how to create a boxplot with physicochemical variables?

OSDIAZ · August 26, 2019, 2:33am

Hello everyone, I am new in R, and I would like to know if you can help me. I attached an image with an example of what I would like to do in R. I have several physicochemical variables, such as pH, temperature, dissolved oxygen, etc. I took them at different depths of a lagoon in Mexico ( surface, in the middle and bottom). In the photo example they also took those depths (bottom, middle and surface). At the same time through molecular techniques I took samples of the microorganisms present at these depths. What I want is to know how to associate the presence of these microorganisms with the physicochemical variables. I don't know what commands and functions to use.

Thnks

FJCC · August 26, 2019, 5:06am

Your title asks one question and the text of your post asks another. To help with either one, we would need to see an example of your data to understand how it is laid out. Some guidance on how to show data can be found here:

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.…

It may then be fairly easy to answer your question "how to create a boxplot with physicochemical variables?"

Your other question, "What I want is to know how to associate the presence of these microorganisms with the physicochemical variables", might be too broad to answer completely. If you can show a sample of both the physiochemical values and the microorganism data, and explain to what extent you want to associate them, someone may be able to provide some guidance. If you just want to make graphs of, say, dissolved oxygen versus the density of each organism, that might be straightforward. If you want to develop a model of many physiochemical variables predicting organism presence, that is probably more than can be done on a forum, though people will be able to point you towards literature from which you can learn how to do that.

OSDIAZ · August 26, 2019, 4:46pm

Sorry I couldn't attach the documents cause Im a new user, and
I can only attach a single image.

I am working with Excel.

In the first image, they are the results of the family of my microorganisms, in the second image they are the physicochemical parameters. I seek to make a relationship by sampling point (CAJ-1, CAJ-2, etc.), by the sampling period (JULY, AUGUST, SEPTEMBER), as well as by depth (80 cm and interstitial). I have already obtained some results such as relative abundance, permanova, histograms per sample. But I still have to do that boxplot as well as an RDA.

All support will be appreciated, and we can collaborate in the publication of the article, but I need help with this part of programming.

OSDIAZ · August 26, 2019, 4:47pm

andresrcs · August 26, 2019, 5:36pm

Please share your sample data on a copy/paste friendly format (screenshots are not very useful and also not a good thing to do here), here is a nice blog post by Mara that explains how to do it.

OSDIAZ · August 26, 2019, 6:49pm

I couldn't do it. I found u on fb, and I just sent the files by inbox. If this bother you, no worries I understand if don't reply me.

Thanks

andresrcs · August 27, 2019, 4:38am

You could have shared a link to your files here, but anyways I'm going to help you with the question in your topic title (you are not supposed to make different questions on the same thread) and later you can open a new topic for the other question.

This is a reproducible example of how to make a similar boxplot with your data

# Sample data on a copy/paste friendly format
metadata <- data.frame(stringsAsFactors=FALSE,
            SampleID = c("1A", "1B", "1C", "1D", "1E", "1F", "1G", "1H", "2A",
                         "2B", "2C", "2D", "2E", "2F", "2G", "2H", "3A", "3B",
                         "3C", "3D", "3E", "3F", "3G", "3H", "4A", "4B", "4C",
                         "4D", "4E", "4F", "4G", "4H", "5A", "5B", "5C", "5D",
                         "5E", "5F", "5G", "5H", "6A", "6B", "6C", "6D", "6E", "6F",
                         "6G", "6H", "7A", "7B", "7C", "7D", "7E", "7F", "7G",
                         "7H", "8A", "8B", "8C", "8D", "8E", "8F", "8G", "8H",
                         "9A", "9B", "9C", "9D", "9E", "9F", "9G", "9H", "10A",
                         "10B", "10C", "10D", "10E", "10F", "10G", "10H", "11A",
                         "11B", "11C", "11D", "11E", "11F", "11G", "11H", "12A",
                         "12B", "12C", "12D", "12E", "12F", "12G", "12H"),
       SamplingPoint = c("CAJ-1", "CAJ-2", "CAJ-4", "CAJ-1", "CAJ-3", "CAJ-5",
                         "CAJ-2", "CAJ-4", "CAJ-1", "CAJ-2", "CAJ-4", "CAJ-1",
                         "CAJ-3", "CAJ-5", "CAJ-2", "CAJ-4", "CAJ-1", "CAJ-2",
                         "CAJ-4", "CAJ-1", "CAJ-3", "CAJ-5", "CAJ-2", "CAJ-4",
                         "CAJ-1", "CAJ-3", "CAJ-4", "CAJ-1", "CAJ-3", "CAJ-5",
                         "CAJ-2", "CAJ-4", "CAJ-1", "CAJ-3", "CAJ-4", "CAJ-1", "CAJ-3",
                         "CAJ-5", "CAJ-2", "CAJ-4", "CAJ-1", "CAJ-3", "CAJ-5",
                         "CAJ-1", "CAJ-3", "CAJ-5", "CAJ-2", "CAJ-4", "CAJ-1",
                         "CAJ-3", "CAJ-5", "CAJ-2", "CAJ-4", "CAJ-1", "CAJ-3",
                         "CAJ-5", "CAJ-1", "CAJ-3", "CAJ-5", "CAJ-2", "CAJ-4",
                         "CAJ-1", "CAJ-3", "CAJ-5", "CAJ-2", "CAJ-3", "CAJ-5", "CAJ-2",
                         "CAJ-4", "CAJ-1", "CAJ-3", "CAJ-5", "CAJ-2", "CAJ-3",
                         "CAJ-5", "CAJ-2", "CAJ-4", "CAJ-1", "CAJ-3", "CAJ-5",
                         "CAJ-2", "CAJ-4", "CAJ-5", "CAJ-2", "CAJ-4", "CAJ-1",
                         "CAJ-3", "CAJ-5", "CAJ-2", "CAJ-4", "CAJ-1", "CAJ-2", "CAJ-4",
                         "CAJ-1", "CAJ-3", "CAJ-5"),
               Depth = c("80 cm", "80 cm", "Interstitial", "80 cm", "80 cm",
                         "80 cm", "80 cm", "80 cm", "80 cm", "Interstitial",
                         "Interstitial", "80 cm", "80 cm", "80 cm", "80 cm",
                         "80 cm", "Interstitial", "Interstitial", "80 cm",
                         "Interstitial", "Interstitial", "Interstitial", "Interstitial",
                         "Interstitial", "Interstitial", "80 cm", "Interstitial",
                         "Interstitial", "Interstitial", "Interstitial",
                         "Interstitial", "Interstitial", "80 cm", "80 cm", "Interstitial",
                         "80 cm", "80 cm", "80 cm", "80 cm", "80 cm", "80 cm",
                         "Interstitial", "80 cm", "80 cm", "Interstitial",
                         "Interstitial", "Interstitial", "Interstitial", "Interstitial",
                         "Interstitial", "80 cm", "80 cm", "80 cm", "80 cm",
                         "80 cm", "80 cm", "Interstitial", "80 cm", "Interstitial",
                         "80 cm", "80 cm", "80 cm", "80 cm", "80 cm", "80 cm",
                         "Interstitial", "Interstitial", "Interstitial",
                         "Interstitial", "Interstitial", "Interstitial", "Interstitial",
                         "80 cm", "Interstitial", "80 cm", "Interstitial",
                         "Interstitial", "Interstitial", "Interstitial", "Interstitial",
                         "Interstitial", "80 cm", "Interstitial", "80 cm", "80 cm",
                         "80 cm", "80 cm", "80 cm", "Interstitial", "80 cm",
                         "Interstitial", "Interstitial", "Interstitial",
                         "Interstitial", "Interstitial", "Interstitial"),
               Month = c("July", "July", "July", "August", "August", "August",
                         "September", "September", "July", "July", "July",
                         "August", "August", "August", "September", "September",
                         "July", "July", "July", "August", "August", "August",
                         "September", "September", "July", "July", "July", "August",
                         "August", "August", "September", "September", "July",
                         "July", "July", "August", "August", "August", "September",
                         "September", "July", "July", "July", "August", "August",
                         "August", "September", "September", "July", "July",
                         "July", "August", "August", "September", "September",
                         "September", "July", "July", "July", "August", "August",
                         "September", "September", "September", "July", "July",
                         "July", "August", "August", "September", "September",
                         "September", "July", "July", "July", "August", "August",
                         "September", "September", "September", "July", "July", "July",
                         "August", "August", "September", "September",
                         "September", "July", "July", "August", "August", "August",
                         "September", "September", "September"),
              Filter = c("20-25 um", "0.45 um", "20-25 um", "20-25 um",
                         "20-25 um", "20-25 um", "20-25 um", "20-25 um",
                         "0.45 um", "20-25 um", "0.45 um", "0.45 um", "0.45 um",
                         "0.45 um", "0.45 um", "0.45 um", "20-25 um", "0.45 um",
                         "0.45 um", "20-25 um", "20-25 um", "20-25 um", "20-25 um",
                         "20-25 um", "0.45 um", "20-25 um", "20-25 um", "0.45 um",
                         "0.45 um", "0.45 um", "0.45 um", "0.45 um", "20-25 um",
                         "0.45 um", "0.45 um", "0.45 um", "0.45 um", "0.45 um",
                         "0.45 um", "0.45 um", "0.45 um", "20-25 um", "20-25 um",
                         "20-25 um", "0.45 um", "0.45 um", "0.45 um", "0.45 um",
                         "20-25 um", "0.45 um", "0.45 um", "20-25 um", "20-25 um",
                         "20-25 um", "20-25 um", "20-25 um", "0.45 um",
                         "0.45 um", "20-25 um", "0.45 um", "0.45 um", "0.45 um",
                         "0.45 um", "0.45 um", "20-25 um", "20-25 um", "0.45 um",
                         "20-25 um", "20-25 um", "20-25 um", "20-25 um", "20-25 um",
                         "0.45 um", "0.45 um", "0.45 um", "0.45 um", "0.45 um",
                         "0.45 um", "0.45 um", "0.45 um", "20-25 um", "20-25 um",
                         "20-25 um", "0.45 um", "0.45 um", "0.45 um", "0.45 um",
                         "0.45 um", "0.45 um", "0.45 um", "0.45 um", "0.45 um",
                         "0.45 um", "0.45 um", "0.45 um", "0.45 um"),
     SampleorReplica = c("Sample", "Sample", "Sample", "Sample", "Sample",
                         "Sample", "Sample", "Sample", "Sample", "Sample",
                         "Sample", "Sample", "Sample", "Sample", "Sample", "Sample",
                         "Sample", "Sample", "Sample", "Sample", "Sample",
                         "Sample", "Sample", "Sample", "Sample", "Sample", "Replica",
                         "Sample", "Sample", "Sample", "Sample", "Sample",
                         "Replica", "Sample", "Replica", "Replica", "Replica",
                         "Replica", "Replica", "Replica", "Replica", "Sample", "Sample",
                         "Replica", "Replica", "Replica", "Replica", "Replica",
                         "Replica", "Sample", "Sample", "Sample", "Sample",
                         "Sample", "Sample", "Sample", "Replica", "Replica", "Sample",
                         "Sample", "Sample", "Sample", "Sample", "Sample",
                         "Sample", "Replica", "Sample", "Sample", "Sample", "Sample",
                         "Sample", "Sample", "Replica", "Replica", "Replica",
                         "Sample", "Sample", "Sample", "Sample", "Sample", "Replica",
                         "Sample", "Replica", "Replica", "Replica", "Replica",
                         "Replica", "Replica", "Replica", "Replica", "Replica",
                         "Replica", "Replica", "Replica", "Replica", "Replica"),
    Dissolved_oxygen = c(4.24, 2.58, 2.85, 3.81, 2.64, 4.61, 5.74, 3.69, 4.24,
                         2.66, 2.85, 3.81, 2.64, 4.61, 5.74, 3.69, 2.51, 2.66,
                         3.14, 2.92, 1.83, 1.82, 3.02, 3.3, 2.51, 3.04, 2.85,
                         2.92, 1.83, 1.82, 3.02, 3.3, 4.24, 3.04, 2.85, 3.81, 2.64,
                         4.61, 5.74, 3.69, 4.24, 2.09, 2.98, 3.81, 1.83, 1.82,
                         3.02, 3.3, 2.51, 2.09, 2.98, 8.17, 2.63, 7.69, 3.07, 3.7,
                         2.51, 3.04, 2.18, 8.17, 2.63, 7.69, 3.07, 3.7, 2.58,
                         2.09, 2.18, 2.16, 1.7, 6.8, 1.95, 4.28, 2.58, 2.09, 2.98,
                         2.16, 1.7, 6.8, 1.95, 4.28, 2.66, 3.14, 2.18, 8.17, 2.63,
                         7.69, 3.07, 3.7, 2.66, 3.14, 2.92, 2.16, 1.7, 6.8,
                         1.95, 4.28),
                  pH = c(9.94, 10.06, 9.98, 9.07, 8.99, 8.93, 9.24, 9.32, 9.94,
                         10, 9.98, 9.07, 8.99, 8.93, 9.24, 9.32, 10.04, 10, 10,
                         9.06, 8.99, 8.92, 9.18, 9.32, 10.04, 9.96, 9.98, 9.06,
                         8.99, 8.92, 9.18, 9.32, 9.94, 9.96, 9.98, 9.07, 8.99,
                         8.93, 9.24, 9.32, 9.94, 9.95, 10.09, 9.07, 8.99, 8.92,
                         9.18, 9.32, 10.04, 9.95, 10.09, 9.04, 9, 9.53, 9.31, 9.14,
                         10.04, 9.96, 9.97, 9.04, 9, 9.53, 9.31, 9.14, 10.06,
                         9.95, 9.97, 8.96, 9.02, 9.51, 9.39, 8.85, 10.06, 9.95,
                         10.09, 8.96, 9.02, 9.51, 9.39, 8.85, 10, 10, 9.97, 9.04, 9,
                         9.53, 9.31, 9.14, 10, 10, 9.06, 8.96, 9.02, 9.51, 9.39,
                         8.85),
   Water_temperature = c(24.48, 24.95, 24.01, 26.67, 24.01, 23.5, 24.46, 24.65,
                         24.48, 24.92, 24.01, 26.67, 24.01, 23.5, 24.46, 24.65,
                         24.35, 24.92, 24, 26.46, 23.99, 23.43, 24.14, 24.67,
                         24.35, 24.04, 24.01, 26.46, 23.99, 23.43, 24.14, 24.67,
                         24.48, 24.04, 24.01, 26.67, 24.01, 23.5, 24.46, 24.65,
                         24.48, 24.01, 24.36, 26.67, 23.99, 23.43, 24.14, 24.67,
                         24.35, 24.01, 24.36, 24.88, 24.7, 26.14, 24.19, 22.65,
                         24.35, 24.04, 24.4, 24.88, 24.7, 26.14, 24.19, 22.65, 24.95,
                         24.01, 24.4, 24.3, 24.72, 26.15, 23.9, 20.65, 24.95,
                         24.01, 24.36, 24.3, 24.72, 26.15, 23.9, 20.65, 24.92, 24,
                         24.4, 24.88, 24.7, 26.14, 24.19, 22.65, 24.92, 24,
                         26.46, 24.3, 24.72, 26.15, 23.9, 20.65),
           Turbidity = c(87.3, 95.2, 98.8, 24.9, 43.1, 49.1, 68.6, 69.8, 87.3,
                         113, 98.8, 24.9, 43.1, 49.1, 68.6, 69.8, 87.7, 113,
                         96.9, 39.7, 49, 47.6, 66.6, 74.1, 87.7, 98.5, 98.8, 39.7,
                         49, 47.6, 66.6, 74.1, 87.3, 98.5, 98.8, 24.9, 43.1,
                         49.1, 68.6, 69.8, 87.3, 95.9, 97.2, 24.9, 49, 47.6, 66.6,
                         74.1, 87.7, 95.9, 97.2, 46.9, 37.2, 74.2, 69.9, 71.3,
                         87.7, 98.5, 100.6, 46.9, 37.2, 74.2, 69.9, 71.3, 95.2, 95.9,
                         100.6, 42, 36.1, 74.4, 44.4, 71.3, 95.2, 95.9, 97.2,
                         42, 36.1, 74.4, 44.4, 71.3, 113, 96.9, 100.6, 46.9, 37.2,
                         74.2, 69.9, 71.3, 113, 96.9, 39.7, 42, 36.1, 74.4, 44.4,
                         71.3),
                 ORP = c(97, 108.4, 102.9, 94, 63.9, 64.7, 40.3, 48.1, 97,
                         111.9, 102.9, 94, 63.9, 64.7, 40.3, 48.1, 91.3, 111.9,
                         108, 23.7, 64.1, 60.4, 40.6, 49.8, 91.3, 98.9, 102.9,
                         23.7, 64.1, 60.4, 40.6, 49.8, 97, 98.9, 102.9, 94, 63.9,
                         64.7, 40.3, 48.1, 97, 92.8, 106.9, 94, 64.1, 60.4, 40.6,
                         49.8, 91.3, 92.8, 106.9, 90.4, 74.9, 67.7, 42, 37.1,
                         91.3, 98.9, 102.7, 90.4, 74.9, 67.7, 42, 37.1, 108.4,
                         92.8, 102.7, 53, 63.4, 73.9, 42, 37.5, 108.4, 92.8, 106.9,
                         53, 63.4, 73.9, 42, 37.5, 111.9, 108, 102.7, 90.4, 74.9,
                         67.7, 42, 37.1, 111.9, 111.9, 23.7, 53, 63.4, 73.9, 42,
                         37.5),
            Ammonium = c(4.46, 4.62, 4.37, 5.6, 3.38, 3.21, 1.93, 2.21, 4.46,
                         4.75, 4.37, 5.6, 3.38, 3.21, 1.93, 2.21, 4.5, 4.75,
                         4.48, 7.64, 3.18, 3.09, 2.19, 2.14, 4.5, 3.97, 4.37, 7.64,
                         3.18, 3.09, 2.19, 2.14, 4.46, 3.97, 4.37, 5.6, 3.38,
                         3.21, 1.93, 2.21, 4.46, 4.06, 4.43, 5.6, 3.18, 3.09, 2.19,
                         2.14, 4.5, 4.06, 4.43, 2.81, 4.2, 4.5, 1.99, 2.07, 4.5,
                         3.97, 5.47, 2.81, 4.2, 4.5, 1.99, 2.07, 4.62, 4.06,
                         5.47, 3.19, 3.97, 3.3, 3.38, 1.18, 4.62, 4.06, 4.43, 3.19,
                         3.97, 3.3, 3.38, 1.18, 4.75, 4.48, 5.47, 2.81, 4.2, 4.5,
                         1.99, 2.07, 4.75, 4.48, 7.64, 3.19, 3.97, 3.3, 3.38,
                         1.18),
            Nitrates = c(3.6, 3.98, 3.57, 3.53, 2.55, 2.28, 0.71, 1.2, 3.6,
                         3.21, 3.57, 3.53, 2.55, 2.28, 0.71, 1.2, 3.36, 3.21,
                         3.76, 3.66, 2.44, 2.06, 0.67, 0.87, 3.36, 4.35, 3.57,
                         3.66, 2.44, 2.06, 0.67, 0.87, 3.6, 4.35, 3.57, 3.53, 2.55,
                         2.28, 0.71, 1.2, 3.6, 3.68, 3.34, 3.53, 2.44, 2.06,
                         0.67, 0.87, 3.36, 3.68, 3.34, 2.25, 2.99, 1.3, 0.74, 0.68,
                         3.36, 4.35, 4.11, 2.25, 2.99, 1.3, 0.74, 0.68, 3.98,
                         3.68, 4.11, 2.1, 2.55, 1.11, 0.69, 0.69, 3.98, 3.68, 3.34,
                         2.1, 2.55, 1.11, 0.69, 0.69, 3.21, 3.76, 4.11, 2.25,
                         2.99, 1.3, 0.74, 0.68, 3.21, 3.76, 3.66, 2.1, 2.55, 1.11,
                         0.69, 0.69),
    Blue_Green_Algae = c(279133, 279113, 265304, 11603, 218471, 226658, 267389,
                         267144, 279133, 270193, 265304, 11603, 218471, 226658,
                         267389, 267144, 267716, 270193, 279119, 66608, 213497,
                         242331, 267007, 261363, 267716, 279109, 265304, 66608,
                         213497, 242331, 267007, 261363, 279133, 279109, 265304,
                         11603, 218471, 226658, 267389, 267144, 279133, 279100,
                         279099, 11603, 213497, 242331, 267007, 261363, 267716,
                         279100, 279099, 246979, 169175, 272332, 269519, 272096,
                         267716, 279109, 278137, 246979, 169175, 272332, 269519,
                         272096, 279113, 279100, 278137, 174271, 159046, 271503,
                         261124, 271303, 279113, 279100, 279099, 174271, 159046,
                         271503, 261124, 271303, 270193, 279119, 278137, 246979,
                         169175, 272332, 269519, 272096, 270193, 279119, 66608,
                         174271, 159046, 271503, 261124, 271303),
          Chlrophyll = c(36.6, 38.9, 40, 44, 35, 32.8, 44, 44.8, 36.6, 39.8,
                         40, 44, 35, 32.8, 44, 44.8, 39.6, 39.8, 38.5, 45.1,
                         42.2, 50.2, 43.6, 45.1, 39.6, 43, 40, 45.1, 42.2, 50.2,
                         43.6, 45.1, 36.6, 43, 40, 44, 35, 32.8, 44, 44.8, 36.6,
                         50, 43, 44, 42.2, 50.2, 43.6, 45.1, 39.6, 50, 43, 34,
                         38.4, 58.5, 44.3, 40, 39.6, 43, 53.8, 34, 38.4, 58.5, 44.3,
                         40, 38.9, 50, 53.8, 50.3, 55.9, 51.3, 68.2, 34.2, 38.9,
                         50, 43, 50.3, 55.9, 51.3, 68.2, 34.2, 39.8, 38.5, 53.8,
                         34, 38.4, 58.5, 44.3, 40, 39.8, 38.5, 45.1, 50.3, 55.9,
                         51.3, 68.2, 34.2)
)

library(tidyverse)

metadata %>% 
    select(Depth, Dissolved_oxygen:Chlrophyll) %>% 
    gather(Parameter, Value, -Depth) %>% 
    ggplot(aes(Depth, Value, fill = Depth)) +
    geom_boxplot(show.legend = FALSE) +
    facet_wrap(~Parameter, scales = "free_y") +
    theme_light()

^{Created on 2019-08-27 by the reprex package (v0.3.0.9000)}

OSDIAZ · September 2, 2019, 7:21pm

Muchas gracias Andres, fue de mucha ayuda el script que me enviaste. Mil mil gracias.

system · September 11, 2019, 8:56pm

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