单细胞数据复现-肺癌文章代码复现5
原创单细胞数据复现-肺癌文章代码复现5
原创
小胡子刺猬的生信学习123
发布于 2022-05-22 17:16:40
发布于 2022-05-22 17:16:40
单细胞数据复现-肺癌文章代码复现1/developer/article/1992648
单细胞数据复现-肺癌文章代码复现2/developer/article/1995619
单细胞数据复现-肺癌文章代码复现3/developer/article/1996043
单细胞数据复现-肺癌文章代码复现4/developer/article/2006654
教程3和4主要是分别对epi细胞亚群进行的分析，也是将亚群细分，然后去找里面比较重要的基因。今天的代码是对str亚群进行的分析。
ps：我发现放上图片后所占的版面过长，因此我就不放自己做出来的图了，是基本和原文一致的，基本按照我相关的代码是可以出来的，大家可以下载这篇文章的附图，进行比较，是不是自己需要调参数，因此我在后面有一个讲解的教程里面，单独进行拼图，与原文进行比较。
R环境的包及颜色配置加载
### load libraries
library(Seurat)
library(dplyr)
library(reticulate)
library(sctransform)
library(cowplot)
library(ggplot2)
library(viridis)
library(tidyr)
library(magrittr)
library(reshape2)
library(readxl)
library(readr)
library(stringr)
library(gplots)
library(grid)
library(rlang)
library(tibble)
theme_set(theme_cowplot())
#color scheme
use_colors <- c(
Tumor = "brown2",
Normal = "deepskyblue2",
G1 = "#46ACC8",
G2M = "#E58601",
S = "#B40F20",
Epithelial = "seagreen",
Immune = "darkgoldenrod2",
Stromal = "steelblue",
p018 = "#E2D200",
p019 = "#46ACC8",
p023 = "#E58601",
p024 = "#B40F20",
p027 = "#0B775E",
p028 = "#E1BD6D",
p029 = "#35274A",
p030 = "#F2300F",
p031 = "#7294D4",
p032 = "#5B1A18",
p033 = "#9C964A",
p034 = "#FD6467",
Endothelial1 = "#FED976",
Endothelial2 = "#FEB24C",
Endothelial3 = "#fd8d3C",
Endothelial4 = "#FC4E2A",
Endothelial5 = "#E31A1C",
Endothelial6 = "#BD0026",
Endothelial7 = "#800026",
Lymphaticendothelial = "salmon",
Fibroblast1 = "#2166AC",
Fibroblast2 = "#4393C3",
Myofibroblast1 = "#5AAE61",
Myofibroblast2 = "#1B7837",
Smoothmuscle1 = "#9970AB",
Smoothmuscle2 = "#762A83",
Mesothelial = "#40004B")亚群分析
读取在一开始做分群的时候保存的rdata数据。
str_anno <- readRDS("seurat_objects/str_anno.RDS")通过读取meta中的数据，然后选择自己需要的几种细胞的水平，来进行后面的分析。
str_anno@meta.data$cell_type_str <- factor(str_anno@meta.data$cell_type_str, levels = c("Endothelial1",
"Endothelial2",
"Endothelial3",
"Endothelial4",
"Endothelial5",
"Endothelial6",
"Endothelial7",
"Lymphaticendothelial",
"Fibroblast1",
"Fibroblast2",
"Myofibroblast1",
"Myofibroblast2",
"Smoothmuscle1",
"Smoothmuscle2",
"Mesothelial"))
##画图，主要是根据group的参数，这里选择的有组织、病人来源、细胞类型；还根据featuregene进行点图绘制，这个图也是单细胞组学文章中进行出镜的图
DimPlot(str_anno, group.by = "tissue_type", cols = use_colors)
#ggsave2("DimPlot_str_Normal_Tumor.pdf", path = "output/fig3", width = 15, height = 15, units = "cm")
DimPlot(str_anno, group.by = "patient_id", cols = use_colors, pt.size = 0.5)
ggsave2("SuppFig1C_str_patients.pdf", path = "../results", width = 15, height = 15, units = "cm")
DimPlot(str_anno, group.by = "cell_type_str", label = F, split.by = "tissue_type", cols = use_colors, pt.size = 0.5)
ggsave2("Fig3A_umap.pdf", path = "../results", width = 30, height = 15, units = "cm")
DotPlot(str_anno, features = c("WT1", "UPK3B", "MYH11", "PDGFRB", "ACTA2", "MYLK", "LUM", "PDGFRA", "CCL21", "PROX1", "PECAM1", "VWF"), group.by = "cell_type_str") +
theme(axis.text.x = element_text(angle = 90, hjust = 1)) +
coord_flip() +
scale_color_viridis()
ggsave2("Fig3B.pdf", path = "../results", width = 16, height = 12, units = "cm")###subsetting
##前面提到了在进行亚群在细分的时候，由于将自己需要的亚群进行了提取，所以需要在进行标准化，符合后面分析的要求。
str_endo <- subset(str_anno, subset = cell_type_str %in% c("Endothelial1",
"Endothelial2",
"Endothelial3",
"Endothelial4",
"Endothelial5",
"Endothelial6",
"Endothelial7",
"Lymphaticendothelial"))
str_endo <- ScaleData(str_endo)
str_fibro <- subset(str_anno, subset = cell_type_str %in% c("Fibroblast1",
"Fibroblast2",
"Myofibroblast1",
"Myofibroblast2",
"Smoothmuscle1",
"Smoothmuscle2",
"Mesothelial"))
str_fibro <- ScaleData(str_fibro)
endo_counts <- FetchData(str_endo, vars = c("tissue_type", "cell_type_str", "sample_id", "patient_id")) %>%
mutate(tissue_type = factor(tissue_type, levels = c("Tumor", "Normal")))
endo_counts_tbl <- endo_counts %>%
dplyr::count(cell_type_str, patient_id, tissue_type)
write_csv(endo_counts_tbl, path = "../results/SuppTable1.csv")
fibro_counts <- FetchData(str_fibro, vars = c("tissue_type", "cell_type_str", "sample_id", "patient_id")) %>%
mutate(tissue_type = factor(tissue_type, levels = c("Tumor", "Normal")))
fibro_counts_tbl <- fibro_counts %>%
dplyr::count(cell_type_str, patient_id, tissue_type)
write_csv(fibro_counts_tbl, path = "../results/SuppTable2.csv")
##作者很多的绘图的代码都很好看，自己在绘图的后期，可以自己粘贴过来，进行颜色和输入的修改就可以
ggplot(data = endo_counts, aes(x = tissue_type, fill = cell_type_str)) +
geom_bar(position = "fill") +
scale_fill_manual(values = use_colors) +
coord_flip() +
scale_y_reverse()
ggsave2("Fig3A_barplot_endothelial.pdf", path = "../results", width = 20, height = 5, units = "cm")
ggplot(data = fibro_counts, aes(x = tissue_type, fill = cell_type_str)) +
geom_bar(position = "fill") +
scale_fill_manual(values = use_colors) +
coord_flip() +
scale_y_reverse()
ggsave2("Fig3A_barplot_fibroblastic.pdf", path = "../results", width = 20, height = 5, units = "cm")
endo_counts %>%
filter(tissue_type == "Tumor") %>%
ggplot(aes(x = sample_id, fill = cell_type_str)) +
geom_bar(position = "fill") +
scale_fill_manual(values = use_colors) +
coord_flip() +
scale_y_reverse()
ggsave2("Fig3A_barplot_endothelial_per_patient.pdf", path = "../results", width = 30, height = 30, units = "cm")
fibro_counts %>%
filter(tissue_type == "Tumor") %>%
ggplot(aes(x = sample_id, fill = cell_type_str)) +
geom_bar(position = "fill") +
scale_fill_manual(values = use_colors) +
coord_flip() +
scale_y_reverse()
ggsave2("Fig3A_barplot_fibroblastic_per_patient.pdf", path = "../results", width = 30, height = 30, units = "cm")
endo_counts %>%
filter(tissue_type == "Normal") %>%
ggplot(aes(x = sample_id, fill = cell_type_str)) +
geom_bar(position = "fill") +
scale_fill_manual(values = use_colors) +
coord_flip() +
scale_y_reverse()
ggsave2("SuppFig6A_endothelial.pdf", path = "../results", width = 30, height = 30, units = "cm")
fibro_counts %>%
filter(tissue_type == "Normal") %>%
ggplot(aes(x = sample_id, fill = cell_type_str)) +
geom_bar(position = "fill") +
scale_fill_manual(values = use_colors) +
coord_flip() +
scale_y_reverse()
ggsave2("SuppFig6A_fibroblastic.pdf", path = "../results", width = 30, height = 30, units = "cm")热图绘制
在进行单细胞热图绘制的时候，seurat的heatmap只是可以看到亚群和基因号，不可以添加其他的参数，但是这个脚本可以添加其他很多的参数，如分组、样本来源等，文章作者也给出了参考来源-https://github.com/satijalab/seurat/issues/2201，主要的代码参考如下，自己在github的网站上查看源码根据自己的需求进行更改。
DoMultiBarHeatmap <- function (object,
features = NULL,
cells = NULL,
group.by = "ident",
additional.group.by = NULL,
additional.group.sort.by = NULL,
cols.use = NULL,
group.bar = TRUE,
disp.min = -2.5,
disp.max = NULL,
slot = "scale.data",
assay = NULL,
label = TRUE,
size = 5.5,
hjust = 0,
angle = 45,
raster = TRUE,
draw.lines = TRUE,
lines.width = NULL,
group.bar.height = 0.02,
combine = TRUE)
{
cells <- cells %||% colnames(x = object)
if (is.numeric(x = cells)) {
cells <- colnames(x = object)[cells]
}
assay <- assay %||% DefaultAssay(object = object)
DefaultAssay(object = object) <- assay
features <- features %||% VariableFeatures(object = object)
## Why reverse???
features <- rev(x = unique(x = features))
disp.max <- disp.max %||% ifelse(test = slot == "scale.data",
yes = 2.5, no = 6)
possible.features <- rownames(x = GetAssayData(object = object,
slot = slot))
if (any(!features %in% possible.features)) {
bad.features <- features[!features %in% possible.features]
features <- features[features %in% possible.features]
if (length(x = features) == 0) {
stop("No requested features found in the ", slot,
" slot for the ", assay, " assay.")
}
warning("The following features were omitted as they were not found in the ",
slot, " slot for the ", assay, " assay: ", paste(bad.features,
collapse = ", "))
}
if (!is.null(additional.group.sort.by)) {
if (any(!additional.group.sort.by %in% additional.group.by)) {
bad.sorts <- additional.group.sort.by[!additional.group.sort.by %in% additional.group.by]
additional.group.sort.by <- additional.group.sort.by[additional.group.sort.by %in% additional.group.by]
if (length(x = bad.sorts) > 0) {
warning("The following additional sorts were omitted as they were not a subset of additional.group.by : ",
paste(bad.sorts, collapse = ", "))
}
}
}
data <- as.data.frame(x = as.matrix(x = t(x = GetAssayData(object = object,
slot = slot)[features, cells, drop = FALSE])))
object <- suppressMessages(expr = StashIdent(object = object,
save.name = "ident"))
group.by <- group.by %||% "ident"
groups.use <- object[[c(group.by, additional.group.by[!additional.group.by %in% group.by])]][cells, , drop = FALSE]
plots <- list()
for (i in group.by) {
data.group <- data
if (!is_null(additional.group.by)) {
additional.group.use <- additional.group.by[additional.group.by!=i]
if (!is_null(additional.group.sort.by)){
additional.sort.use = additional.group.sort.by[additional.group.sort.by != i]
} else {
additional.sort.use = NULL
}
} else {
additional.group.use = NULL
additional.sort.use = NULL
}
group.use <- groups.use[, c(i, additional.group.use), drop = FALSE]
for(colname in colnames(group.use)){
if (!is.factor(x = group.use[[colname]])) {
group.use[[colname]] <- factor(x = group.use[[colname]])
}
}
if (draw.lines) {
lines.width <- lines.width %||% ceiling(x = nrow(x = data.group) *
0.0025)
placeholder.cells <- sapply(X = 1:(length(x = levels(x = group.use[[i]])) *
lines.width), FUN = function(x) {
return(Seurat:::RandomName(length = 20))
})
placeholder.groups <- data.frame(rep(x = levels(x = group.use[[i]]), times = lines.width))
group.levels <- list()
group.levels[[i]] = levels(x = group.use[[i]])
for (j in additional.group.use) {
group.levels[[j]] <- levels(x = group.use[[j]])
placeholder.groups[[j]] = NA
}
colnames(placeholder.groups) <- colnames(group.use)
rownames(placeholder.groups) <- placeholder.cells
group.use <- sapply(group.use, as.vector)
rownames(x = group.use) <- cells
group.use <- rbind(group.use, placeholder.groups)
for (j in names(group.levels)) {
group.use[[j]] <- factor(x = group.use[[j]], levels = group.levels[[j]])
}
na.data.group <- matrix(data = NA, nrow = length(x = placeholder.cells),
ncol = ncol(x = data.group), dimnames = list(placeholder.cells,
colnames(x = data.group)))
data.group <- rbind(data.group, na.data.group)
}
order_expr <- paste0('order(', paste(c(i, additional.sort.use), collapse=','), ')')
group.use = with(group.use, group.use[eval(parse(text=order_expr)), , drop=F])
plot <- Seurat:::SingleRasterMap(data = data.group, raster = raster,
disp.min = disp.min, disp.max = disp.max, feature.order = features,
cell.order = rownames(x = group.use), group.by = group.use[[i]])
if (group.bar) {
pbuild <- ggplot_build(plot = plot)
group.use2 <- group.use
cols <- list()
na.group <- Seurat:::RandomName(length = 20)
for (colname in rev(x = colnames(group.use2))) {
if (colname == i) {
colid = paste0('Identity (', colname, ')')
} else {
colid = colname
}
# Default
cols[[colname]] <- c(scales::hue_pal()(length(x = levels(x = group.use[[colname]]))))
#Overwrite if better value is provided
if (!is_null(cols.use[[colname]])) {
req_length = length(x = levels(group.use))
if (length(cols.use[[colname]]) < req_length){
warning("Cannot use provided colors for ", colname, " since there aren't enough colors.")
} else {
if (!is_null(names(cols.use[[colname]]))) {
if (all(levels(group.use[[colname]]) %in% names(cols.use[[colname]]))) {
cols[[colname]] <- as.vector(cols.use[[colname]][levels(group.use[[colname]])])
} else {
warning("Cannot use provided colors for ", colname, " since all levels (", paste(levels(group.use[[colname]]), collapse=","), ") are not represented.")
}
} else {
cols[[colname]] <- as.vector(cols.use[[colname]])[c(1:length(x = levels(x = group.use[[colname]])))]
}
}
}
# Add white if there's lines
if (draw.lines) {
levels(x = group.use2[[colname]]) <- c(levels(x = group.use2[[colname]]), na.group)
group.use2[placeholder.cells, colname] <- na.group
cols[[colname]] <- c(cols[[colname]], "#FFFFFF")
}
names(x = cols[[colname]]) <- levels(x = group.use2[[colname]])
y.range <- diff(x = pbuild$layout$panel_params[[1]]$y.range)
y.pos <- max(pbuild$layout$panel_params[[1]]$y.range) + y.range * 0.015
y.max <- y.pos + group.bar.height * y.range
pbuild$layout$panel_params[[1]]$y.range <- c(pbuild$layout$panel_params[[1]]$y.range[1], y.max)
plot <- suppressMessages(plot +
annotation_raster(raster = t(x = cols[[colname]][group.use2[[colname]]]), xmin = -Inf, xmax = Inf, ymin = y.pos, ymax = y.max) +
annotation_custom(grob = grid::textGrob(label = colid, hjust = 0, gp = gpar(cex = 0.75)), ymin = mean(c(y.pos, y.max)), ymax = mean(c(y.pos, y.max)), xmin = Inf, xmax = Inf) +
coord_cartesian(ylim = c(0, y.max), clip = "off"))
if ((colname == i) && label) {
x.max <- max(pbuild$layout$panel_params[[1]]$x.range)
x.divs <- pbuild$layout$panel_params[[1]]$x.major %||% pbuild$layout$panel_params[[1]]$x$break_positions()
group.use$x <- x.divs
label.x.pos <- tapply(X = group.use$x, INDEX = group.use[[colname]],
FUN = median) * x.max
label.x.pos <- data.frame(group = names(x = label.x.pos),
label.x.pos)
plot <- plot + geom_text(stat = "identity",
data = label.x.pos, aes_string(label = "group",
x = "label.x.pos"), y = y.max + y.max *
0.03 * 0.5, angle = angle, hjust = hjust,
size = size)
plot <- suppressMessages(plot + coord_cartesian(ylim = c(0,
y.max + y.max * 0.002 * max(nchar(x = levels(x = group.use[[colname]]))) *
size), clip = "off"))
}
}
}
plot <- plot + theme(line = element_blank())
plots[[i]] <- plot
}
if (combine) {
plots <- CombinePlots(plots = plots)
}
return(plots)
}根据上面的热图的源码进行分组的热图高表达基因的绘制。基本的代码跟前面的epi的代码是类似的。
###DEGs endothelial
Idents(str_endo) <- str_endo@meta.data$cell_type_str
endo_markers <- FindAllMarkers(str_endo, only.pos = T, min.pct = 0.25, min.diff.pct = 0.25)
top_endo_markers <- endo_markers %>% group_by(cluster) %>% top_n(10, wt = avg_log2FC)
DoMultiBarHeatmap(str_endo, features = top_endo_markers$gene, group.by = "cell_type_str", additional.group.by = "tissue_type",additional.group.sort.by = "tissue_type", cols.use = list(tissue_type = use_colors), draw.lines = F) +
scale_fill_viridis()
ggsave2("SuppFig6B.png", path = "../results", width = 30, height = 40, units = "cm")
#ggsave2("HeatMap_Endo.pdf", path = "output/fig3", width = 30, height = 40, units = "cm")
#ggsave2("HeatMap_Endo.emf", path = "output/fig3", width = 30, height = 40, units = "cm")这里是对另一种细胞类型进行的差异分析，如果想要求严格一些，可以放p_value值进行筛选。
###DEGs fibroblastic
Idents(str_fibro) <- str_fibro@meta.data$cell_type_str
fibro_markers <- FindAllMarkers(str_fibro, only.pos = T, min.pct = 0.25, min.diff.pct = 0.25)
top_fibro_markers <- fibro_markers %>% group_by(cluster) %>% top_n(10, wt = avg_log2FC)
DoMultiBarHeatmap(str_fibro, features = top_fibro_markers$gene, group.by = "cell_type_str", additional.group.by = "tissue_type",additional.group.sort.by = "tissue_type", cols.use = list(tissue_type = use_colors), draw.lines = F) +
scale_fill_viridis()
ggsave2("Fig6C.png", path = "../results", width = 30, height = 40, units = "cm")
#ggsave2("HeatMap_Fibro.pdf", path = "output/fig3", width = 30, height = 40, units = "cm")
#ggsave2("HeatMap_Fibro.emf", path = "output/fig3", width = 30, height = 40, units = "cm")主要将3个不同的细胞类型进行细分，是主要想看在不同微环境下，肿瘤基因的相关通路，所以可以发现在3个亚群最后一步分析当中都带入了progeny scores参数，具体做肿瘤的友友可以参考这篇文章-https://www.jianshu.com/p/4058050d546e，由于我是做植物的，来源也不一样，所以不进行讲解了。
###progeny scores
str_fibro2 <- subset(str_anno, subset = cell_type_str %in% c("Fibroblast1",
"Fibroblast2",
"Myofibroblast1",
"Myofibroblast2",
"Smoothmuscle1",
"Smoothmuscle2"))
progeny_scores <- as.data.frame(t(GetAssayData(str_fibro2, assay = "progeny", slot = "scale.data")))
progeny_scores$cell_id <- rownames(progeny_scores)
progeny_scores <- gather(progeny_scores, Pathway, Activity, -cell_id)
cells_clusters <- FetchData(str_anno, c("cell_type_str"))
cells_clusters$cell_id <- rownames(cells_clusters)
progeny_scores <- inner_join(progeny_scores, cells_clusters)
summarized_progeny_scores <- progeny_scores %>%
group_by(Pathway, cell_type_str) %>%
summarise(avg = mean(Activity), std = sd(Activity), .groups = 'drop') %>%
pivot_wider(id_cols = Pathway, names_from = cell_type_str, values_from = avg) %>%
column_to_rownames("Pathway") %>%
as.matrix()
heatmap.2(summarized_progeny_scores, trace = "none", density.info = "none", col = bluered(100), margins = c(10,10))
ggsave("Fig3D.pdf", width = 7, height = 10)总结
可以发现这篇与上两篇的对epi分析的思路很像，都是对亚群进行细分以及细胞通路的查看，去看一些基因的表达情况，将里面的基因根据不同表达水平进行划分。这个时候发现单细胞的分析在前面还是很像的，但是根据自己研究的样本以及生物学问题的来源不一样，后面是需要进行不同的包的调取，还有个性化分析的，所以无论是做植物还是动物的，多读一些最新的单细胞组学的文章都是能学到很多的内容的，不断的将自己的文章提高一个新的思路。
原创声明：本文系作者授权腾讯云开发者社区发表，未经许可，不得转载。
如有侵权，请联系 cloudcommunity@tencent.com 删除。
原创声明：本文系作者授权腾讯云开发者社区发表，未经许可，不得转载。
如有侵权，请联系 cloudcommunity@tencent.com 删除。
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