Fixing Removed rows containing missing values for ggplot()

So I'm trying to make a histogram with ggplot where I am trying to zoom in the axis on the a graph, but I still want all my bars to be present. So I have the dataframe below:

> dput(organic_acids_28day_merged_numeric)
structure(list(Sample = c("Ana 28day", "Ana 28day", "Ana 28day", 
"Ana 28day", "Ana 28day", "Ana 28day", "Ana 28day", "CA 28day", 
"CA 28day", "CA 28day", "CA 28day", "CA 28day", "CA 28day", "CA 28day"
), Acid = c("Acetic Acid", "Butyric Acid", "Isovaleric Acid", 
"Lactic Acid", "Propionic Acid", "Succinic Acid", "Valeric Acid", 
"Acetic Acid", "Butyric Acid", "Isovaleric Acid", "Lactic Acid", 
"Propionic Acid", "Succinic Acid", "Valeric Acid"), Percent = c(3.06, 
2.5, 0.42, 0.3, 2.78, 1.01, 0, 2.49, 0.03, 2.48, 1.3, 2.09, 29.68, 
0), stdev = c(0.78, 0.34, 0.23, 0.13, 0.37, 0.3, 0, 0.41, 0.05, 
1.28, 0.32, 0.19, 6.81, 0)), class = "data.frame", row.names = c(NA, 

And when I don't try to fix the axes I get all the data points showing up fine. But when I zoom into the axis, as with the code below (adjusting the y-axis to be betwen 0 and 5) it completely removes the bar that goes up to about 30%. And I get the error after it:

> ggplot(organic_acids_28day_merged_numeric,
+                   aes(x=factor(Sample,level=c("Ana 28day","CA 28day")),
+                       y=Percent,fill=factor(Acid,level=c("Acetic Acid",
+                                                          'Butyric Acid',
+                                                          'Isovaleric Acid',
+                                                          'Lactic Acid',
+                                                          'Propionic Acid',
+                                                          'Valeric Acid',
+                                                          'Succinic Acid'))))+
+   geom_col(position=position_dodge())+
+   labs(x="None",y="% of Dry Matter by Mass")+
+   scale_x_discrete(labels=c("UT\n28d","CA\n28d"))+
+   scale_y_continuous(limits=c(0,5))+
+   geom_errorbar(aes(ymin=Percent-stdev,
+                     ymax=Percent+stdev),
+                 position=position_dodge())+
+   scale_fill_manual(values=c("#D95F02","#7570B3","#E7298A","#66A61E","#E6AB02",
+                              "#A6761D","#666666"))+
+   # scale_fill_brewer(palette="Dark2")+
+   theme_classic()+
+   theme(axis.title.x=element_blank(),legend.title=element_blank(),
+         legend.text =element_text(size=12),axis.title.y=element_text(size=12),
+         legend.position="bottom",axis.text.x=element_text(size=12),
+         axis.text.y=element_text(size=12),
+         panel.grid.major.y=element_line(color=1,size=0.5,linetype=2),
+         panel.grid.minor.y=element_line(color="black",size=0.25,linetype=3))
Warning message:
Removed 1 rows containing missing values (`geom_col()`). 

And I know it's removed because the value is outside the y-axis limit. But I wanted to know if there is a way to fix this so that it still shows that last bar being present, even if it would be cut off, if that makes sense.

One way to achieve this is to first mutate Percent to be 5 if it is originally greater than 5 (or any threshold). Then plot the data frame. You could also add a caption to the plot so your audience knows the bar is actually greater than 5% (just to be safe).

organic_acids_28day_merged_numeric = organic_acids_28day_merged_numeric %>%
  mutate(Percent = ifelse(Percent > 5, 5, Percent))

Created on 2023-01-18 with reprex v2.0.2.9000

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