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update fig 1 with final datasets
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@Michael-Geuenich
Michael-Geuenich committed Oct 21, 2023
1 parent 7c360d8 commit 204e58a
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Showing 2 changed files with 55 additions and 52 deletions.
66 changes: 33 additions & 33 deletions pipeline/figures/figure1.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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)

Expand Down Expand Up @@ -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$cell_type |>
table() |>
as.data.frame() |>
Expand All @@ -83,21 +80,22 @@ cytof_bar <- CyTOF$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$CellType |>
Expand All @@ -116,7 +114,8 @@ scrna_bar <- scRNA$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))

Expand All @@ -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))

Expand All @@ -162,31 +162,33 @@ 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)) +
geom_bar(stat = "identity") +
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")
Expand All @@ -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()

41 changes: 22 additions & 19 deletions pipeline/whatsthatcell-helpers.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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(
Expand Down Expand Up @@ -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"){
Expand All @@ -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
}
}

Expand Down

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