Data Plots

Looking for ways to analyze your dataset? Need help with a software package?
Computational image analysis of multiplexed Imaging Mass Cytometry acquisitions
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Scott
Posts: 2
Joined: Tue Jul 31, 2018 1:09 pm

Data Plots

Post by Scott » Wed Aug 01, 2018 1:03 pm

Hello,

I have managed to segment the images on Histocat++ and get values, for example for the cell median which nicely populate the Data Values tab. However, if I try to use the Plot option after installing the two R packages (ggplot2 and RColorBrewer) and choose two different channels for the x and y axis, Histocat++ becomes unresponsive and no plots are generated.

I was wondering whether anyone else has had similar issues and if there is a way of extracting the data values from Histocat++ to process them in R separately.

Would be grateful for any help and ideas.

Scott

RaulCatena
Posts: 30
Joined: Mon Nov 27, 2017 12:49 pm

Re: Data Plots

Post by RaulCatena » Mon Aug 06, 2018 10:41 am

Hi Scott,

The functions are not well documented yet. Again, it will all be explained in detail in the upcoming manual.
Meanwhile, let me just give you a pointer on how it basically works.

Double click on the channels that you are interested. The rows will become orange. Double click to remove them from the list of channels of interest.

You may select any of the channels as X, Y, color or shape. It will probably break it you select a color but not X, and or Y.
Depending on the type of plot that you select above, it will require Y or not.

For the sake of giving an example. Select scatter plot. Get two channels in orange by double clicking, and then select as X and Y those channels. click the refresh button in the lower-right corner and you should see the plot.

In the list selectors below, you will see that there is an option called CompId. This allows you to use the cell data objects as variables.
Cell data objects are the cell feature extractions. They are all listed under "Cell data" in the explorer column in the top left.

If you select only one cell data object (the data coming from one mask) the you see that data in the plot. If you select several, then you will see one plot will all the data together. If you select several, and you do for instance CompId as the TilesX factor, then you will get plot faceting (I assume that you are somewhat familiar with ggplot2).

Remember to click the refresh button on the lower right of the plot tab anytime you do a change.

Let me know whether this leads you somewhere.

Scott
Posts: 2
Joined: Tue Jul 31, 2018 1:09 pm

Re: Data Plots

Post by Scott » Wed Aug 08, 2018 2:46 pm

Thank you for the quick response!

This has indeed helped andthe program is not freezing anymore however, I am still struggling to have a graph appear.
I am able to select two different channels and choose one for the x and y but when I press the refresh button to produce a graph there is a short pause but no graphs appear. Is there a possible plug-in I might be missing?

RaulCatena
Posts: 30
Joined: Mon Nov 27, 2017 12:49 pm

Re: Data Plots

Post by RaulCatena » Wed Aug 08, 2018 2:51 pm

Hi Scott,

Please contact me at raulcatena@gmail.com and let's try to quickly troubleshoot this offline the forum.

Regards,

Raúl

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