HelenaLC
commented
4 years ago - The default argument is
features = "state". In your case, all features are type, hence "No features matched he specified marker class". UsingplotPbExprs(sce, facet_by = "antigen", ncol = 4)withfeatures = "type"or= NULL(= plot all features) should resolve this. - I ran your function call with the example data from the package and did not get an error, so not sure why this is failing. What's the output for
colData(sce)? What do thesample_ids look like (table(sce$sample_id))? If you could come up with a minimal example with the example data from the package that'd help!
# this doesn't fail
data(PBMC_fs, PBMC_panel, PBMC_md)
sce <- prepData(PBMC_fs, PBMC_panel, PBMC_md)
sce <- cluster(sce, verbose = FALSE)
plotPbExprs(sce, features = "type",
facet_by = "antigen", color_by = "sample_id",
size_by = TRUE, geom = "points", jitter = FALSE, ncol = 5)
bioguy2018
JudithBernett
Dear developers, I have faced a problem while running the function plotPbExprs() on my dataset. I get the following error:
plotPbExprs(sce, facet_by = "antigen", ncol = 4)I have checked my panel and my md files and everything looks fine there and I do have a col as antigen followed another col to specify type or state (in my case all are types) so I can't get why is it happening.
I also get the error message in the following modified version of the code:
> plotPbExprs(sce, features = "type", facet_by = "antigen", color_by = "condition", size_by = TRUE, geom = "points", jitter = FALSE, ncol = 5)I am not sure why it is happening cause with color_by = "sample_id" the code works.