", TRUE, - a1_start = -37, a1_end = -27, a1_y = -29, - a2_start = -29, a2_end = -19, a2_x = -37) + a1_start = -35, a1_end = -25, a1_y = -33, + a2_start = -33, a2_end = -23, a2_x = -35) cytof_bar <- CyTOF$cell_type |> table() |> as.data.frame() |> @@ -83,21 +80,22 @@ cytof_bar <- CyTOF$cell_type |> angle = 45, hjust = 0, vjust = 0), position = position_stack(vjust = 1.03)) + scale_fill_manual(values = cell_type_colours("CyTOF", FALSE)) + - ylim(0, 3050) + + ylim(0, 2800) + labs(x = "Cell type", y = "Number of cells", fill = "Cell type") + whatsthatcell_theme() + theme(axis.text.x = element_blank(), axis.ticks.x = element_blank()) -cytof_plot <- (wrap_elements(full = cytof_tsne, ignore_tag = TRUE) & labs(title = "CyTOF")) / - cytof_bar + plot_layout(heights = c(3,1.5)) +cytof_plot <- (wrap_elements(full = cytof_tsne, ignore_tag = TRUE) & + labs(title = "CyTOF - Bone marrow")) / + cytof_bar + plot_layout(heights = c(3,1.8)) ### scRNASeq scrna_tsne <- plot_dim_red(scRNA, "scRNASeq", TRUE, - a1_start = -38, a1_end = -28, a1_y = -33, - a2_start = -33, a2_end = -23, a2_x = -38, + a1_start = -40, a1_end = -30, a1_y = -49, + a2_start = -49, a2_end = -39, a2_x = -40, l_nrow = 5) scrna_bar <- scRNA$CellType |> @@ -116,7 +114,8 @@ scrna_bar <- scRNA$CellType |> axis.ticks.x = element_blank()) -scrna_plot <- ((wrap_elements(full = scrna_tsne, ignore_tag = TRUE) & labs(title = "scRNASeq")) / +scrna_plot <- ((wrap_elements(full = scrna_tsne, ignore_tag = TRUE) & + labs(title = "scRNASeq - Breast cancer cell lines")) / scrna_bar) + plot_layout(heights = c(3,1)) @@ -140,7 +139,8 @@ snrna_bar <- snRNA$cell_type |> axis.ticks.x = element_blank()) -snrna_plot <- ((wrap_elements(full = snrna_tsne, ignore_tag = TRUE) & labs(title = "snRNASeq")) / +snrna_plot <- ((wrap_elements(full = snrna_tsne, ignore_tag = TRUE) & + labs(title = "snRNASeq - Pancreas cancer")) / snrna_bar) + plot_layout(heights = c(3,1)) @@ -162,14 +162,15 @@ scRNALung_bar <- scRNALung$CellType |> theme(axis.text.x = element_blank(), axis.ticks.x = element_blank()) -scrna_lung_plot <- ((wrap_elements(full = scrna_lung_tsne, ignore_tag = TRUE) & labs(title = "scRNALung")) / +scrna_lung_plot <- ((wrap_elements(full = scrna_lung_tsne, ignore_tag = TRUE) & + labs(title = "scRNASeq - Lung cancer cell lines")) / scRNALung_bar) + plot_layout(heights = c(3,1)) ## Tabula Liver -tabulaLiver_tsne <- plot_dim_red(tabulaLiver, "tabulaLiver") +liverAtlas_tsne <- plot_dim_red(liverAtlas, "liverAtlas") -tabulaLiver_bar <- tabulaLiver$CellType |> +liverAtlas_bar <- liverAtlas$CellType |> table() |> as.data.frame() |> ggplot(aes(x = reorder(Var1, -Freq), y = Freq, fill = Var1)) + @@ -177,16 +178,17 @@ tabulaLiver_bar <- tabulaLiver$CellType |> geom_text(aes(label = Freq, x = reorder(Var1, -Freq), y = Freq + 40, angle = 45, hjust = 0, vjust = 0), position = position_stack(vjust = 1.03)) + - scale_fill_manual(values = cell_type_colours("tabulaLiver", FALSE)) + - ylim(0, 2000) + + scale_fill_manual(values = cell_type_colours("liverAtlas", FALSE)) + + ylim(0, 4200) + labs(x = "Cell type", y = "Number of cells", fill = "Cell type") + whatsthatcell_theme() + theme(axis.text.x = element_blank(), axis.ticks.x = element_blank()) -tabulaLiver_plot <- ((wrap_elements(full = tabulaLiver_tsne, ignore_tag = TRUE) & labs(title = "tabulaLiver")) / - tabulaLiver_bar) + - plot_layout(heights = c(3,1.5)) +liverAtlas_plot <- ((wrap_elements(full = liverAtlas_tsne, ignore_tag = TRUE) & + labs(title = "scRNASeq - Liver")) / + liverAtlas_bar) + + plot_layout(heights = c(3,1.8)) ## Tabula Vasc tabulaVasc_tsne <- plot_dim_red(tabulaVasc, "tabulaVasc") @@ -200,26 +202,24 @@ tabulaVasc_bar <- tabulaVasc$CellType |> angle = 45, hjust = 0, vjust = 0), position = position_stack(vjust = 1.03)) + scale_fill_manual(values = cell_type_colours("tabulaVasc", FALSE)) + - ylim(0, 7200) + + ylim(0, 7000) + labs(x = "Cell type", y = "Number of cells", fill = "Cell type") + whatsthatcell_theme() + theme(axis.text.x = element_blank(), axis.ticks.x = element_blank()) -tabulaVasc_plot <- ((wrap_elements(full = tabulaVasc_tsne, ignore_tag = TRUE) & labs(title = "tabulaVasc")) / +tabulaVasc_plot <- ((wrap_elements(full = tabulaVasc_tsne, ignore_tag = TRUE) & + labs(title = "scRNASeq - Vasculature")) / tabulaVasc_bar) + - plot_layout(heights = c(3,1.5)) + plot_layout(heights = c(3,1.8)) ## Combine figures row1 <- wrap_elements((scrna_plot | scrna_lung_plot | snrna_plot) + plot_layout(widths = c(1, 1.2, 1))) -row2 <- wrap_elements((cytof_plot | tabulaLiver_plot | tabulaVasc_plot) + plot_layout(widths = c(1, 1.2, 1))) - -pdf(snakemake@output$fig1, height = 22, width = 17) -wrap_elements(row1 / plot_spacer() / row2 + plot_layout(heights= c(1, 0.1, 1))) / - #wrap_elements(schematic) + - #plot_layout(heights = c(5, 0.9)) + - plot_annotation(tag_levels = 'A') & - theme(plot.tag = element_text(size = 22)) +row2 <- wrap_elements((cytof_plot | liverAtlas_plot | tabulaVasc_plot) + plot_layout(widths = c(1, 1.2, 1))) + +pdf(snakemake@output$fig1, height = 18, width = 17) + wrap_elements(row1 / plot_spacer() / row2 + plot_layout(heights= c(1, 0.05, 1))) / + theme(plot.tag = element_text(size = 22)) dev.off() diff --git a/pipeline/whatsthatcell-helpers.R b/pipeline/whatsthatcell-helpers.R index b646dc9..d14cfa3 100644 --- a/pipeline/whatsthatcell-helpers.R +++ b/pipeline/whatsthatcell-helpers.R @@ -676,20 +676,22 @@ cell_type_colours <- function(modality, include_unassigned = TRUE) { "HCC827" = pal[12] ) - tabulaLiver_colours <- c( - "endothelial cell" = pal[9], - "endothelial cell of hepatic sinusoid" = pal[13], - "erythrocyte" = pal[14], - "fibroblast" = pal[19], - "hepatocyte" = pal[3], - "intrahepatic cholangiocyte" = pal[18], - "liver dendritic cell" = pal[4], - "macrophage" = pal[8], - "monocyte" = pal[16], - "neutrophil" = pal[20], - "nk cell" = pal[10], - "plasma cell" = pal[2], - "t cell" = pal[12] + liverAtlas_colours <- c( + "Endothelial cells" = pal[9], + #"endothelial cell of hepatic sinusoid" = pal[13], + "Basophils" = pal[14], + "Fibroblasts" = pal[19], + "Hepatocytes" = pal[3], + "Cholangiocytes" = pal[18], + "Dendritic cells" = pal[4], + "Macrophages" = pal[8], + "Mono+mono derived cells" = pal[16], + "Neutrophils" = pal[13], + "Resident NK" = pal[10], + "Plasma cells" = pal[2], + "T cells" = pal[12], + "B cells" = pal[11], + "pDCs" = pal[20] ) tabulaVasc_colours <- c( @@ -717,14 +719,13 @@ cell_type_colours <- function(modality, include_unassigned = TRUE) { "HCC827" = pal[12] ) - tabulaLiver_colours <- c() - if(include_unassigned){ scRNASeq_colours <- c(scRNASeq_colours, c('unassigned' = "grey60")) snRNASeq_colours <- c(snRNASeq_colours, c('unassigned' = "grey60")) CyTOF_colours <- c(CyTOF_colours, c('unassigned' = "grey60")) scRNALung_colours <- c(scRNALung_colours, c('unassigned' = "grey60")) - tabulaLiver_colours <- c(tabulaLiver_colours, c('unassigned' = "grey60")) + liverAtlas_colours <- c(liverAtlas_colours, c('unassigned' = "grey60")) + tabulaVasc_colours <- c(tabulaVasc_colours, c('unassigned' = "grey60")) } if(modality == "scRNASeq"){ @@ -735,8 +736,10 @@ cell_type_colours <- function(modality, include_unassigned = TRUE) { CyTOF_colours }else if(modality == "scRNALung"){ scRNALung_colours - }else if(modality == "tabulaLiver"){ - tabulaLiver_colours + }else if(modality == "liverAtlas"){ + liverAtlas_colours + }else if(modality == "tabulaVasc"){ + tabulaVasc_colours } }