<p>Axes for <code>ggplot</code>s can be controlled via <code>xlim()</code> and <code>ylim()</code> functions. You can try:</p>

<pre><code>your_ggplot_object +
  ylim(-5,20) # assuming that you want the gene labels to be readabe, not clear from your post
</code></pre>

CC BY-SA 4.0
2019-09-19T12:31:14.763Z
> p1 +
+     xlim() +
+     ylim(-5,20) 
Error in UseMethod("limits") : 
  no applicable method for 'limits' applied to an object of class "NULL"
>
Zizogolu
CC BY-SA 4.0
2019-09-19T12:40:21.220Z
I have realized that the function EnhancedVolcano has a "ylim" argument and its lower limit is 0, please try "ylim = c(-5, max(-log10(toptable[,y]), na.rm=TRUE) + 5)" within EnhancedVolcano.
haci
CC BY-SA 4.0
2019-09-19T12:52:22.373Z
Sorry what is the y here? when I am placing pvalue, says that Error in `[.data.frame`(res_responders, , pvalue) : 
  object 'pvalue' not found
Zizogolu
CC BY-SA 4.0
2019-09-19T13:24:05.473Z
Please check the documentation of the function EnhancedVolcano() and play a little bit different arguments. For you case ssetting the ylim argument "ylim = (-5,20)" might help.
haci
CC BY-SA 4.0
2019-09-19T12:18:06.333Z
2019-09-19T14:46:12.947Z
2019-09-19T14:46:12.947Z
haci
<p>By EnhancedVolcano R package I have this plot with this code</p>

<pre><code>    &gt; head(res1)
         baseMean log2FoldChange     lfcSE        stat     pvalue      padj
SAMD11   237.7975     0.03584334 1.3244737  0.02706233 0.97841002 0.9971691
NOC2L   4751.0381    -0.62090622 0.6500115 -0.95522347 0.33946470 0.9239759
KLHL17   735.0849    -0.95126291 0.8417444 -1.13010892 0.25843033 0.8926461
PLEKHN1 1117.5598    -2.11321359 1.0411108 -2.02976816 0.04238011 0.6350143
PERM1    409.0061    -2.32444927 1.1255813 -2.06511000 0.03891259 0.6285916
HES4    1088.7549     0.28395931 0.9091259  0.31234320 0.75477971 0.9866881
&gt;
p= EnhancedVolcano(res1,
    lab = rownames(res1),
    x = 'log2FoldChange',
    y = 'pvalue',
    xlim = c(-5, 8))
</code></pre>

<p>I have stored my plot in an object</p>

<pre><code>&gt; class(p)
[1] "gg"     "ggplot"
</code></pre>

<p><a href="https://i.sstatic.net/X32hE.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/X32hE.png" alt="enter image description here"></a></p>

<p>I want to limit the axis length in this plot in the other word shrining my plot more but I don't know how to do that. <code>For example y axis be from 0 to 10 instead of 20</code></p>

<p>Any help please </p>

CC BY-SA 4.0
2019-09-19T12:11:00.443Z
Could you clarify what do you man by "limit the axis length"?  Do you want it for instance to reach just from -4 to 4 or do you want a wider plot? What kind of searches did you make? Also if you could include a reproducible example, see [reprex](https://reprex.tidyverse.org/), it would be easier for people to understand and work with your problem
llrs
<r><rna-seq><ggplot2>
Changing the axis limits of ggplot objects
# Changing the axis limits of ggplot objects

(Asked by: username_0 on 2019-09-19)

By EnhancedVolcano R package I have this plot with this code
    > head(res1)
         baseMean log2FoldChange     lfcSE        stat     pvalue      padj
SAMD11   237.7975     0.03584334 1.3244737  0.02706233 0.97841002 0.9971691
NOC2L   4751.0381    -0.62090622 0.6500115 -0.95522347 0.33946470 0.9239759
KLHL17   735.0849    -0.95126291 0.8417444 -1.13010892 0.25843033 0.8926461
PLEKHN1 1117.5598    -2.11321359 1.0411108 -2.02976816 0.04238011 0.6350143
PERM1    409.0061    -2.32444927 1.1255813 -2.06511000 0.03891259 0.6285916
HES4    1088.7549     0.28395931 0.9091259  0.31234320 0.75477971 0.9866881
>
p= EnhancedVolcano(res1,
    lab = rownames(res1),
    x = 'log2FoldChange',
    y = 'pvalue',
    xlim = c(-5, 8))

I have stored my plot in an object
> class(p)
[1] "gg"     "ggplot"


I want to limit the axis length in this plot in the other word shrining my plot more but I don't know how to do that. For example y axis be from 0 to 10 instead of 20
Any help please

**Tags:** r, rna-seq, ggplot2
> **Comments:**
> **username_1**: Could you clarify what do you man by "limit the axis length"?  Do you want it for instance to reach just from -4 to 4 or do you want a wider plot? What kind of searches did you make? Also if you could include a reproducible example, see [reprex](https://reprex.tidyverse.org/), it would be easier for people to understand and work with your problem  

---

## 1 answers

### Answer by username_2 on 2019-09-19. Score: 4

Axes for ggplots can be controlled via xlim() and ylim() functions. You can try:
your_ggplot_object +
  ylim(-5,20) # assuming that you want the gene labels to be readabe, not clear from your post

> **Comments:**
> **username_0**: > p1 + +     xlim() + +     ylim(-5,20)  Error in UseMethod("limits") :    no applicable method for 'limits' applied to an object of class "NULL" >  
> **username_2**: I have realized that the function EnhancedVolcano has a "ylim" argument and its lower limit is 0, please try "ylim = c(-5, max(-log10(toptable[,y]), na.rm=TRUE) + 5)" within EnhancedVolcano.  
> **username_0**: Sorry what is the y here? when I am placing pvalue, says that Error in `[.data.frame`(res_responders, , pvalue) :    object 'pvalue' not found  
> **username_2**: Please check the documentation of the function EnhancedVolcano() and play a little bit different arguments. For you case ssetting the ylim argument "ylim = (-5,20)" might help.  

---

