#I couldn't install Monocle3.
#JupyterHub also doesn't have Monocle3
library(Seurat)
library(dplyr)
library(monocle)
sessionInfo()
load("190414MouseLimb10X.Robj")
updated_MouseLimb10X = UpdateSeuratObject(object = MouseLimb10X)
str(updated_MouseLimb10X)
DeepGenes <- read.table("190220DeepTree4000genes.txt",sep="_")
DeepGenes2=as.vector(unlist(DeepGenes[,2]))
updated_MouseLimb10X<-BuildClusterTree(updated_MouseLimb10X, reorder=FALSE, reorder.numeric = TRUE,dims = 1:42)
Tool(object = updated_MouseLimb10X, slot = 'BuildClusterTree')
PlotClusterTree(updated_MouseLimb10X)
updated_MouseLimb10X<-BuildClusterTree(updated_MouseLimb10X, reorder=FALSE, reorder.numeric = TRUE,
features = DeepGenes2)
Tool(object = updated_MouseLimb10X, slot = 'BuildClusterTree')
PlotClusterTree(updated_MouseLimb10X)
sed -i -e $'s/,/\t/g' genes.tsv
MouseLimbC1.data <- Read10X(data.dir="C1FPKM/")
MouseLimbC1 <- CreateSeuratObject(counts = MouseLimbC1.data, min.cells = 1, min.features = 0, project = "MouseLimbC1")
MouseLimbC1[["percent.mt"]] <- PercentageFeatureSet(object = MouseLimbC1, pattern = "^mt-")
#These were done on MATLAB:
#CellType=readtable('180408Disp1000PCells.txt','ReadVariableNames',false);
#CellType.Properties.RowNames=ValidizeNames(CellType{:,1});
#CellType2=CellType(get(CFPKMcorfildm,'ColNames'),3);
#writetable(CellType2,'190422Cells.txt','WriteRowNames',true);
#mappedX=importdata('180322Disp1000MappedXDim30.mat');
#writetable(array2table(mappedX),'190422C1TSNEcoordinates.txt');
#These were done on Sanger Mac:
#mib113001i:Downloads ph12$ scp 190422C* ETA:/mnt/190308Hongbohindlimb/mouse/C1FPKM/
C1_MATLAB_type <- read.table("C1FPKM/190422Cells.txt",sep=",",header = TRUE)
MouseLimbC1 <- AddMetaData(object = MouseLimbC1, metadata = C1_MATLAB_type$Var3,col.name = "MATLABtype")
Idents(MouseLimbC1, cells = NULL, drop = FALSE) <- 0
VlnPlot(object = MouseLimbC1, features = c("nFeature_RNA", "nCount_RNA", "percent.mt"), ncol = 3)
plot1 <- FeatureScatter(object = MouseLimbC1, feature1 = "nCount_RNA", feature2 = "percent.mt")
plot2 <- FeatureScatter(object = MouseLimbC1, feature1 = "nCount_RNA", feature2 = "nFeature_RNA")
CombinePlots(plots = list(plot1, plot2))
MouseLimbC1 <- NormalizeData(object = MouseLimbC1, normalization.method = "LogNormalize", scale.factor = 1000000)
In order to create the tsne slot, I'm running these codes:
MouseLimbC1 <- FindVariableFeatures(object = MouseLimbC1, selection.method = "vst", nfeatures = 1000)
MouseLimbC1 <- ScaleData(object = MouseLimbC1, features=MouseLimbC1@assays$RNA@var.features)
MouseLimbC1 <- RunPCA(object = MouseLimbC1, features = VariableFeatures(object = MouseLimbC1))
MouseLimbC1 <- RunTSNE(MouseLimbC1, reduction = "pca", cells = NULL,
dims = 1:5, features = NULL, seed.use = 1, tsne.method = "Rtsne",
add.iter = 0, dim.embed = 2, distance.matrix = NULL,
reduction.name = "tsne", reduction.key = "tSNE_")
C1_MATLAB_tsne <- read.table("C1FPKM/190422C1TSNEcoordinates.txt",sep=",",header = TRUE)
MouseLimbC1@reductions$tsne@cell.embeddings[,'tSNE_1']<-C1_MATLAB_tsne[,'mappedX1']
MouseLimbC1@reductions$tsne@cell.embeddings[,'tSNE_2']<-C1_MATLAB_tsne[,'mappedX2']
DimPlot(object = MouseLimbC1, reduction = "tsne",group.by = 'MATLABtype')+scale_color_manual(values=c('black',
'blue','cyan','darkred','green','gray','magenta','orange','purple','red','yellow','yellowgreen'))
DimPlot(object = MouseLimbC1, reduction = "tsne",group.by = 'MATLABtype')+scale_color_manual(values=c('#000000',
'#0118FA','#00FFFF','#ff0000','#00FF00','#000000','#9834E7','#FBC83C','#C39CFB','#FF8380','#FFFA2C',
'#8B8A1D'))
ggsave('C1tsne.eps', plot = last_plot(), device = "eps", path = "./Figures",
scale = 1, width = NA, height = NA, dpi = 300)
limb.anchors <- FindTransferAnchors(reference = updated_MouseLimb10X, query = MouseLimbC1, dims = 1:42, npcs=NULL)
predictions <- TransferData(anchorset = limb.anchors, refdata = updated_MouseLimb10X@active.ident, dims = 1:42)
MouseLimbC1 <- AddMetaData(object = MouseLimbC1, metadata = predictions)
DimPlot(object = MouseLimbC1, reduction = "tsne",group.by = 'predicted.id',
order=c(24:0))+scale_color_manual(values=c("black",
"blue","gray","cyan","#FF8380","yellowgreen","khaki3", "#FFFA2C","#C39CFB", "slategray",
"#871F4E", "#9834E7", "red","darkgreen", "#FBC83C",
"#016edb"))
DimPlot(object = updated_MouseLimb10X,reduction = "tsne",order=c(24:0),
label = TRUE,pt.size=0.1)+scale_color_manual(values=c("#000000", "#0118FA","#C0C0C0","#00FFFF",
"#FF8380","#8B8A1D","#CAC379","#00FF00","#FFFA2C","#C39CFB","#7762F0","#717E8D","#A71206","#35B5E2","#9834E7",
"#995432","#483F84","#ff0000","#216407","#ff42ef","#FBC83C","#FF9A21","#B4246E","#09658A","#016edb"))
ggsave('10Xtsne.eps', plot = last_plot(), device = "eps", path = "./Figures",
scale = 1, width = NA, height = NA, dpi = 300)
save(MouseLimbC1,file="190423MouseLimbC1.Robj")
write.csv(MouseLimbC1@meta.data['MATLABtype'],'C1FPKM/190425Cells.txt')
devtools::dev_mode(path='~/tools/Seurat2/')
library(Seurat)
MouseLimbC1.data <- Read10X(data.dir="C1FPKM/")
MouseLimbC1 <- CreateSeuratObject(raw.data = MouseLimbC1.data, min.cells = 0, min.genes = 0, project = "MouseLimbC1")
mito.genes <- grep(pattern = "^mt-", x = rownames(x = MouseLimbC1@data), value = TRUE)
percent.mito <- Matrix::colSums(MouseLimbC1@raw.data[mito.genes, ])/Matrix::colSums(MouseLimbC1@raw.data)
MouseLimbC1 <- AddMetaData(object = MouseLimbC1, metadata = percent.mito, col.name = "percent.mito")
MouseLimbC1 <- NormalizeData(object = MouseLimbC1, normalization.method = "LogNormalize", scale.factor = 1000000)
MouseLimbC1 <- FindVariableGenes(object = MouseLimbC1, mean.function = ExpMean, dispersion.function = LogVMR,x.low.cutoff = 0.0125, x.high.cutoff = 3, y.cutoff = 0.5)
C1_MATLAB_type <- read.table("C1FPKM/190425Cells.txt",sep=",",header = TRUE)
MouseLimbC1 <- AddMetaData(object = MouseLimbC1, metadata = C1_MATLAB_type,col.name = "MATLABtype")
C1_MATLAB_tsne <- read.table("C1FPKM/190422C1TSNEcoordinates.txt",sep=",",header = TRUE)
MouseLimbC1 <- ScaleData(object = MouseLimbC1, genes.use=MouseLimbC1@var.genes, vars.to.regress = c("nUMI", "percent.mito"))
MouseLimbC1 <- RunPCA(object = MouseLimbC1, pc.genes = MouseLimbC1@var.genes, pcs.compute=100, do.print = TRUE, pcs.print = 1:5,genes.print = 5)
MouseLimbC1 <- RunTSNE(object = MouseLimbC1, dims.use = 1:5,do.fast = TRUE)
MouseLimbC1@dr$tsne@cell.embeddings[,'tSNE_1']<-C1_MATLAB_tsne[,'mappedX1']
MouseLimbC1@dr$tsne@cell.embeddings[,'tSNE_2']<-C1_MATLAB_tsne[,'mappedX2']
Convert(from = MouseLimbC1, to = "anndata", X.slot = "data", raw.slot = "@raw.data", filename = "190423MouseLimbC1.h5ad")
StageInfo <- read.table("C1FPKM/190430CTime.csv",sep="_")
rownames(StageInfo) <- rownames(MouseLimbC1@meta.data)
colnames(StageInfo) <- 'stage'
MouseLimbC1 <- AddMetaData(object = MouseLimbC1, metadata = StageInfo, col.name = 'stage')
save(MouseLimbC1,file="190423MouseLimbC1Seurat2.Robj")
updated_MouseLimb10X <- AddMetaData(object = updated_MouseLimb10X, metadata = updated_MouseLimb10X@active.ident,col.name = "ident")
write.csv(updated_MouseLimb10X@meta.data[c('nGene','ident')],'190425MouseLimb10XMeta.csv')
help(FindIntegrationAnchors)
Limb.list=list(MouseLimbC1,updated_MouseLimb10X)
names(Limb.list) <- c("C1","10X")
reference.list <- Limb.list[c("C1","10X")]
reference.list
Limb.anchors <- FindIntegrationAnchors(object.list = reference.list,
dims = 1:50, anchor.features = DeepGenes2)
Limb.integrated <- IntegrateData(anchorset = Limb.anchors, dims = 1:50)
library(ggplot2)
library(cowplot)
DefaultAssay(Limb.integrated) <- "integrated"
Limb.integrated <- ScaleData(Limb.integrated, verbose = FALSE)
Limb.integrated <- RunPCA(Limb.integrated, npcs = 50, verbose = FALSE)
Limb.integrated <- RunUMAP(Limb.integrated, reduction = "pca", dims = 1:50)
Limb.integrated <- RunTSNE(Limb.integrated, reduction = "pca", dims = 1:50)
table(!is.na(Limb.integrated@meta.data$stage))
Limb.integrated@active.ident[1:5]
C1index<-is.na(Limb.integrated@meta.data$stage)
CellIdentities<-MouseLimbC1@meta.data['MATLABtype']
CellIdentities[CellIdentities=="grey"] <- "black"
CellIdentities <- factor(as.integer(CellIdentities$MATLABtype)+24)
attributes(CellIdentities)$names<-attributes(Limb.integrated@active.ident[C1index])$names
CellIdentities[1:5]
active.ident=as.character(Limb.integrated@active.ident)
active.ident[C1index]<-as.character(CellIdentities)
table(active.ident)
table(CellIdentities,MouseLimbC1@meta.data$MATLABtype)
active.ident<-factor(active.ident)
attributes(active.ident)$names<-attributes(Limb.integrated@active.ident)$names
Limb.integrated@active.ident <- active.ident
batch<-as.character(Limb.integrated@meta.data$batch)
batch[C1index]='C1'
batch[!C1index]='10X'
Limb.integrated@meta.data$batch<-batch
DimPlot(Limb.integrated, reduction = "umap", group.by = "batch")
DimPlot(Limb.integrated, reduction = "umap",cells.highlight=Cells(MouseLimbC1))
ggsave('joint_C1_10X_UMAP.eps', plot = last_plot(), device = "eps", path = "./Figures",
scale = 1, width = NA, height = NA, dpi = 300)
p1<-DimPlot(Limb.integrated, reduction = "umap",cells=Cells(MouseLimbC1))+scale_color_manual(values=c('#000000',
'#0118FA','#00FFFF','#ff0000','#00FF00','#9834E7','#FBC83C','#C39CFB','#FF8380','#FFFA2C','#8B8A1D'))+
NoLegend() + NoAxes()
DimPlot(Limb.integrated, reduction = "umap",cells=Cells(MouseLimbC1))+scale_color_manual(values=c('#000000',
'#0118FA','#00FFFF','#ff0000','#00FF00','#9834E7','#FBC83C','#C39CFB','#FF8380','#FFFA2C','#8B8A1D'))
ggsave('joint_C1_UMAP.eps', plot = last_plot(), device = "eps", path = "./Figures",
scale = 1, width = NA, height = NA, dpi = 300)
FeaturePlot(object = Limb.integrated, features = c("Pax3","Pax7","Myog","Myot"),
reduction = "umap",pt.size=0.2,cells = Cells(MouseLimbC1))
FeaturePlot(object = Limb.integrated, features = c("Pax3","Pax7","Myog","Myot"),
reduction = "umap",pt.size=0.2)
FeaturePlot(object = Limb.integrated, features = c("Ebf2","Twist2","Osr1","Col1a1"),
reduction = "umap",pt.size=0.2)
p2<-DimPlot(Limb.integrated, reduction = "umap",cells=Cells(updated_MouseLimb10X))+scale_color_manual(values=c(
"#000000","#0118FA","#7762F0","#717E8D","#A71206","#35B5E2","#9834E7","#995432","#483F84","#ff0000",
"#216407","#ff42ef","#C0C0C0","#FBC83C","#FF9A21","#B4246E","#09658A","#016edb","#00FFFF","#FF8380",
"#8B8A1D","#CAC379","#00FF00","#FFFA2C","#C39CFB"))+
NoLegend() + NoAxes()
DimPlot(Limb.integrated, reduction = "umap",cells=Cells(updated_MouseLimb10X))+scale_color_manual(values=c(
"#000000","#0118FA","#7762F0","#717E8D","#A71206","#35B5E2","#9834E7","#995432","#483F84","#ff0000",
"#216407","#ff42ef","#C0C0C0","#FBC83C","#FF9A21","#B4246E","#09658A","#016edb","#00FFFF","#FF8380",
"#8B8A1D","#CAC379","#00FF00","#FFFA2C","#C39CFB"))
ggsave('joint_10X_UMAP.eps', plot = last_plot(), device = "eps", path = "./Figures",
scale = 1, width = NA, height = NA, dpi = 300)
plot_grid(p1, p2)
DimPlot(Limb.integrated, reduction = "tsne", group.by = "batch")
DimPlot(Limb.integrated, reduction = "tsne",cells.highlight=Cells(MouseLimbC1))
p1 <- DimPlot(Limb.integrated, reduction = "tsne",cells=Cells(MouseLimbC1))+scale_color_manual(values=c('#000000',
'#0118FA','#00FFFF','#ff0000','#00FF00','#9834E7','#FBC83C','#C39CFB','#FF8380','#FFFA2C','#8B8A1D'))+
NoLegend() + NoAxes()
DimPlot(Limb.integrated, reduction = "tsne",cells=Cells(MouseLimbC1))+scale_color_manual(values=c('#000000',
'#0118FA','#00FFFF','#ff0000','#00FF00','#9834E7','#FBC83C','#C39CFB','#FF8380','#FFFA2C','#8B8A1D'))
p2<-DimPlot(Limb.integrated, reduction = "tsne",cells=Cells(updated_MouseLimb10X))+scale_color_manual(values=c(
"#000000","#0118FA","#7762F0","#717E8D","#A71206","#35B5E2","#9834E7","#995432","#483F84","#ff0000",
"#216407","#ff42ef","#C0C0C0","#FBC83C","#FF9A21","#B4246E","#09658A","#016edb","#00FFFF","#FF8380",
"#8B8A1D","#CAC379","#00FF00","#FFFA2C","#C39CFB"))+
NoLegend() + NoAxes()
DimPlot(Limb.integrated, reduction = "tsne",cells=Cells(updated_MouseLimb10X))+scale_color_manual(values=c(
"#000000","#0118FA","#7762F0","#717E8D","#A71206","#35B5E2","#9834E7","#995432","#483F84","#ff0000",
"#216407","#ff42ef","#C0C0C0","#FBC83C","#FF9A21","#B4246E","#09658A","#016edb","#00FFFF","#FF8380",
"#8B8A1D","#CAC379","#00FF00","#FFFA2C","#C39CFB"))
plot_grid(p1, p2)
MarkerGenes <- read.table("markergenes.txt",sep=",")
MarkerGenes2=unique(as.vector(unlist(MarkerGenes[,1])))
MouseLimbC1@active.ident=MouseLimbC1@meta.data$MATLABtype
DoHeatmap(MouseLimbC1, features = MarkerGenes2) + NoLegend()
DoHeatmap(updated_MouseLimb10X, features = MarkerGenes2) + NoLegend()
# It didn't work?
table(updated_MouseLimb10X@active.ident,updated_MouseLimb10X@meta.data$stage)
save(Limb.integrated,'190414LimbIntegratedSeurat')
updated_MouseLimb10X
ConfusedCells0 <- read.table("190519Monocle3ConfusedCells.csv",sep="_",header = TRUE)
ConfusedCells=as.vector(unlist(ConfusedCells0[,1]))
length(ConfusedCells)
# devtools::dev_mode(path='~/tools/Seurat3.0.1/')
# Installing new Seurat 3.0.1 didn't work
Muscle2<-WhichCells(updated_MouseLimb10X,idents = 4)
Muscle3<-WhichCells(updated_MouseLimb10X,idents = 17)
Col1a1_Muscle4<-WhichCells(updated_MouseLimb10X,idents = 22)
Muscle4<-WhichCells(updated_MouseLimb10X,idents = 12)
Perichondrial<-WhichCells(updated_MouseLimb10X,idents = 1)
Col1a1_Muscle4.vs.Muscle4<-FindMarkers(updated_MouseLimb10X,
ident.1 = 22, ident.2 = 12, min.pct = 0.25)
Col1a1_Muscle4.vs.Peri<-FindMarkers(updated_MouseLimb10X,
ident.1 = 22, ident.2 = 1, min.pct = 0.25)
updated_MouseLimb10X <- SetIdent(object = updated_MouseLimb10X,
cells = intersect(ConfusedCells,Muscle2), value = '4B')
updated_MouseLimb10X <- SetIdent(object = updated_MouseLimb10X,
cells = intersect(ConfusedCells,Muscle3), value = '17B')
updated_MouseLimb10X <- SetIdent(object = updated_MouseLimb10X,
cells = intersect(ConfusedCells,Muscle4), value = '12B')
Confused2.vs.2<-FindMarkers(updated_MouseLimb10X,
ident.1 = '4B', ident.2 = 4, min.pct = 0.25)
Confused3.vs.3<-FindMarkers(updated_MouseLimb10X,
ident.1 = '17B', ident.2 = 17, min.pct = 0.25)
Confused4.vs.4<-FindMarkers(updated_MouseLimb10X,
ident.1 = '12B', ident.2 = 12, min.pct = 0.25)
write.table(Col1a1_Muscle4.vs.Muscle4,file="190519Col1a1_Muscle4.vs.Muscle4.markers")
write.table(Col1a1_Muscle4.vs.Peri,file="190519Col1a1_Muscle4.vs.Peri.markers")
write.table(Confused2.vs.2,file="190519Confused2.vs.2.markers")
write.table(Confused3.vs.3,file="190519Confused3.vs.3.markers")
write.table(Confused4.vs.4,file="190519Confused4.vs.4.markers")
#ubuntu@190403eta:/mnt/190308Hongbohindlimb/mouse$
#for file in 190519*markers;
#do awk '{if($3>0){print $0}}' $file | sort -k2,2g -k3,3gr - > $file.+.txt;
#awk '{if($3<0){print $0}}' $file | sort -k2,2g -k3,3g - > $file.-.txt; done
Col1a1_Muscle4.vs.Muscle4.0.4<-FindMarkers(updated_MouseLimb10X,
ident.1 = 22, ident.2 = c('12','12B'), min.pct = 0.25,min.diff.pct = 0.4)
Col1a1_Muscle4.vs.Peri.0.4<-FindMarkers(updated_MouseLimb10X,
ident.1 = 22, ident.2 = 1, min.pct = 0.25,min.diff.pct = 0.4)
Confused2.vs.2.0.4<-FindMarkers(updated_MouseLimb10X,
ident.1 = '4B', ident.2 = 4, min.pct = 0.25, min.diff.pct = 0.4)
Confused3.vs.3.0.4<-FindMarkers(updated_MouseLimb10X,
ident.1 = '17B', ident.2 = 17, min.pct = 0.25, min.diff.pct = 0.4)
Confused4.vs.4.0.4<-FindMarkers(updated_MouseLimb10X,
ident.1 = '12B', ident.2 = 12, min.pct = 0.25, min.diff.pct = 0.4)
write.table(Col1a1_Muscle4.vs.Muscle4.0.4,file="190519Col1a1_Muscle4.vs.Muscle4.markers0.4")
write.table(Col1a1_Muscle4.vs.Peri.0.4,file="190519Col1a1_Muscle4.vs.Peri.markers0.4")
write.table(Confused2.vs.2.0.4,file="190519Confused2.vs.2.markers0.4")
write.table(Confused3.vs.3.0.4,file="190519Confused3.vs.3.markers0.4")
write.table(Confused4.vs.4.0.4,file="190519Confused4.vs.4.markers0.4")
#ubuntu@190403eta:/mnt/190308Hongbohindlimb/mouse$
#for file in 190519*markers0.4;
#do awk '{if($3>0){print $0}}' $file | sort -k2,2g -k3,3gr - > $file.+.txt;
#awk '{if($3<0){print $0}}' $file | sort -k2,2g -k3,3g - > $file.-.txt; done
save()
cell_type_color <- c('0'='#000000',
'1'='#0118FA',
'2'='#C0C0C0',
'3'='#00FFFF',
'4'='#FF8380',
'5'='#8B8A1D',
'6'='#CAC379',
'7'='#00FF00',
'8'='#FFFA2C',
'9'='#C39CFB',
'10'='#7762F0',
'11'='#717E8D',
'12'='#A71206',
'13'='#35B5E2',
'14'='#9834E7',
'15'='#995432',
'16'='#483F84',
'17'='#ff0000',
'18'='#216407',
'19'='#ff42ef',
'20'='#FBC83C',
'21'='#FF9A21',
'22'='#B4246E',
'23'='#09658A',
'24'='#016edb')
VlnPlot(updated_MouseLimb10X,features = c("Pax3","Myod1","Pax7","Myog"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(updated_MouseLimb10X,features = c("Pax3","Myod1","Pax7","Myog"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),slot="counts",
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Pax3","Myod1","Pax7","Myog"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Car14","Ccne1","Cdkn1a","Chchd4"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Car14","Ccne1","Cdkn1a","Chchd4"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Chd7","Eya1","Eya2","Fam195a"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Chd7","Eya1","Eya2","Fam195a"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Itga4","Lbx1","Macrod2","Met"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Itga4","Lbx1","Macrod2","Met"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Mn1","Myf5","Pax3","Pcdh17"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Mn1","Myf5","Pax3","Pcdh17"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Pcdh19","Pdgfc","Pitx2","Sim2"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Pcdh19","Pdgfc","Pitx2","Sim2"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Six1","Snhg4","Sp5","Tcf15 "),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Six1","Snhg4","Sp5","Tcf15 "),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Sept11","2610318N02Rik","2810408I11Rik","2810417H13Rik"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Sept11","2610318N02Rik","2810408I11Rik","2810417H13Rik"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Aars","Adh5","Ahsa1","Ak2"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Aars","Adh5","Ahsa1","Ak2"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Akirin2","Akr1b3","Alyref","Anp32e"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Akirin2","Akr1b3","Alyref","Anp32e"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Apex1","Asb4","Atp2b1","Birc5"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Apex1","Asb4","Atp2b1","Birc5"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Bola3","Bzw2","C1qbp","Casd1"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Bola3","Bzw2","C1qbp","Casd1"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Cct3","Cct7","Cct8","Cdc20"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Cct3","Cct7","Cct8","Cdc20"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Cdc34","Cenpe","Cited2","Clns1a"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Cdc34","Cenpe","Cited2","Clns1a"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Cotl1","Cs","Cyc1","Dctpp1"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Cotl1","Cs","Cyc1","Dctpp1"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Dkc1","Dnaja2","Dnajc2","Dusp9"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Dkc1","Dnaja2","Dnajc2","Dusp9"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Dut","Dynll2","E130012A19Rik","Ebna1bp2"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Dut","Dynll2","E130012A19Rik","Ebna1bp2"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Eif1ad","Eif4ebp1","Elovl6","Eno3"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Eif1ad","Eif4ebp1","Elovl6","Eno3"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Fhl1","Fkbp4","Foxd2os","Gar1"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Fhl1","Fkbp4","Foxd2os","Gar1"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Gcsh","Glrx5","Gmnn","Got2"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Gcsh","Glrx5","Gmnn","Got2"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Gtpbp4","H2afx","Hmga1","Hmga1-rs1"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Gtpbp4","H2afx","Hmga1","Hmga1-rs1"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Hmga2","Hoxa11","Hspa4","Hspa9"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Hmga2","Hoxa11","Hspa4","Hspa9"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Hspd1","Id2","Igdcc3","Igf2bp1"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Hspd1","Id2","Igdcc3","Igf2bp1"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Kpnb1","Llph","Lsm3","Lyar"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Kpnb1","Llph","Lsm3","Lyar"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Magoh","Mapk12","Mdh2","Mrpl11"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Magoh","Mapk12","Mdh2","Mrpl11"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
VlnPlot(updated_MouseLimb10X,features = c("Mrpl12","Mrpl28","Mrpl34","Mrps15"),
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = c("Mrpl12","Mrpl28","Mrpl34","Mrps15"),
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
Genes1=c("Mrto4","Mthfd2","Mtx2","Nabp2","Nasp","Ndufa12","Nhp2","Nolc1","Nsun2","Nudt4","Odc1","Pa2g4","Pabpc4","Parl","Pcbp4","Phgdh","Plk2","Pno1","Ppa1","Ppif","Ppp1r14b","Prdx6","Prmt1","Psme3","Ptpla","Rangrf","Rbp1","Rrm2","Rrs1","Rsl1d1","Sdhd","Slc25a5","Smarca4","Sms","Snrpa1","Srm","Ssrp1","Sssca1","Stip1","Suclg1","Sulf2","Tcf12","Tmem160","Tomm40","Trp53","Tubb2b","Txnl4a","Ube2m","Uchl3","Wdr18","Wfdc2","Ybx3","Zfp428")
i=1
VlnPlot(updated_MouseLimb10X,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=2
VlnPlot(updated_MouseLimb10X,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=3
VlnPlot(updated_MouseLimb10X,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=4
VlnPlot(updated_MouseLimb10X,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=5
VlnPlot(updated_MouseLimb10X,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=6
VlnPlot(updated_MouseLimb10X,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=7
VlnPlot(updated_MouseLimb10X,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=8
VlnPlot(updated_MouseLimb10X,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=9
VlnPlot(updated_MouseLimb10X,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=10
VlnPlot(updated_MouseLimb10X,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=11
VlnPlot(updated_MouseLimb10X,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=12
VlnPlot(updated_MouseLimb10X,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=13
VlnPlot(updated_MouseLimb10X,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=14
VlnPlot(updated_MouseLimb10X,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes1[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
Genes2 = c("2310015B20Rik","2410004N09Rik","2810442N19Rik","9630033F20Rik","AC118721.1","Acta2","Arhgdig","Atp2a1","Bdnf","Ccdc141","Ccdc171","Cd59a","Cdc6","Cdh15","Cdk5r1","Cep41","Cerkl","Chac2","Cldn9","Crym","Cxcr4","D130040H23Rik","Dcdc2a","Dmrt2","Dpysl4","Dtna","Epb4.1l4a","Epb4.1l5","Fgf9","Fgfr4","Fitm1","Fst","Gamt","Gm10184","Gm10499","Gm11451","Gm13502","Gm15773","Gm7332","Gria2","Hes6","Hey1","Hk2","Hotairm1","Hpgd","Iigp1","Isl1","Kcne1l","Lfng","Lmo3","Msc","Mybpc1","Myc","Myl1","Myo5b","Myod1","Nav2","Neb","Nexn","Ntf3","Nudt19","Pdgfa","Pdss2","Pgam2","Pgf","Pitx3","Pknox2","Ppargc1b","Ppp1r1a","Pvt1","Rab3ip","Rapsn","Rbm20","Rbm24","RP24-396E16.1","Rragd","Rtn2","Rxrg","Sct","Sgcg","Shmt1","Smtnl2","Snap91","Stk26","Stra6","Synpo2l","Tmem30b","Tnnt1","Tpm2","Tppp3","Ttn","Tuba4a","Vgll2")
i=1
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=2
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=3
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=4
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=5
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=6
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=7
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=8
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=9
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=10
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=11
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=12
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=13
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=14
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=15
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=16
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=17
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=18
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=19
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=20
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=21
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=22
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=23
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=24
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=25
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
i=26
VlnPlot(updated_MouseLimb10X,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,idents=c("7","4","17","12","22"),
group.by="ident", cols=cell_type_color[c("7","4","17","12","22")])
VlnPlot(MouseLimbC1,features = Genes2[c(i*4-3,i*4-2,i*4-1,i*4)],
pt.size=0.005,ncol=2,
group.by="MATLABtype"
, cols=as.vector(cell_type_color[c("0","1","3","17","7","2","14","20","9","4","8","5")])
)
length(Genes1)
help(HTODemux)