How to Ignore one of the factors in a Column

I think you can replace "" and 9999 by NA values before plotting. There is several ways to do that depending on the tools you want to use.

naniar :package: has really good tools for dealing with missing values. Among theme, you'll find naniar::replace_with_na that will do the job.

You can also recode your column (with dplyr's recode, if_else or case_when) to replace the values.

As you deal with factor, you may need more factors oriented tools. There are dplyr::recode_factor or even forcats::fct_recode where you can remove levels easily. forcats is the toolbox for factors in the tidyverse.

Indeed, you can also do it with base R too. At the end, it is as you like. :wink:

If you manage to provide a reprex, we can be sure it is the issue and we can work on an example for you.

rem: I also edited your post for formatting purposes