Question

Error when plotting flow cytometry data

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alex • 0

@222f89de

Last seen 2.1 years ago

Germany

Hi everyone, I just started to use R for flow cytometry analysis and its hard for me to get behind. I never asked any question online and hope that I managed to post here accordingly, but I have a problem that I can't fix.

I'm using read.flowSet to read my .fcs files from an experiment. After gating and transformation of the flowset, I try to plot my flowset as stacked density plots as described here: https://www.bioconductor.org/packages/devel/bioc/vignettes/ggcyto/inst/doc/ggcyto.flowSet.html

When I try to plot however with

ggcyto(T_Singlets_MyFlowSet, aes(x="BV421-A")) + geom_density_ridges(aes(y=name))

I get an error:

Error in max(data$y) - min(data$y) : 
  non-numeric argument to binary operator

Could this error occur because my "name" vector in the phenodata dataframe is off the class " 'AsIs' chr" and not "chr" ?? This is at least the most obvious difference for me between teh flowset from I get from reading my experiment files vs. the flowset I get from https://www.bioconductor.org/packages/devel/bioc/vignettes/ggcyto/inst/doc/ggcyto.flowSet.html

I would be super happy if someone could help me. I really don't know a lot about this kind of stuff

FlowCytometry flowCore ggcyto • 2.1k views

ADD COMMENT • link updated 2.2 years ago by SamGG ▴ 350 • written 2.2 years ago by alex • 0

score 0 · Answer 1 · 2022-09-23

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SamGG ▴ 350

@samgg-6428

Last seen 10 hours ago

France/Marseille/Inserm

Welcome!

The most obvious solution sounds to use a backtick ` instead of double quote ".

Check carefully the vignette I think this is the point.

Best.

ADD COMMENT • link 2.2 years ago SamGG ▴ 350

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Thanks for the reply! I get the same error when using backticks instead of quotes.

ADD REPLY • link 2.2 years ago alex • 0

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ggplot(T_Singlets_MyFlowSet, aes(x = `BV421-A`, fill = name)) + geom_density(alpha = 0.2)

same error with previous code?

ADD REPLY • link 2.2 years ago SamGG ▴ 350

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This works!

ADD REPLY • link 2.2 years ago alex • 0

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ggplot(T_Singlets_MyFlowSet, aes(x = `BV421-A`)) + geom_density_ridges(aes(y=name))

also works?

ADD REPLY • link 2.2 years ago SamGG ▴ 350

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Nope. This again results in the error

Error in max(data$y) - min(data$y) : 
  non-numeric argument to binary operator

ADD REPLY • link 2.2 years ago alex • 0

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Test your hypothesis. Change the type of the name column.

pData(T_Singlets_MyFlowSet)[,"name"] = as.character(pData(T_Singlets_MyFlowSet)[,"name"])

If the display still fails, please run the following code and return the result.

sapply(pData(T_Singlets_MyFlowSet), class)
sapply(pData(T_Singlets_MyFlowSet), typeof)

ADD REPLY • link 2.2 years ago SamGG ▴ 350

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It worked!!! I can also use

ggcyto(T_Singlets_MyFlowSet, aes(x="BV421-A")) + geom_density_ridges(aes(y=name)) + facet_null()

now to plot as I intented. I guess then, the problem was that "name" wasn't classified as character, but I didn't know how to fix it. Thank you so so much!! this was giving me so much headaches

ADD REPLY • link 2.2 years ago alex • 0

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Great! If the error occurs again, it would be useful to understand where it comes from.

Best.

ADD REPLY • link 2.2 years ago SamGG ▴ 350