Open Doc-R-J opened 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
Hi @Doc-R-J,
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Thanks, Maddy
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