<p>You can use the <code>cells</code> argument to only display the data for a specific subset of cells.  </p>

<p>For example to extract the values for a cluster 2:</p>

<pre><code># The cluster identity is stored in the meta.data
# In this example there is a clustering column called "RNA_snn_res.0.7" 
# but any metadata column can be used

clust2.cells &lt;- rownames(Seurat.data@meta.data[Seurat.data$RNA_snn_res.0.7 == 2, ])

FeatureScatter(Seurat.data, feature1 = "gene_A", feature2 = "gene_B", cells = clust2.cells)
</code></pre>

CC BY-SA 4.0
2020-05-20T14:06:06.673Z
Thank you so much.
raiora
CC BY-SA 4.0
2020-08-11T17:45:39.167Z
You can also subset your Seurat object within the call to `FeatureScatter`, such as `FeatureScatter(subset(Seurat.data, idents = "2"), "gene_A", "gene_B")`
Dave Ross
CC BY-SA 4.0
2020-05-20T12:36:11.130Z
2020-05-20T14:26:02.863Z
2020-05-20T14:26:02.863Z
PPK
<p>Nowadays, I am trying to calculate Pearson correlation values between two genes of my interest from single-cell RNA-data (features.tsv, barcodes.tsv, and matrix.mtx files) which are obtained from the 10xgenomics cellranger. </p>

<p>FYI, The filtered_feature_bc_matrix includes an aggregated population of tumor-infiltrating immune cells that are derived from 6 different syngeneic mouse tumors (<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE121861" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE121861</a>). I downloaded fastq files and ran "cellranger count" and "cellranger aggr" commands to obtain combined data.</p>

<p>My strategy includes the use of the "feature scatter" function deposited in the library(Seurat). Finally, I ended up getting results below. </p>

<p><a href="https://i.sstatic.net/0OLyF.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/0OLyF.png" alt="FeatureScatter plot"></a></p>

<p>My question is that can we select a specific cluster(s) or identity on this plot? For example, I want to see correlation values in cluster 2 only.
The usage of Feature scatter is as follows. </p>

<p>FeatureScatter(
  object,
  feature1,
  feature2,
  cells = NULL,
  group.by = NULL,
  cols = NULL,
  pt.size = 1,
  shape.by = NULL,
  span = NULL,
  smooth = FALSE,
  combine = TRUE,
  slot = "data"
)</p>

<p>Do you know how to get the Pearson correlation of my two genes using Seurat? This is the best I can do.</p>

<p>Thank you.</p>

<seurat><correlation>
How to specifically select cluster on Featurescatter on Seurat?
# How to specifically select cluster on Featurescatter on Seurat?

(Asked by: username_0 on 2020-05-20)

Nowadays, I am trying to calculate Pearson correlation values between two genes of my interest from single-cell RNA-data (features.tsv, barcodes.tsv, and matrix.mtx files) which are obtained from the 10xgenomics cellranger.

FYI, The filtered\_feature\_bc\_matrix includes an aggregated population of tumor-infiltrating immune cells that are derived from 6 different syngeneic mouse tumors (<https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE121861>). I downloaded fastq files and ran "cellranger count" and "cellranger aggr" commands to obtain combined data.

My strategy includes the use of the "feature scatter" function deposited in the library(Seurat). Finally, I ended up getting results below.

[![FeatureScatter plot](https://i.sstatic.net/0OLyF.png)](https://i.sstatic.net/0OLyF.png)

My question is that can we select a specific cluster(s) or identity on this plot? For example, I want to see correlation values in cluster 2 only.
The usage of Feature scatter is as follows.

FeatureScatter(
object,
feature1,
feature2,
cells = NULL,
group.by = NULL,
cols = NULL,
pt.size = 1,
shape.by = NULL,
span = NULL,
smooth = FALSE,
combine = TRUE,
slot = "data"
)

Do you know how to get the Pearson correlation of my two genes using Seurat? This is the best I can do.

Thank you.

**Tags:** seurat, correlation

---

## 1 answers

### Answer by username_1 on 2020-05-20. Score: 3 | Accepted answer

You can use the cells argument to only display the data for a specific subset of cells.  
For example to extract the values for a cluster 2:
# The cluster identity is stored in the meta.data
# In this example there is a clustering column called "RNA_snn_res.0.7" 
# but any metadata column can be used

clust2.cells <- rownames(Seurat.data@meta.data[Seurat.data$RNA_snn_res.0.7 == 2, ])

FeatureScatter(Seurat.data, feature1 = "gene_A", feature2 = "gene_B", cells = clust2.cells)

> **Comments:**
> **username_0**: Thank you so much.  
> **username_2**: You can also subset your Seurat object within the call to `FeatureScatter`, such as `FeatureScatter(subset(Seurat.data, idents = "2"), "gene_A", "gene_B")`  

---

