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Without having a look at the whole `user_interaction_input_no_duplicates.csv` it's hard to tell. But, like the error suggests, perhaps there are duplicated `id_cp_interaction` in the input file.

Hi @pidoc, could you provide a minimal set of input files to reproduce this error? That would help us debug the issue.

@msalaciak @DrMaestre could you provide sample files to reproduce this error? (`meta.txt`, `means.txt` and `pvalues.txt`)

Hi @TehseusKunka "Plan shapes are not aligned" is a pandas error. Does the test data work on your environment or you get the same error? Before looking more into this,...

Hi @nobie666 thank you for using CellPhoneDB. Looks like you've got the order of the arguments wrong. You need to provide the **meta first** and then **counts second** like this:...

@lyuguol if installed using conda then @jariwalask solution is the correct one, but if you already had an R environment then you need to install the packages with`install.packages(c("ggplot2","pheatmap"))` from R.

Hi @Pedramto89 since running the plot commands from the output folder you need to use it like this: - `cellphonedb plot dot_plot --means-path ./means.txt --pvalues-path ./pvalues.txt` - `cellphonedb plot heatmap_plot...

You're missing the first half of the command _(the `cellphonedb plot heatmap_plot` part)_ and also, there's no `--meta-path` option, it's just the argument. Your command (assuming you're going to run...

Without having a look at your input it's hard to tell. But if you only had two clusters defined in meta, that's pretty much all you're going to get. What...

Hi @henryeahhh, what's the original format of your data? Can you convert it to `h5ad` using something like [sceasy](https://github.com/cellgeni/sceasy) and work with that as an input count file?