cellphonedb plot heatmap_plot

[dianadom]

Hi,

While running command cellphonedb plot heatmap_plot.... I am getting the following error R Runtime Exception: error in '[.data.frame(all_intr, , pairs1[i])': undefined columns selected

How should it be fixed?

[lyuguol]

Hi,

When running cellphonedb dot_plot or cellphonedb plot heatmap_plot test_meta.txt, I encountered the following erros, repectively: no package named ''ggplot2' or no package name 'pheatmap'.

Do you have any idea in solving the problem?

Many thanks and wish you all a Merry Christmas.

Best,

Guoliang

[jariwalask]

@lyuguol try

conda install -c conda-forge r-base=3.6.2 # if not installed already
conda install -c conda-forge  r-ggplot2
conda install -c conda-forge r-pheatmap

[prete]

@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 withinstall.packages(c("ggplot2","pheatmap")) from R.

[Pedramto89]

I try to plot the results using heatmap or dotplot but getting the errors. The error as showed in the image is :Error: Invalid value for "--pvalues-path": Path "./out/pvalues.txt" does not exist.

[prete]

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 --pvalues-path ./pvalues.txt PATH_TO_THE_META _(where PATH_TO_META is the input meta file you used for running the analysis)_

You can read more about all the plotting arguments here

[Pedramto89]

Thank you @prete I run it and got the dotplot but for the heatmap does not work

[prete]

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 it from ~/analysis/venv) should be like this:

cellphonedb plot heatmap_plot --pvalues-path ./out/new_project/pvalues.txt ./meta_subtype1new.txt

[Pedramto89]

Thank you @prete for your quick response and answer. I run it but the output is a bit weird.

[prete]

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 info would you like to obtain from your data? What questions you are looking to answer? Knowing that would make it easier for us to give you more options.

[Pedramto89]

The dotplot looks interesting but the heatmap not. I am looking for ligand-receptor interactions based on my data. I have two other subtypes two. Maybe I can get more meaningful output