Multiple different errors using Plot2

[k-ohare]

I have been trying to use Compass to analyze an experiment with multiple stimulation conditions to look at 4 different markers. I have created Compass results for two conditions and am trying to plot them together using the plot2 function.

The first error I encountered was:

Error in plot2(fit_tcr, fit_vim) :
Internal error: could not match categories between the matrices from 'x' and 'y'
In addition: Warning message:
In colnames(M_x) == colnames(M_y) :
longer object length is not a multiple of shorter object length

Looking back, it seems that when the compass results were generated, one condition generated 16 categories and the other only generated 15 categories despite coming from the same CompassContainer and having the category filter set to 0, so that no categories get filtered out.

Is there a work around to enforce that the same number of categories are tested for each analysis?

Additionally, when I attempted to plot 2 conditions that both tested 16 categories I encountered this error:

Error in if (any(0 > rgb) || any(rgb > 1)) stop("rgb values must be in [0, maxColorValue]") :
missing value where TRUE/FALSE needed
In addition: There were 15 warnings (use warnings() to see them)

The expanded warnings showed:
In FUN(X[[i]], ...) : NAs introduced by coercion (repeated 15 times)

Is there a TRUE/FALSE argument that I am missing in the function causing this?

Thanks in advance.