Help adding significant difference bars to plot in R

Smartell · March 5, 2021, 3:47pm

Hi, I'm a bit of a newbie to R. I have a violin plot comparing measured lengths and widths and would like to put if any of these differences are significant in the plot. Any help with code would be sooo much appreciated.

Thanks

nirgrahamuk · March 5, 2021, 5:31pm

Hi!

To help us help you, could you please prepare a reproducible example (reprex) illustrating your issue? Please have a look at this guide, to see how to create one:

FAQ: How to do a minimal reproducible example ( reprex ) for beginners Guides & FAQs

A minimal reproducible example consists of the following items: A minimal dataset, necessary to reproduce the issue The minimal runnable code necessary to reproduce the issue, which can be run on the given dataset, and including the necessary information on the used packages. Let's quickly go over each one of these with examples: Minimal Dataset (Sample Data) You need to provide a data frame that is small enough to be (reasonably) pasted on a post, but big enough to reproduce your issue. Let's say, as an example, that you are working with the iris data frame head(iris) #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.…

Smartell · March 5, 2021, 7:01pm

Hi
I put my code below as well as a sample of my dataset. Is there anything I can provide?

library(rlang)
library(ggplot2)
library(svglite)
library(Hmisc)
read.csv("Leptothrix_lw.csv", header = TRUE)
data <- read.csv("Leptothrix_lw.csv", header = TRUE)
summary(data)
plot <- plot + geom_violin(aes(color = "Cell_W"))
q <- plot + geom_violin(aes(y =Cell_L , colour = "Cell_L"))
q + labs(y= "Cell Measurements (um)", title= "Cell Length & Width Measurements", colour= "Cell L or W") + stat_summary(
  fun.data="mean_sdl", mult=1, geom="crossbar", width=0.2)

|Name|Cell_L|Cell_W|

|L. cholodnii|2.569|1.082|
|L. cholodnii|3.015|1.029|
|L. cholodnii|2.674|1.137|
|L. cholodnii|2.397|1.123|
|L. cholodnii|2.645|1.197|
|L. mobilis|1.882|0.925|
|L. mobilis|1.931|1.072|
|L. mobilis|1.940|1.049|
|L. mobilis|1.998|0.904|
|L. mobilis|2.366|0.908|

nirgrahamuk · March 5, 2021, 7:12pm

What portion of the guide says to share data in this way? Please advise me so I can correct the guide.

Smartell · March 5, 2021, 7:56pm

Thanks for replying to my post again to help. my bad on the data format being wrong. Like I said before, I'm a newbie to R, R language, and posting (in proper format) to this R community. Also I don't fully follow your head(iris) example. Is that code? is that how the data looks before going into R? once being in R? If I tried to follow an example I don't understand the data may get messed up in the miscommunication? I just thought I'd copy and paste from my excel so at least the data in the proper categories is there. My advise would be to not expect everyone to follow your guide or know R language enough to follow. Maybe try the example again using the data I provided?

nirgrahamuk · March 5, 2021, 8:12pm

Ok let's talk it through nice and slow.

Iris is a built in dataset in R.
That means you can open r.
Type

iris

and expect to see it.
You should try this and report back.
With it being a special case, something everyone has, there's little need to share it but I show you how to share it.

Run

dput(iris)

This is runnable shareable code that can recreate iris.

Copy the output of the dput into your console and see what happens.

Smartell · March 5, 2021, 8:29pm

alright, alright! slow definitely works better for me! So I think I did it correctly now but it has all of my data and not just a small sample like I copied and pasted before. Is that ok?

dput(data)
structure(list(Name = c("L. cholodnii", "L. cholodnii", "L. cholodnii",
"L. cholodnii", "L. cholodnii", "L. cholodnii", "L. cholodnii",
"L. cholodnii", "L. cholodnii", "L. cholodnii", "L. cholodnii",
"L. cholodnii", "L. cholodnii", "L. cholodnii", "L. cholodnii",
"L. cholodnii", "L. cholodnii", "L. cholodnii", "L. cholodnii",
"L. cholodnii", "S. natans", "S. natans", "S. natans", "S. natans",
"S. natans", "S. natans", "S. natans", "S. natans", "S. natans",
"S. natans", "S. natans", "S. natans", "S. natans", "S. natans",
"S. natans", "S. natans", "S. natans", "S. natans", "S. natans",
"S. natans", "L. mobilis", "L. mobilis", "L. mobilis", "L. mobilis",
"L. mobilis", "L. mobilis", "L. mobilis", "L. mobilis", "L. mobilis",
"L. mobilis", "L. mobilis", "L. mobilis", "L. mobilis", "L. mobilis",
"L. mobilis", "L. mobilis", "L. mobilis", "L. mobilis", "L. mobilis",
"L. mobilis", "I", "I", "I", "I", "I", "I", "I", "I", "I", "I",
"I", "I", "I", "I", "I", "I", "I", "I", "I", "I", "I", "I", "I",
"I", "I", "I", "I", "I", "I", "I", "I", "I", "I", "I", "I", "I",
"I", "I", "I", "I", "I", "I", "I", "I", "I", "I", "I", "I", "I",
"I", "I", "I", "I", "I", "I", "I", "I", "I", "I", "I", "II",
"II", "II", "II", "II", "II", "II", "II", "II", "II", "II", "II",
"II", "II", "II", "II", "II", "II", "II", "II", "II", "II", "II",
"II", "II", "II", "II", "II", "II", "II", "II", "II", "II", "II",
"II", "II", "II", "II", "II", "II", "II", "II", "II", "II", "II",
"II", "II", "II", "II", "II", "II", "II", "II", "II", "II", "II",
"II", "II", "II", "II", "III", "III", "III", "III", "III", "III",
"III", "III", "III", "III", "III", "III", "III", "III", "III",
"III", "III", "III", "III", "III", "III", "III", "III", "III",
"III", "III", "III", "III", "III", "III", "III", "III", "III",
"III", "III", "III", "III", "III", "III", "III", "III", "III",
"III", "III", "III", "III", "III", "III", "III", "III", "III",
"III", "III", "III", "III", "III", "III", "III", "III", "III",
"III", "III", "III", "III", "III", "III", "III", "III", "III",
"III", "III", "III", "III", "III", "III", "III", "III", "III",
"III", "III", "III", "III", "III", "III", "III", "III", "III",
"III", "III", "III", "III", "III", "III", "III", "III", "III",
"III", "III", "III", "III", "III", "III", "III", "III", "III",
"III", "III", "III", "III", "III", "III", "III", "III", "III",
"III", "III", "III", "III", "III", "III", "III", "III", "III",
"III", "III", "III", "III", "III", "III", "III", "III", "III",
"III", "III", "III", "III", "III", "III", "III", "III"), Cell_L = c(2.569,
3.015, 2.674, 2.397, 2.645, 2.395, 2.472, 2.643, 2.582, 2.428,
2.715, 2.59, 2.596, 2.796, 2.627, 2.467, 2.616, 2.439, 2.361,
2.564, 2.669, 3.117, 2.795, 2.789, 2.947, 2.896, 3.254, 2.933,
2.842, 2.689, 3.299, 2.824, 2.693, 2.986, 2.927, 2.947, 2.694,
3.201, 2.963, 3.188, 1.882, 1.931, 1.94, 1.998, 2.366, 2.01,
2.441, 2.028, 1.995, 2.241, 1.892, 1.831, 1.74, 1.798, 2.166,
2.01, 2.041, 2.028, 1.995, 2.141, 2.481, 2.538, 2.21, 2.207,
2.137, 2.22, 2.433, 2.185, 2.179, 2.279, 2.519, 2.531, 2.326,
2.519, 2.652, 2.222, 2.279, 2.505, 2.346, 2.394, 2.157, 2.45,
2.224, 2.328, 2.515, 2.5, 2.549, 2.418, 2.36, 2.418, 2.442, 2.744,
2.494, 2.418, 2.713, 2.549, 2.543, 2.413, 2.467, 2.67, 2.386,
2.597, 2.271, 2.22, 2.38, 2.676, 2.567, 2.869, 2.732, 2.342,
2.443, 2.361, 2.754, 2.522, 2.334, 2.721, 2.6, 2.597, 2.326,
2.574, 2.961, 3.023, 2.878, 2.127, 2.043, 2.628, 2.764, 2.623,
2.828, 2.636, 2.337, 2.949, 2.796, 2.55, 2.679, 2.411, 2.511,
1.973, 2.965, 2.801, 1.922, 2.444, 2.159, 2.247, 2.534, 2.167,
2.025, 2.404, 2.308, 2.067, 2.483, 2.402, 2.569, 2.464, 2.296,
2.434, 2.54, 2.412, 2.442, 2.393, 2.247, 2.534, 2.167, 2.325,
2.434, 2.628, 2.764, 2.643, 2.827, 2.411, 2.847, 2.574, 2.467,
2.385, 2.534, 2.61, 2.664, 2.643, 2.837, 2.413, 2.386, 2.511,
2.593, 2.501, 2.652, 2.611, 2.865, 2.627, 2.74, 2.517, 2.586,
2.571, 2.693, 2.531, 2.752, 2.681, 2.765, 2.637, 2.44, 2.537,
2.21, 2.308, 2.244, 2.214, 2.326, 2.344, 2.39, 2.29, 2.286, 2.443,
2.21, 2.315, 2.387, 2.315, 2.453, 2.598, 2.522, 2.261, 2.326,
2.517, 2.67, 2.482, 2.543, 2.535, 2.649, 2.611, 2.865, 2.627,
2.74, 2.677, 2.543, 2.842, 2.618, 2.434, 2.808, 2.411, 2.905,
2.512, 2.574, 2.811, 2.27, 2.454, 2.812, 2.354, 2.394, 2.3, 2.916,
2.851, 2.97, 2.34, 2.593, 2.501, 2.652, 2.703, 2.742, 2.916,
2.864, 2.508, 2.522, 2.51, 2.596, 2.505, 2.59, 2.815, 2.613,
2.157, 2.386, 2.511, 2.564, 2.569, 2.921, 2.317, 2.472, 2.442,
2.516, 2.429, 2.5, 2.524, 2.68, 2.851, 1.901, 2.064, 1.925, 1.919,
1.689, 1.986, 2.002, 1.843, 1.9, 1.94, 1.924, 1.927, 1.803, 1.946,
1.656, 1.615, 1.775, 2.001, 1.593, 1.627, 2.759, 2.555, 2.606,
2.323, 2.743, 2.916, 2.676, 2.679, 2.346, 2.865, 2.678, 2.528,
2.895, 2.655, 2.385, 2.549, 2.598, 2.602, 2.923, 2.912), Cell_W = c(1.082,
1.029, 1.137, 1.123, 1.197, 0.989, 1.109, 1.026, 1.055, 1.054,
1.02, 1.079, 1.145, 1.107, 0.995, 0.999, 1.042, 1.142, 1.042,
1.094, 1.111, 1.097, 1, 1.275, 1.222, 1.117, 1.092, 1.081, 1.164,
1.199, 1.117, 1.097, 1.326, 1.163, 1.397, 1.124, 1.252, 1.097,
1.163, 1.072, 0.925, 1.072, 1.049, 0.904, 0.908, 1.198, 0.934,
1.014, 1.113, 1.076, 0.985, 1.002, 1.149, 0.974, 0.978, 1.118,
0.934, 1.014, 1.131, 1.076, 1.072, 1.086, 1.078, 1.088, 1.088,
1.049, 1.211, 1.163, 1.13, 1.023, 1.15, 1.011, 1.166, 1.094,
1.132, 1.111, 1.04, 1.096, 1.006, 1.078, 1.072, 1.124, 1.058,
1.204, 1.172, 1.069, 1.047, 1.145, 1.044, 1.156, 1.211, 1.204,
1.179, 1.152, 1.124, 1.103, 1.102, 1.11, 1.127, 1.169, 1.186,
1.14, 1.241, 1.151, 1.044, 1.111, 1.124, 1.3, 1.299, 1.008, 1.24,
1.29, 1.202, 1.092, 1.092, 1.271, 1.263, 1.207, 1.357, 1.342,
1.103, 0.996, 1.206, 1.163, 1.199, 1.099, 1.236, 1.203, 1.236,
1.163, 1.11, 1.392, 0.961, 1.263, 1.398, 1.235, 1.258, 1.316,
1.377, 1.455, 1.047, 1.066, 1.041, 1.08, 1.091, 1.102, 1.169,
1.179, 1, 1.064, 1.054, 1.165, 1.129, 1.172, 1.059, 1.014, 1.086,
1.086, 1.047, 1.102, 1.091, 1.102, 1.169, 1.179, 1.203, 1.236,
1.163, 1.11, 1.263, 1.198, 1.235, 1.091, 1.102, 1.169, 1.379,
1.213, 1.136, 1.163, 1.131, 1.163, 1.199, 1.029, 0.99, 1.004,
1.017, 1.006, 1.096, 1.125, 1.094, 1.127, 1.059, 1.088, 1.104,
1.037, 1.126, 1.066, 1.145, 1.104, 1.147, 1.136, 1.015, 0.937,
0.987, 0.987, 1.199, 1.029, 0.99, 1.004, 0.919, 0.937, 1.118,
1.029, 0.937, 1.072, 0.995, 0.99, 1.067, 1.111, 0.993, 0.99,
1.04, 1.072, 1.03, 1.017, 1.08, 1.163, 1.078, 1.166, 1.017, 1.006,
1.096, 1.125, 1.14, 1.111, 1.132, 1.024, 1.13, 1.058, 1.032,
1.069, 1.074, 1.04, 1.098, 1.011, 1.088, 1.011, 1.086, 1.03,
1.041, 1.119, 1.058, 1.094, 1.127, 1.059, 1.088, 1.145, 1.077,
1.054, 1.011, 1.086, 1, 1.072, 1.154, 1.086, 1.048, 1.072, 0.975,
1.048, 1.04, 1.106, 0.99, 1.029, 1.035, 1.015, 1.067, 1.111,
0.987, 1.199, 1.004, 1.111, 0.959, 1.186, 0.97, 0.981, 1.023,
1.047, 1.088, 0.908, 0.97, 1.034, 0.933, 1.098, 0.969, 1.081,
1.069, 1, 1.141, 1.011, 1.072, 0.988, 1.072, 1.064, 1.102, 1.13,
1.102, 1.135, 1.163, 1.04, 1.008, 1.145, 1.125, 1.15, 1.183,
1.077, 1.092, 1.13, 1.047, 1.165, 1.032, 1.067)), class = "data.frame", row.names = c(NA,
-320L))

nirgrahamuk · March 5, 2021, 8:36pm

ok wonderful, I have your 'data'.
Now lets scrutinise your code.
after you load your 'data' and show yourself a summary of it ...
theres a statement with plot on both side, not in reference to your data, and not the way a ggplot is typically begun (with ggplot)
Perhaps you redacted too much of your code ?

Smartell · March 5, 2021, 8:50pm

OH! so maybe I was running it wrong? So, I think I just found it?

plot <- ggplot(data=data, mapping = aes(x=Name, y=Cell_W))

q + labs(y= "Cell Measurements (um)", title= "Cell Length & Width Measurements", colour= "Cell L or W") + stat_summary(
  fun.data="mean_sdl", mult=1, geom="crossbar", width=0.2)

Smartell · March 5, 2021, 8:51pm

oops bottom part was a note to myself about something else. I think just the top part is what you wanted =)

system · March 26, 2021, 8:51pm

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