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plot_genes_in_pseudotime error #171

Open csbbcompbio opened 6 years ago

csbbcompbio commented 6 years ago

Hi Monocle Developers !!

I am facing this error when using plot_genes_in_pseudotime. Error in attributes(out) <- attributes(col) : 'names' attribute [2404] must be the same length as the vector [1]

Can you please help with this.

Cheers !!

Praneet

tkiehl commented 6 years ago

Several folks looking for solutions to the problem, myself included see #88 and #153

Xiaojieqiu commented 6 years ago

hi @tkiehl and @csbbcompbio, the error is kind cryptic for me. This may happen when the function tries to assign the row or column names for some dataframe but the things to be assigned has inconsistent length to the dimension of data frame. My guess is that you are only applying plot_genes_in_pseudotime on a single gene? Can you try to plot multiple genes at once?

Alternatively, if you can share a subset of your data with me to reproduce the error, I can then take a more close look for you soon.

tkiehl commented 6 years ago

I got the error when I was trying to plot multiple genes. I'm not sure it's feasible for me to share my data at this time.

ghost commented 5 years ago

Hey, @tkiehl @csbbcompbio @Xiaojieqiu, If the parameter "data" in phenoData and featureData were constructed step by step, for example,

  1. variables <- data.frame(Va = c(x, x, x), Vb = c(y, y, y))

  2. rownames(variables) <- colnames(expr_matrix)

  3. pd <- new('AnotateDataFrame', data = variables ) ,

everything would be fine. But if "data" was just a subset or slices of existed data frame or transfered from other data type, like matrix, there would be "Error in attributes(out) <- attributes(col) : 'names' attribute [...] must be the same length as the vector [1]" when runing _plot_genes_inpseudotime.

saeedfc commented 5 years ago

@MushanLie Nice fix! Worked Thanks