Adding median to Violin Plots ggplot2

Question

[Anupam]

Hello All,

I want to make grouped violin plots from a table. I have a table of the following format:

Cell_Id         Cell_Type     nox4_expr        TP53
AAA1_AAACCCAAGGCCGCTT-1         Fibroblasts no_NOX4_Cells  0.42292722
AA1_AAACCCAGTATTTCGG-1 Smooth_Muscle_Cells no_NOX4_Cells -1.02533342
AAA1_AAACGAACAGGCTATT-1   Endothelial_Cells no_NOX4_Cells -1.23918040
AAA1_AAACGCTCACAAGTGG-1 Smooth_Muscle_Cells no_NOX4_Cells -0.30592846
AAA1_AAAGAACAGGAAAGGT-1 Smooth_Muscle_Cells no_NOX4_Cells -0.73323183
AAA1_AAAGGGCAGATGCCGA-1 Smooth_Muscle_Cells no_NOX4_Cells  0.75156034
AAA1_AAAGGTATCTGTCCCA-1   Endothelial_Cells no_NOX4_Cells -0.52521605
AAA1_AAAGTCCTCTTGGTCC-1 Smooth_Muscle_Cells no_NOX4_Cells -0.19304152
AAA1_AACAAAGCATGTGTCA-1   Endothelial_Cells no_NOX4_Cells -0.28536052
AAA1_AACAAAGTCCTGTTGC-1   Endothelial_Cells no_NOX4_Cells -0.48373745
AAA1_AACAAGATCGCCATAA-1         Fibroblasts no_NOX4_Cells -0.54716342
AAA1_AACACACTCACTCGAA-1         Fibroblasts no_NOX4_Cells  0.07636655
AAA1_AACAGGGCAGAGGAAA-1 Smooth_Muscle_Cells no_NOX4_Cells -1.96604142
AAA1_AACAGGGTCTACTATC-1 Smooth_Muscle_Cells no_NOX4_Cells -0.97004485
AAA1_AACCAACAGTGAGTGC-1   Endothelial_Cells NOX4_Cells -1.06456474
AAA1_AACCAACCATACCAGT-1 Smooth_Muscle_Cells no_NOX4_Cells -0.04470668
AAA1_AACCAACGTCACCGCA-1         Fibroblasts no_NOX4_Cells  1.51190518
AAA1_AACCAACGTGAATTGA-1         Fibroblasts no_NOX4_Cells -0.76614605
AAA1_AACCATGAGGATTCAA-1 Smooth_Muscle_Cells no_NOX4_Cells  0.71925013
AAA1_AACCTGAAGATGACAT-1 Smooth_Muscle_Cells no_NOX4_Cells -0.98475028
AAA1_AACCTGATCGCACGGT-1 Smooth_Muscle_Cells no_NOX4_Cells -1.09628709
AAA1_AACCTTTTCGGTGAAG-1         Fibroblasts NOX4_Cells -0.45117008
AAA1_AACGAAATCTCGTGGG-1 Smooth_Muscle_Cells NOX4_Cells -1.14700998
AAA1_AACGGGACATGAAGCG-1         Fibroblasts no_NOX4_Cells -0.34016949
AAA1_AACGTCACACAAGCAG-1 Smooth_Muscle_Cells no_NOX4_Cells -0.17526431
AAA1_AACGTCATCACCATCC-1         Fibroblasts no_NOX4_Cells -0.35808476
AAA1_AACGTCATCCACCTCA-1         Fibroblasts no_NOX4_Cells -0.26573515
AAA1_AAGAACACATATGAAG-1 Smooth_Muscle_Cells no_NOX4_Cells -0.39395033
AAA1_AAGAACAGTCCATACA-1         Fibroblasts no_NOX4_Cells  1.08556113
AAA1_AAGAACAGTTGACTAC-1         Fibroblasts    NOX4_Cells  2.41693267
AAA1_AAGACAACAGCGCTTG-1   Endothelial_Cells no_NOX4_Cells -1.14250292
AAA1_AAGCCATCACATGTTG-1 Smooth_Muscle_Cells no_NOX4_Cells -0.41232271
AAA1_AAGCGAGCAGACCATT-1   Endothelial_Cells no_NOX4_Cells  0.24044021
AAA1_AAGCGAGGTCTTGCGG-1         Fibroblasts NOX4_Cells -0.47326943
AAA1_AAGCGAGGTTATCTGG-1   Endothelial_Cells NOX4_Cells  0.06141235
AAA1_AAGCGAGTCCATACTT-1 Smooth_Muscle_Cells NOX4_Cells -1.00187397
AAA1_AAGCGTTCATTGACCA-1   Endothelial_Cells no_NOX4_Cells -1.98551134
AAA1_AAGGAATAGCTGTTCA-1   Endothelial_Cells no_NOX4_Cells  0.58095744
AAA1_AAGTCGTCACATATCG-1         Fibroblasts no_NOX4_Cells  0.07679935
AAA1_AAGTCGTCAGACCAAG-1         Fibroblasts no_NOX4_Cells -0.79393816
AAA1_AAGTGAACACTCTCGT-1         Fibroblasts no_NOX4_Cells  1.22087911
AAA1_AAGTGAATCTGCCTCA-1 Smooth_Muscle_Cells NOX4_Cells -0.24164262
AAA1_AAGTTCGTCAAACGAA-1 Smooth_Muscle_Cells no_NOX4_Cells -0.61149856
AAA1_AATCACGAGCACGTCC-1   Endothelial_Cells NOX4_Cells  0.90173135
AAA1_AATCACGGTCTCGCGA-1         Fibroblasts no_NOX4_Cells -0.47399920
AAA1_AATCACGGTGATTCTG-1         Fibroblasts no_NOX4_Cells -0.23503119
AAA1_AATCGACGTATCGAGG-1         Fibroblasts no_NOX4_Cells  0.94648594
AAA1_AATCGACGTCGTACTA-1         Fibroblasts    NOX4_Cells  0.98152549
AAA1_AATCGTGCATCGATAC-1 Smooth_Muscle_Cells NOX4_Cells -0.56436443
AAA1_AATGACCTCGCTAATG-1         Fibroblasts NOX4_Cells  1.54377599

Following is my code:

ggplot(t_t,aes(x=Cell_Type,y=TP53,fill=nox4_expr),pt.size=0,y.max=5)+ geom_violin()+ 
 stat_compare_means(aes(group=nox4_expr)) + 
  stat_summary(data=t_t,mapping=aes(x=Cell_Type,y=TP53,fill=nox4_expr),fun.data = "median",geom = "crossbar", width = 0.5,colour = "red")

But I keep getting this error. The first two layers work fine and I get violin plots with p-values. But the stat_summary never works. I need to add median to the violin plots.

Error in `stat_summary()`:
 ! Problem while setting up geom.
  Error occurred in the 3rd layer.
  Caused by error in `compute_geom_1()`:
 ! `geom_crossbar()` requires the following missing aesthetics: y, ymin, and ymax or y, xmin,
     and xmax
    Run `rlang::last_trace()` to see where the error occurred.

Can anyone please help me out?

Thanks in advance

Anupam

[Ram]

Did you build the ggplot2 layers by yourself or get the code from somewhere?

[Anupam]

Whats the point of your question ?

[Ram]

I'm trying to gain more context so I can help you better. If I were you, I'd have tried adding layer by layer until I got to the layer causing the problem, then adding parameter by parameter until I got to the parameter causing the problem - but that will only work if you understand the details of each layer, which can be difficult if you can get the code from somewhere.

You're asking for help on a volunteer forum. Why act offended when asked for details?

[Anupam]

Well, I was trying to the understand the coding context of your question and was in no way offended. I have already stated that I am not getting Error with the first two layers. Its the third layer which is causing the issue.

Answer 1

[Ram]

My bad on my comments - I did not read the part where you specify which layer is causing the problem.

Can you try fun="median" instead of fun.data="median" please?

[Anupam]

Thanks a lot for your response. Works like a charm...

[Ram]

I'll move my comment to an answer. Please accept it to provide closure to the post.