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library(Seurat)
library(ggplot2)
library(ggpubr)
setwd("D:\\KS项目\\公众号文章\\单细胞作图小技巧")
genes <- c("S100a8","Zfhx3","Numb","Ltf",
"S100a9","Trps1", "Cd52","Anxa1",
"Neat1","Ly6g", "Tnf","Il1b")
mouse_data$sex <- ifelse(mouse_data$orig.ident=="10X_ntph_F","F",'M')
VlnPlot(mouse_data,
cols = c("limegreen", "navy"),
pt.size = 0,
group.by = "sex",
features = genes,
ncol = 4,
log = FALSE)&theme(axis.title.x = element_blank(),
panel.border = element_rect(fill=NA,color="black"),
axis.title.y = element_text(color = 'black', size = 12))&
geom_boxplot(width=0.1, fill="white", outlier.shape = NA) &
theme(legend.position = 'none')
#1、差异基因
# unique(human_data$celltype)
celltypes = c("Neutrophil","Macrophage","mDC","T cell")
#结合celltype与分组,做每种celltype两组之间差异基因
deg = c()
Idents(human_data) = paste(human_data$celltype, human_data$group, sep = '_')
for (cell in celltypes)
try({
tmp = FindMarkers(human_data, ident.1 = paste0(cell, '_GM'), ident.2 = paste0(cell, '_BM'))
tmp$gene = rownames(tmp)
tmp$celltype = cell
deg = rbind(deg, tmp)
})
#显著性基因
deg = subset(deg, p_val_adj < 0.05)
deg$DE =''
deg$DE = ifelse(deg$avg_log2FC>0, 'up', 'down')#上下调分组
library(dittoSeq)
VlnPlot(mouse_data,
cols = dittoColors(),
pt.size = 0,
group.by = "sex",
features = genes,
log = FALSE,
stack = T)+
NoLegend()
major_trajectory_color_plate = c("Neuroectoderm_and_glia" = "#f96100",
"Intermediate_neuronal_progenitors" = "#2e0ab7",
"Eye_and_other" = "#00d450",
"Ependymal_cells" = "#b75bff",
"CNS_neurons" = "#e5c000",
"Mesoderm" = "#bb46c5",
"Definitive_erythroid" = "#dc453e",
"Epithelium" = "#af9fb6",
"Endothelium" = "#00a34e",
"Muscle_cells" = "#ffa1f5",
"Hepatocytes" = "#185700",
"White_blood_cells" = "#7ca0ff",
"Neural_crest_PNS_glia" = "#fff167",
"Adipocytes" = "#7f3e39",
"Primitive_erythroid" = "#ffa9a1",
"Neural_crest_PNS_neurons" = "#b5ce92",
"T_cells" = "#ff9d47",
"Lung_and_airway" = "#02b0d1",
"Intestine" = "#ff007a",
"B_cells" = "#01b7a6",
"Olfactory_sensory_neurons" = "#e6230b",
"Cardiomyocytes" = "#643e8c",
"Oligodendrocytes" = "#916e00",
"Mast_cells" = "#005361",
"Megakaryocytes" = "#3f283d",
"Testis_and_adrenal" = "#585d3b")
day_color_plate = c("E8.0" = "#5E4FA2", "E8.25" = "#545BA8", "E8.5" = "#4A68AE", "E8.75" = "#4075B4",
"E9.0" = "#3682BA", "E9.25" = "#398FB9", "E9.5" = "#449DB4", "E9.75" = "#50AAAE",
"E10.0" = "#5CB7A9", "E10.25" = "#69C3A4", "E10.5" = "#78C9A4", "E10.75" = "#88CFA4",
"E11.0" = "#98D5A4", "E11.25" = "#A7DBA4", "E11.5" = "#B5E1A1", "E11.75" = "#C3E69F",
"E12.0" = "#D0EC9C", "E12.25" = "#DDF199", "E12.5" = "#E8F59B", "E12.75" = "#EDF8A4",
"E13.0" = "#F3FAAD", "E13.25" = "#F9FCB6", "E13.5" = "#FFFFBF", "E13.75" = "#FEF7B3",
"E14.0" = "#FEF0A7", "E14.25" = "#FEE99B", "E14.333" ="#FEE28F", "E14.75" = "#FDD985",
"E15.0" = "#FDCD7B", "E15.25" = "#FDC272", "E15.5" = "#FDB768", "E15.75" = "#FCAB5F",
"E16.0" = "#FA9C58", "E16.25" = "#F88D52", "E16.5" = "#F67E4B", "E16.75" = "#F46F44",
"E17.0" = "#EE6445", "E17.25" = "#E75947", "E17.5" = "#E04F4A", "E17.75" = "#D9444D",
"E18.0" = "#CF384D", "E18.25" = "#C32A4A", "E18.5" = "#B71C47", "E18.75" = "#AA0E44",
"P0" = "#9E0142")
#################################
### Somite counts color plate ###
#################################
somite_color_plate = rev(c("#fde725", "#eae51a", "#d5e21a", "#c0df25", "#a8db34",
"#93d741", "#7fd34e", "#6ccd5a", "#58c765", "#48c16e",
"#3aba76", "#2eb37c", "#25ab82", "#20a386", "#1e9c89",
"#1f948c", "#228c8d", "#25848e", "#287d8e", "#2b758e",
"#2e6d8e", "#32658e", "#365d8d", "#3a548c", "#3e4a89",
"#424186", "#453882", "#472e7c", "#482374", "#48186a",
"#470d60", "#440154"))
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