Seurat heatmap across conditions

Hello,

I have a seurat object that has 3 conditions merged. When plotting feature plots I can split them using the " split.by = 'stim' " Would anyone know if there is a way to do this for heatmaps across the conditions for a defined set of genes?

Thanks

seurat single-cell rnaseq

• 5,608 views • link

updated 6.5 years ago by Arup Ghosh

• written 6.5 years ago by V

1 answer

Provide a list of genes to features option and use group.by = 'stim' in Seurat DoHeatmap function.

• 0 views • link

written 6.5 years ago by Arup Ghosh

More posts like this

Can't do runPCA after merging a splited Seurat object before UMAP
written 2.7 years ago by wanaga3166 •

Hi everyone, When I started my analysis, I merged 3 samples. ```r merged_seurat <- merge(x = PC9_1_raw_feature_bc_matrix, y = c(PC9_2_raw_feature_bc_matrix, PC9_3_raw_feature_bc_matrix), add.cell.id = c("PC9_1", "PC9_2", …
Integrated Seurat object change name of the two conditions
written 2.9 years ago by camillab. •

Hi, I have a scRNAseq integrated seurat object composed by my control and my treatment. On this object I did all the analysis and I …
Change transparency/alpha in seurat's vlnPlot()
written 3.0 years ago by acareyhoppe •

Hello, I would like to change the transparency of my violin plots in Seurat. It should be simple yet it seems there isn't a function …
Seurat Sctransform integration errors: Error in scale.data[anchor.features, ] : # no 'dimnames' at…
written 3.8 years ago by sasa •

Hi, I need to integrate the 2 data set. Both have been filtered and SCTransform-ed. However, when I run `PrepSCTIntegration`, I keep getting the following …
Re-arrange conditions in Seurat
written 6.1 years ago by V

Hello, Would anyone know how to re-arrange the output of featureplots/dimplots when using the 'split.by = 'stim'' function? I have 3 conditions, Young, Adult and …
Re-arrange conditions in Seurat
written 6.1 years ago by V

Hello, Would anyone know how to re-arrange the output of featureplots/dimplots when using the 'split.by = 'stim'' function? I have 3 conditions, Young, Adult and …
Remove ensembl identifiers from Seurat
written 6.1 years ago by V

Hello, I took a 10x matrix from a collaborator and created a Seurat object. The issue I am having which I only realised when attempting …
Seurat FeaturePlot across stims
written 6.2 years ago by V

Hello, I have a very basic questions. I have a 'Seurat' file that I've analysed and is a merge of 8 different conditions. When plotting …
Cluster using known marker genes (Seurat)
written 6.4 years ago by V

Hello, Using the seurat pipeline (v3) is there a way to cluster using known marker genes, or a set of genes that you pass into …
R code to plot heatmap/average line plots from Deeptools computeMatrix
written 8.2 years ago by 94133 •

Deeptools is an incredible package, but I want more plotting versatility. Anyone kind enough to share workflow/code for plotting computeMatrix heatmaps and average plots in …