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HaojiaWu / plot1cell

A R package for advanced single cell data viz
MIT License
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Error while using the complex_dotplot_single() function #2

Closed aditisk closed 1 year ago

aditisk commented 1 year ago

Hi @HaojiaWu,

Thank you so much for developing this package with the new plotting capabilities. I am trying to follow the tutorial and running into an error. I have a very large seurat object so I subsetted the object before trying to plot. My code is pasted below with the error message:

Saving the plot since I keep getting an error in RStudio to plot in the plotting window

ggsave(complex_dotplot_single(cd8, feature = "HAVCR2",groups = cd8@meta.data$Treatment,splitby = "Timepoint"),"test.png",device = "png")

Error is pasted below

Warning: Found the following features in more than one assay, excluding the default. We will not include these in the final data frame: HAVCR2 Warning: Could not find RELA in the default search locations, found in RNA assay instead Error in names(x) <- value : 'names' attribute [36604] must be the same length as the vector [3] In addition: Warning message: In FetchData.Seurat(new_seu, slot = data.type, vars = c(features, : The following requested variables were not found: HAVCR2, NIVO, IPI

Please let me know if I am missing something that is triggering this error. If I use the same command without the "splitby" argument, it works just fine, and I am able to generate the plot.

Thanks a lot.

HaojiaWu commented 1 year ago

Thanks for your interest in using our package. Can you try the codes below? Note that the groups argument should be the column name in your Seurat metadata (not the actual values in the column). 

png(filename =  'test.png', width = 4, height = 6, units = 'in', res = 300)
complex_dotplot_single(cd8, feature = "HAVCR2", groups = "Treatment", splitby = "Timepoint")
dev.off()
aditisk commented 1 year ago

Thank you so much, the code above works - specifying the column names was the part I was doing wrong.