# Set themes
mytheme_1 <- theme_bw()+
theme(axis.title = element_text(size=7, color="black"),
axis.text = element_text(size=7, color="black"),
legend.position = "none",
legend.text = element_text(size = 6.5, color="black"),
legend.title = element_text(size = 7, color="black"),
legend.key.width = unit(0.5, "cm"),
plot.title = element_text(hjust = 0.5, size = 7, color="black", face = "bold"),
panel.border = element_rect(size=0.25),
strip.background = element_rect(fill="white", size=0.5),
strip.text = element_text(size=6.5, color="black"),
panel.grid = element_blank()
)
theme_characteristics <- theme(plot.tag = element_text(vjust = -1),
axis.title.x = element_blank(),
panel.border = element_rect(size=0.5))
mytheme_codex <- theme_void()+
theme(legend.position = "none",
plot.title = element_text(color="white", hjust=0.1, size=10,
margin = unit(units = "cm", c(0,0,-0.6,0)), face = "bold"),
panel.background = element_rect(fill = "white", color=NA),
plot.background = element_rect(fill = "white", color=NA))
theme_axis_sub <- theme(
plot.margin = unit(c(0,0.25,0.18,0), units = "cm"),
plot.title = element_text(vjust = -1),
axis.title.x = element_textbox_simple(size = 7,
width = NULL,
padding = margin(1.25, 0, 2.25, 0),
lineheight = 1.25,
halign=0.5),
axis.title.y = element_textbox_simple(size = 7,
width = NULL,
orientation = "left-rotated",
padding = margin(0, 0, 1.25, 0)),
axis.text = element_text(size=7, color="black")
)
theme_axis_sub3 <- theme(
plot.margin = unit(c(0,0.25,0.1,0), units = "cm"),
plot.title = element_text(vjust = -1),
axis.title.x = element_textbox_simple(size = 7,
width = NULL,
margin = unit(units = "cm", c(0.05,0,0,0)),
padding = margin(1.25, 0, 1, 0),
lineheight = 1.25,
halign=0.5),
axis.title.y = element_blank(),
axis.text = element_text(size=7, color="black")
)
# Set colors
colors_characteristics <- c(
"DLBCL"=brewer.pal(5, "Paired")[1],
"FL"=brewer.pal(5, "Paired")[3],
"MCL"=brewer.pal(5, "Paired")[2],
"MZL"=brewer.pal(5, "Paired")[4],
"rLN"=brewer.pal(5, "Paired")[5],
"M"="#fdbb84",
"F"="#e34a33",
"Initial diagnosis"="#9ebcda",
"Relapse"="purple",
"NA"="grey85")
colors_umap_cl <-
c("1"=brewer.pal(9, "Purples")[4],
"2"=brewer.pal(9, "Purples")[6],
"3"=brewer.pal(9, "YlOrRd")[4],
#"4"=brewer.pal(9, "YlOrRd")[8],
"5"=brewer.pal(9, "YlOrRd")[7],
"6"=brewer.pal(9, "Greens")[6],
"8"=brewer.pal(9, "Blues")[3],
"9"=brewer.pal(9, "Purples")[8],
#"10"=brewer.pal(9, "YlOrRd")[5],
"11"=brewer.pal(9, "Blues")[9],
"12"=brewer.pal(9, "YlOrRd")[3],
"13"=brewer.pal(9, "Blues")[5],
"14"=brewer.pal(9, "RdPu")[7],
"15"=brewer.pal(9, "Blues")[7],
"16"=brewer.pal(9, "YlOrRd")[6],
"18"=brewer.pal(9, "YlOrRd")[9],
"19"=brewer.pal(9, "Greys")[4]
)
colors_celltype <-
c("T[Pr]"=brewer.pal(9, "RdPu")[8],
"T[FH]"=brewer.pal(9, "Greens")[5],
"T[H]"=brewer.pal(9, "Purples")[5],
"T[REG]"=brewer.pal(9, "Blues")[5],
"T[TOX]"=brewer.pal(9, "YlOrRd")[7],
"T[DN]"=brewer.pal(9, "Greys")[6]
)
colors_codex <- list(
"B"="#01178B",
"CD4T"=colors_umap_cl[["9"]],
"TFH"="#22d22f",
"TTOX"=brewer.pal(9, "YlOrRd")[5],
"TTOXNaive"=colors_umap_cl[["12"]],
"TTOX_exh"=colors_umap_cl[["5"]],
"Treg"="#FFF201",
"CD4TNaive"=colors_umap_cl[["2"]],
"TPR"=colors_umap_cl[["14"]],
"FDC"="white",
"Myeloid"="brown",
"Stromal cells"="pink",
"Other"="grey50"
)
colors_codex_exp <- list(
"B"="#01178B",
"CD4T"=colors_umap_cl[["9"]],
"TFH"="#22d22f",
"TTOX"=brewer.pal(9, "YlOrRd")[5],
"TTOXNaive"=colors_umap_cl[["12"]],
"TTOX_exh"=colors_umap_cl[["5"]],
"Treg"="#FFF201",
"CD4TNaive"=colors_umap_cl[["2"]],
"TPR"=colors_umap_cl[["14"]],
"FDC"="white",
"Macro"="brown",
"Granulo"="brown",
"DC"="brown",
"Stromal cells"="pink",
"PC"="grey50",
"MC"="grey50",
"NK"="grey50",
"NKT"="grey50"
)
colors_dendrogramm_codex <-
c("1"=colors_umap_cl[["2"]],
"2"=colors_umap_cl[["9"]],
"3"=colors_umap_cl[["3"]],
"5"=colors_umap_cl[["5"]],
"6"="#22d22f",
"12"=brewer.pal(9, "YlOrRd")[3],
"14"=colors_umap_cl[["14"]],
"19"=colors_umap_cl[["19"]],
"TREG"="#FFF201",
"TH"=brewer.pal(9, "Purples")[7],
"TTOX"=brewer.pal(9, "YlOrRd")[5]
)
# Set labels
labels_codex <- list(
"B"=expression("B cells"),
"CD4T"=expression('Memory T'[H]~''),
"TFH"=expression('T'[FH]~''),
"TTOX"=expression('Memory T'[TOX]~''),
"TTOXNaive"=expression('CD8'^'+'~'Naive'),
"TTOX_exh"=expression('Exhausted T'[TOX]~''),
"Treg"=expression('T'[REG]~''),
"CD4TNaive"=expression('CD4'^'+'~'Naive'),
"TPR"=expression('T'[Pr]~''),
"Myeloid"=expression("Myeloid cells"),
"FDC"=expression("FDC"),
"Stroma"=expression("Stromal cells"),
"Other"=expression("Other")
)
labels_codex_exp <- list(
"B"=expression("B cells"),
"CD4T"=expression('Memory T'[H]),
"TFH"=expression('T'[FH]),
"TTOX"=expression('Memory T'[TOX]),
"TTOXNaive"=expression('CD8'^'+'~'Naive'),
"TTOX_exh"=expression('Exhausted T'[TOX]),
"Treg"=expression('T'[REG]),
"CD4TNaive"=expression('CD4'^'+'~'Naive'),
"TPR"=expression('T'[Pr]),
"Myeloid"=expression("Myeloid cells"),
"FDC"=expression("FDC"),
"Stroma"=expression("Stromal cells"),
"Other"=expression("Other"),
"FDC"=expression("FDC"),
"Macro"=expression("Macrophages"),
"Granulo"=expression("Granulocytes"),
"DC"=expression("DC"),
"Stromal cells"=expression("Stromal cells"),
"PC"=expression("Plasma cells"),
"MC"=expression("Mast cells"),
"NK"=expression("NK cells"),
"NKT"=expression("NKT cells")
)
labels_codex_parsed <- list(
"B"="B cells",
"CD4T"=expression('T'[H]~' '),
"TFH"=expression('T'[FH]~' '),
"TTOX"=expression('T'[TOX]~' '),
"TTOXNaive"=expression('CD8'^'+'~'Naive '),
"TTOX_exh"=expression('T'[TOX]~'Exhausted'),
"Treg"=expression('T'[REG]~' '),
"CD4TNaive"=expression('CD4'^'+'~'Naive '),
"TPR"=expression('T'[Pr]~' ')#,
#"nonBT"=expression("Other ")
)
labels_cl <- list(
"14"=expression('T'[Pr]),
"1"=expression('T'[H]~'Naive'),
"2"=expression('T'[H]~'CM'[1]),
"9"=expression('T'[H]~'CM'[2]),
"6"=expression('T'[FH]),
"8"=expression('T'[REG]~'CM'[1]),
"13"=expression('T'[REG]~'CM'[2]),
"15"=expression('T'[REG]~'EM'[1]),
"11"=expression('T'[REG]~'EM'[2]),
"12"=expression('T'[TOX]~'Naive'),
"3"=expression('T'[TOX]~'EM'[1]),
"16"=expression('T'[TOX]~'EM'[2]),
"5"=expression('T'[TOX]~'EM'[3]),
"19"=expression('T'[DN])
)
labels_cl_parsed <- list(
"14"='T'[Pr]~'',
"1"='T'[H]~'Naive',
"2"='T'[H]~'CM'[1]~'',
"9"='T'[H]~'CM'[2]~'',
"6"='T'[FH]~'',
"8"='T'[REG]~'CM'[1]~'',
"13"='T'[REG]~'CM'[2]~'',
"15"='T'[REG]~'EM'[1]~'',
"11"='T'[REG]~'EM'[2]~'',
"12"='T'[TOX]~'Naive',
"3"='T'[TOX]~'EM'[1]~'',
"16"='T'[TOX]~'EM'[2]~'',
"5"='T'[TOX]~'EM'[3]~'',
"19"='T'[DN]~''
)
labels_cl <- list(
"14"=expression('T'[Pr]),
"1"=expression('T'[H]~'Naive'),
"2"=expression('T'[H]~'CM'[1]),
"9"=expression('T'[H]~'CM'[2]),
"6"=expression('T'[FH]),
"8"=expression('T'[REG]~'CM'[1]),
"13"=expression('T'[REG]~'CM'[2]),
"15"=expression('T'[REG]~'EM'[1]),
"11"=expression('T'[REG]~'EM'[2]),
"12"=expression('T'[TOX]~'Naive'),
"3"=expression('T'[TOX]~'EM'[1]),
"16"=expression('T'[TOX]~'EM'[2]),
"5"=expression('T'[TOX]~'EM'[3]),
"19"=expression('T'[DN])
)
# Set other
limits_codex <- c("B", "TPR", "CD4TNaive", "CD4T", "TFH", "Treg", "TTOXNaive", "TTOX_exh", "TTOX", "Stromal cells", "Myeloid", "FDC", "Other")
order_nn <- c( "B", "FDC", "TFH", "CD4T", "Treg", "CD4TNaive", "TTOXNaive", "TPR", "TTOX", "TTOX_exh", "Myeloid", "Stroma")
cluster_order <- c(14, 1, 2, 9, 6, 8, 13, 15, 11, 12, 3, 16, 5, 19)
colors_nn <- c( "#80B1D3", "#D9D9D9", "#BEBADA", "#FFFFB3", "#8DD3C7", "#BC80BD", "#B3DE69", "#FDB462", "#FCCDE5", "#FB8072")
names(colors_nn) <- c( "1" , "9" , "8" , "3" , "7" , "5" , "10" , "6" , "4" , "2" )
celltypes <- c("Proliferating T-cells", "Conventional T-cells", "Follicular T helper cells", "Regulatory T-cells", "Cytotoxic T-cells", "CD4-CD8- T-cells")
labels_celltypes_pars <- c("T[Pr]", "T[H]", "T[FH]", "T[REG]", "T[TOX]", "T[DN]")
labels_celltypes_expr <- list(expression('T'[Pr]), expression('T'[H]), expression('T'[FH]), expression('T'[REG]), expression('T'[TOX]), expression('T'[DN]))
df_celltypes <- data.frame(IdentI=c(cluster_order)) %>%
mutate(CellType=case_when(IdentI==19 ~ celltypes[6],
IdentI %in% c(3,5,12,16,18) ~ celltypes[5],
IdentI %in% c(1,2,9) ~ celltypes[2],
IdentI %in% c(6,17) ~ celltypes[3],
IdentI %in% c(8,11,13,15) ~ celltypes[4],
IdentI==14 ~ celltypes[1])) %>%
mutate(IdentI=as.factor(IdentI))
labels_celltypes_expr <-
list(expression('T'[Pr]),
expression('T'[H]),
expression('T'[FH]),
expression('T'[REG]),
expression('T'[TOX]),
expression('T'[DN]))
df_pop <- data.frame(Population=c("TPR", "THNaive", "THCM1", "THCM2", "TFH", "TREGCM1",
"TREGCM2", "TREGEM1", "TREGEM2", "TTOXNaive",
"TTOXEM1", "TTOXEM2", "TTOXEM3", "TDN"),
IdentI=cluster_order)
Datasets
Models
