<p>The "identities" can be accessed with the <code>Idents()</code> function in Seurat v3.</p>

<p>You should change <code>cell.num &lt;- table(shox2crepos_mtmg@ident)</code> to </p>

<p><code>cell.num &lt;- table(Idents(shox2crepos_mtmg))</code></p>

CC BY-SA 4.0
2019-10-29T08:27:32.547Z
2019-10-29T15:03:11.893Z
2019-10-29T15:03:11.893Z
haci
<p>I was supposed to use the code below to get the number of cells per cluster. The code works with Seurat version 2, but while using version 3 I got the error <code>no slot of name "ident" for this object of class "Seurat"</code>. Does anyone have any idea about how to deal with this?</p>

<pre><code># Calculate number of cells per cluster from object@ident

cell.num &lt;- table(shox2crepos_mtmg@ident)

# Add cell number per cluster to cluster labels

ClusterLabels = paste("Cluster", names(cell.num), paste0("(n = ", cell.num, ")"))

# Order legend labels in plot in the same order as 'ClusterLabels'

ClusterBreaks = names(cell.num)

# Plot tSNE with new legend labels for clusters

TSNEPlot(object = shox2crepos_mtmg, do.return = T) +
  scale_colour_discrete(breaks = ClusterBreaks,
                        labels = ClusterLabels) +
  labs(x = "t-SNE 1",
       y = "t-SNE 2")
</code></pre>

CC BY-SA 4.0
2019-11-05T15:08:53.327Z
The official seurat website (https://satijalab.org/seurat/essential_commands.html) has a `cheat sheet` page with all the different commands between `v2` and `v3` (`Seurat v2.X vs v3.X`).
fra
<scrnaseq>
How to calculate the number of cells in different cell clusters with Seurat v3?
# How to calculate the number of cells in different cell clusters with Seurat v3?

(Asked by: username_0 on 2019-10-28)

I was supposed to use the code below to get the number of cells per cluster. The code works with Seurat version 2, but while using version 3 I got the error no slot of name "ident" for this object of class "Seurat". Does anyone have any idea about how to deal with this?
# Calculate number of cells per cluster from object@ident

cell.num <- table(shox2crepos_mtmg@ident)

# Add cell number per cluster to cluster labels

ClusterLabels = paste("Cluster", names(cell.num), paste0("(n = ", cell.num, ")"))

# Order legend labels in plot in the same order as 'ClusterLabels'

ClusterBreaks = names(cell.num)

# Plot tSNE with new legend labels for clusters

TSNEPlot(object = shox2crepos_mtmg, do.return = T) +
  scale_colour_discrete(breaks = ClusterBreaks,
                        labels = ClusterLabels) +
  labs(x = "t-SNE 1",
       y = "t-SNE 2")

**Tags:** scrnaseq
> **Comments:**
> **username_1**: The official seurat website (https://satijalab.org/seurat/essential_commands.html) has a `cheat sheet` page with all the different commands between `v2` and `v3` (`Seurat v2.X vs v3.X`).  

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## 1 answers

### Answer by username_2 on 2019-10-29. Score: 2 | Accepted answer

The "identities" can be accessed with the `Idents()` function in Seurat v3.

You should change `cell.num <- table(shox2crepos_mtmg@ident)` to

`cell.num <- table(Idents(shox2crepos_mtmg))`


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