###### tags: `ノート` `TS` `解析` `single-cell RNA-seq` # 22-07： ES由来セルトリ細胞scRNAseq解析　FTSLC_scRNAseq 第２弾 (aggrしない) その他 補足 <br> #### 2026/6/9 #### 【 作業場所＆保存場所 】 • 作業場所 　~/osc-fs/22_TS_FTSLC_scRNAseq_2022/Seurat_Non_aggr --- #### ※ aggrしないでSeuratした方 【参考】 scRNA-seqデータの解析(応用編) https://hackmd.io/@takahirosuzuki/ByoEBNVPL --- p１　全細胞UMAPと各FeaturePlot ```r= library(Seurat) library(dplyr) library(patchwork) library(MAST) library(ggsci) library("ComplexHeatmap") library("circlize") library("RColorBrewer") library(scales) library(tidyverse) load("05_20220516_cl02.RData") #220609_all_UMAP.pdf (7.5x10) DimPlot(object = data.integrated , reduction = "umap" , label = TRUE)+ scale_color_ucscgb() # 20220609_all_FeaturePlot_Pou5f1 (8x10) FeaturePlot(object=data.integrated, features= "Pou5f1", col=c("gray", "red"), min.cutoff=0.1, pt.size=1) # 20220609_all_FeaturePlot_Ddx4 FeaturePlot(object=data.integrated, features= "Ddx4", col=c("gray", "red"), min.cutoff=0.1, pt.size=1) # 20220609_all_FeaturePlot_Pecam1 FeaturePlot(object=data.integrated, features= "Pecam1", col=c("gray", "red"), min.cutoff=0.1, pt.size=1) # 20220609_all_FeaturePlot_Flt1 FeaturePlot(object=data.integrated, features= "Flt1", col=c("gray", "red"), min.cutoff=0.1, pt.size=1) # 20220609_all_FeaturePlot_Hbb-y FeaturePlot(object=data.integrated, features= "Hbb-y", col=c("gray", "red"), min.cutoff=0.1, pt.size=1) # 20220609_all_FeaturePlot_Hba-a1 FeaturePlot(object=data.integrated, features= "Hba-a1", col=c("gray", "red"), min.cutoff=0.1, pt.size=1) # 20220609_all_FeaturePlot_Ppbp FeaturePlot(object=data.integrated, features= "Ppbp", col=c("gray", "red"), min.cutoff=0.1, pt.size=1) # 20220609_all_FeaturePlot_Plek FeaturePlot(object=data.integrated, features= "Plek", col=c("gray", "red"), min.cutoff=0.1, pt.size=1) ``` <br> p3 gscの色を揃えたUMAP ```r= load("09_gsc_res03_20220516.RData") #20220609_gsc_UMAP.pdf (7.5x10) DimPlot(object = data.integrated.gsc, reduction = "umap" , label = TRUE) + scale_color_aaas() ``` <br> p4 各クラスターの割合barplot ```r= load("11_data.integrated.gsc16_02.RData") #確認 DimPlot(object = data.integrated.gsc16_02, reduction = "umap" , label = TRUE) #XX_conposition #割合の計算 prop_cluster <- prop.table(x=table(data.integrated.gsc16_02@active.ident, data.integrated.gsc16_02@meta.data$sample), margin =2) #XX_plot用にデータフレームに変換 Cluster_name=factor(rownames(prop_cluster), levels=rownames(prop_cluster)) df <- data.frame(Cluster=Cluster_name,XX_10.5=prop_cluster[,1], XX_11.5=prop_cluster[,2], XX_12.5=prop_cluster[,3], XX_FOSLCs=prop_cluster[,4]) df2 <- tidyr::gather(df, key=Sample, value=Proportion, -Cluster, factor_key = TRUE) #ggplotでvidualization theme <- theme(panel.background = element_blank(), panel.border = element_blank(), panel.grid.major = element_blank(), panel.grid.minor = element_blank(), strip.background = element_blank(), plot.title = element_text(size = 10,hjust = 0.5), axis.text.x = element_text(size=10, angle=90), axis.text.y = element_text(size=10), axis.title.x = element_blank(), axis.title.y = element_text(size=10), axis.ticks = element_line(size=0.5), axis.line = element_line(size=0.5), plot.margin = unit(c(1,1,1,1),"line") ) g <- ggplot(df2, aes(x= Sample, y = Proportion, fill=Cluster)) g <- g + geom_bar(stat = "identity") g <- g + scale_y_continuous(labels = percent) # display as % g <- g + theme #20220609_XX_conposition_barplot (7x10) g #割合の計算 prop_cluster <- prop.table(x=table(data.integrated.gsc16_02@active.ident, data.integrated.gsc16_02@meta.data$sample), margin =2) #XY_plot用にデータフレームに変換 Cluster_name=factor(rownames(prop_cluster), levels=rownames(prop_cluster)) df <- data.frame(Cluster=Cluster_name,XY_10.5=prop_cluster[,5], XY_11.5=prop_cluster[,6], XY_12.5=prop_cluster[,7], XY_FTSLCs=prop_cluster[,8]) df2 <- tidyr::gather(df, key=Sample, value=Proportion, -Cluster, factor_key = TRUE) #ggplotでvidualization theme <- theme(panel.background = element_blank(), panel.border = element_blank(), panel.grid.major = element_blank(), panel.grid.minor = element_blank(), strip.background = element_blank(), plot.title = element_text(size = 10,hjust = 0.5), axis.text.x = element_text(size=10, angle=90), axis.text.y = element_text(size=10), axis.title.x = element_blank(), axis.title.y = element_text(size=10), axis.ticks = element_line(size=0.5), axis.line = element_line(size=0.5), plot.margin = unit(c(1,1,1,1),"line") ) g <- ggplot(df2, aes(x= Sample, y = Proportion, fill=Cluster)) g <- g + geom_bar(stat = "identity") g <- g + scale_y_continuous(labels = percent) g <- g + theme #20220609_XY_conposition_barplot g ``` <br> p7 sampleごとに分けないPax8 ```r= # 20220609_gsc16_FeaturePlot_Pax8 FeaturePlot(object=data.integrated.gsc16_02, features= "Pax8", col=c("gray", "red"), min.cutoff=0.1, pt.size=1) ```