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Nanostring-Biostats / GeoMxWorkflows

Workflows for analyzing data with the GeomxTools package and subsequent GeoMx related packages
MIT License
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Plotting genes of interest issue (ggplot plotting random points?) #26

Open Doc-R-J opened 1 year ago

Doc-R-J commented 1 year ago

Hi all,

I'm finding plotting genes of interest using the following code seems to be just randomly assigning values. It also isn't plotting the violin shape.

show expression for a single target: PDHA1 ggplot(pData(target_demoData), aes(x = region, fill = region, y = assayDataElement(target_demoData["PDHA1", ], elt = "q_norm"))) + geom_violin() + geom_jitter(width = .2) + labs(y = "PDHA1 Expression") + scale_y_continuous(trans = "log2") + facet_wrap(~class) + theme_bw()

For clarity: this vignette (https://bioconductor.org/packages/release/workflows/vignettes/GeoMxWorkflows/inst/doc/GeomxTools_RNA-NGS_Analysis.html#10_Session_Information) is showing what I am seeing, whereas the vignette in this link (https://bioconductor.org/packages/devel/workflows/vignettes/GeoMxWorkflows/inst/doc/GeomxTools_RNA-NGS_Analysis.html#10_Session_Information) is showing what I should be seeing.

It looks like there are different versions of ggplot2 being used. I've tried using the older version of ggplot2 but it seems to be incompatible with GeoMx tools.

Any suggestions?

many thanks in advance

maddygriz commented 1 year ago

Hi @Doc-R-J,

Thank you for reaching out. Our customer support team will be able to help you with this. Please email support@nanostring.com with your issue.

Thanks, Maddy