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saeyslab / CytoNorm

R library to normalize cytometry data
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Error in rep(NA, (width - length(x))) : invalid 'times' argument #2

Open SansMorel opened 4 years ago

SansMorel commented 4 years ago

Hi, I am having a problem running testCV. After running prepareFlowSOM on my reference samples I try to run testCV but get the error in the title.

I believe the error originates from this line: https://github.com/saeyslab/CytoNorm/blob/ab58f29f29812a9f0b0bc721787c41cf2b75426e/R/evaluation.R#L211 Perhaps because length(x)>width.

SansMorel commented 4 years ago

I think the error might be caused by the default value of cluster_values parameter in testCV. If cluster_values is set to a cluster that doesn't exist (for example through using the default parameter) the error seems to occur. Perhaps an error message could be displayed if cluster_values is set to a nonexistent cluster?

tomashhurst commented 4 years ago

@SansMorel I came up with the same error. After pulling the function apart, the first problem comes up in this part of testCV, at the end of the function:

res <- named.list(pctgs, cvs, meta_cl) if(plot){ PlotOverviewCV(fsom, res) }

and specifically: PlotOverviewCV(fsom, res) returns:

Error in rep(NA, (width - length(x))) : invalid 'times' argument

So the issues is in the PlotOverviewCV function, which is defined just below it. The issue comes up here:

cv_matrix <- do.call(rbind, lapply(cvs[as.character(cluster_values)], function (x) { c(x, rep(NA, (width - length(x)))) }))

tomashhurst commented 4 years ago

So yes, it carries the cluster_values value the whole way through to that point. If you change it fro c(5, 10, 15) to c(5, 10) then it works fine.

SofieVG commented 4 years ago

@SansMorel @tomashhurst I just pushed a fix for this issue, thanks for pointing it out and figuring out where it went wrong! Let me know if you still run into any related problems.