topic Re: Adding the user-defined error interval option to the graph builder in Discussions

Adding the user-defined error interval option to the graph builder

dainius — Sun, 11 Jun 2023 11:07:21 GMT

Is it possible to plot the mean and then add a summary statistics from Points-Summary Statistic as a separate error interval, which you define Yourself?

Because calculating mean and SD in different columns in JMP is very easy, but then adding them together and plotting them as a dot and error bars does not function. And this is frankly very annoying because this feature is present in many other statistical softwares :).

Hereby is my suggestion for further JMP development - make a 'USER DEFINED STATISTICS' as a possibility to add as an error bar (Error Interval).

Then one could calculate and define SD separately in a separate column from a biological triplicate - and so plot them together on top of each other in all possible conditions and variations, voila.

I could see this feature is lacking for some time already (from discussion trends), and all alternatives to solve this issue around are very clumsy and code-requiring.

Thank you :)

Re: Adding the user-defined error interval option to the graph builder

Dan_Obermiller — Wed, 28 Oct 2020 13:23:27 GMT

Have you seen the Interval drop zone in Graph Builder? I think this is what you are looking for:

Re: Adding the user-defined error interval option to the graph builder

dainius — Wed, 28 Oct 2020 13:48:24 GMT

Aha, now I see what it is doing finally. So you are saying this is a completely user-defined interval?
If so, how can you make it thicker and more visible in on the plot?
Because it appears super finely drawn and I cannot see it nicely.
What should I change in the general preferences to make it always happen - i.e. to always draw a thick line and visible end bars?

Thank you :).

Re: Adding the user-defined error interval option to the graph builder

dainius — Sun, 01 Nov 2020 20:22:20 GMT

I have added the intervals as suggested, but frankly I do not understand what it is.

Now it is plotted as: Mean as a dot +/-SD as bars

And I have zoomed in the graph.

1. Why are they different widths? What else is plotted there as a thick line - a median or a mean of my SD? How do I get rid of it then?

2. Then, how does each bar relate to the mean - how are they connected, which mean belongs to which bars? Can one just make a line going through the center of the points as in all other stat softwares?

I cannot easily understand. I think this could be improved...?

Re: Adding the user-defined error interval option to the graph builder

Dan_Obermiller — Mon, 06 Dec 2021 14:25:22 GMT

I can't really tell how you created your graph, but it looks like you do not have a grouping variable defined, so you are getting intervals for each data point. See this example:

I had a data table with 3 columns: Group, Y, and Interval.

I drug the Y column to the Y-axis. I then drug Group to the X-axis and Interval to the Interval role to create the graph. Note that the Interval column is only needed because you wanted a Custom interval. If you just want something standard, you can drag the Y variable into the Interval role and specify the statistic you want to create the interval.

I believe this is the type of interval graph that most people expect. Perhaps if you share a bit more of your problem setup (or a fictional example of your data), people will be able to help more.

Re: Adding the user-defined error interval option to the graph builder

dainius — Fri, 30 Oct 2020 08:14:13 GMT

Dear Dan,

yes - I would like to get the error bars for each point, correct.

I have created a sample zoo-dataset, where I would like to plot the animal mean weight +/-SD in different temperatures.

And I have SD calculated for each animal in each temperature. That is, I have weighted my elephant three times using the same scales and then calculated the mean and the SD for each animal at each temperature.

Let's agree that SD of a duck kept at 37 C has nothing to do with the SD of the elephant kept in 54 C, because 1. the used scales can be different, 2. days the measurement has been done can also be different and 3. one veterinarian which weighs animals has a better eye to spot things more precisely compared to the other one. So I cannot always agree to use a combined SD from all the means and all temperatures and then put the same one on all experiments in all temperatures and days etc. I know it is easier, but this is incorrect in my particular case. Therefore, I plot SD for each animal independently.

Sorry, the internet was not working yesterday so I could not upload the dataset.

Re: Adding the user-defined error interval option to the graph builder

Dan_Obermiller — Fri, 30 Oct 2020 15:51:37 GMT

Question about your example dataset: Is each row a specific animal? For example, row 1 is a Cow with an average of 200, standard deviation of 3. Was it the same cow measured multiple times? If so, do you have the raw data (that is, each measurement)?

Because you have such a large discrepancy in the means and standard deviations, the graph will always be difficult to read. The ducks around 2.5 with standard deviations around 0.4 are going to look very low and tight since elephants are round 510.

Re: Adding the user-defined error interval option to the graph builder

dainius — Mon, 02 Nov 2020 08:59:09 GMT

My idea is that the cow with the ID 1 has been measured 3 times at 37C and this is how I got the mass and SD from it.

And then experiment ID 2 is another cow, but measured at 54C in the same triplicate way.

So these are two independent cows effectively - and I don't want to join their SDs together from 6 measurements.

Because maybe measurements on cow 1 was done by a sloppy technician and on cow 2 by a good technician.

In my original dataset with bacteria the numbers are more alike each other, so I have no Duck-Elephant comparisons.

But still, I don't want to plot a joint mass SD of all samples. I would want to plot them separately.

Re: Adding the user-defined error interval option to the graph builder

dainius — Mon, 02 Nov 2020 09:18:50 GMT

I have added a dataset with raw data. If you were asking this, cows at row 1 and row 11 are also different cows (let us call them A and B). I just plot them together side by side at 37 with their own means and their own SDs. And cows at row 2 and 12 are also different (let us call them C and D). So I have 4 cows in total, two measured in 37 two at 54 - by random technicians in random days, independent samples etc etc.

Re: Adding the user-defined error interval option to the graph builder

Dan_Obermiller — Mon, 02 Nov 2020 16:21:43 GMT

That is what I thought. In order to keep the intervals from being combined, you need to specify the animal ID as part of the graph. Otherwise there is no way for JMP to know that the first cow is different from the second cow. You can create this from the summary table like this:

But you do not need to have the table summarized. From the raw data, I stacked the measurement columns (data table is attached). I then put the mass measurement as the Y and as the interval, animal as the X-axis and Experiment ID as the nested x-axis variable. Because the animals are so different, the scale is too small to see the error bars, so I added a local data filter that would allow me to choose the animal type to see the graph more easily. That is saved as a script on the data table.

Re: Adding the user-defined error interval option to the graph builder

dainius — Tue, 03 Nov 2020 09:14:02 GMT

Dear Dan,

I could reproduce the plot - thank you. Is it also possible to draw a line in the middle, like I have shown? You could imagine it would be nice to know which intervals belong to which animal, especially if there are close to each other or even overlap.

Is there also another way (in principle) to do it, where the categories do not need to be nested? I have tried to plot it.

Because imagine if I have 200 deers and 200 cows besides each other, then the nested graph becomes quite wide you see :).

I usually have some measurement (size mass diameter) in triplicates, arranged in columns besides - exactly as in the animal example. How to plot the mean and SD graph of this without pain? The only way I see it in JMP is to calculate the Parameter_mean and Parameter_SD as two separate columns and then plot them on top of each other. Or am I wrong, maybe there is a more clever way?

Thanks,
D.

Re: Adding the user-defined error interval option to the graph builder

Dan_Obermiller — Tue, 03 Nov 2020 13:21:04 GMT

I am confused by the line. By default, you do have a line connecting the ends of the interval as shown (made easier to see by choosing one of the animals from the local data filter):

If you are wanting to change the color of the line, you can change the color of the entire error bar (along with other elements of the error bar), by right-clicking the graph and choosing Customize.

I believe the nesting will be necessary because you are wanting to have each animal graphed separately. If you have 200 animals, you are going to need 200 error bars. Even your example is nesting, but you are making the nested variable much closer. JMP just provides the information on WHICH animal you are looking at, which is lost on your example. Further, your example is nice if the animals are quite different. But if they are very close in weight you may not see the intervals even be separated. Ultimately, the more levels/animals you have, the closer JMP will put them. If you double-click the axis you can see some items that you may wish to change to try to make them more legible.

Finally, if each measurement goes into a column, it is easy to get into the format that I used. You use the Tables > Stack Columns command. If you look at the Source script that was in my earlier post, you will see the exact command that was used from your example table. Reading the script should tell you how to fill out the interactive dialog box.

Re: Adding the user-defined error interval option to the graph builder

dainius — Wed, 04 Nov 2020 07:57:27 GMT

Dear Dan,

Thank you. Now I have solved the line thing. When you add on the grid and the x axis and the SD line - and they are of the same width, the grid is put above the line so it disappears. To see it through the grid, the SD line needs to have a thickness of min 2, if the grid has a thickness of 1.

Which, in my opinion, is not an optimal default line arrangement. Can it be changed?

Re: Adding the user-defined error interval option to the graph builder

Dan_Obermiller — Wed, 04 Nov 2020 16:00:31 GMT

I do see the same issue as you. I looked through all of the preferences, both in the Graph section and under Platforms > Graph Builder. I do not see an option to change the default width of the error bar. Perhaps someone else can find an option somewhere? It sounds like you should look at the JMP Wish List. If someone has already suggested this, vote for it. If this item is not there, you should add it.

Of course the "easy" answer is to turn off the grid for the x-axis as you can add dividers between the "animals". But this is not a very good answer in my opinion.