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asteinberger9 / seq_scripts

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Error in kruskal.pretty #2

Closed tbmonica84 closed 3 years ago

tbmonica84 commented 4 years ago

Hi @asteinberger9 , thank you so much for the seq_scripts repo. I successfully ran simper.pretty and now I'd like to use kruskal.pretty. However, I keep getting this error message: Error in[<-.data.frame(*tmp*, , 6, value = numeric(0)) : new columns would leave holes after existing columns Could you please help me to fix it? Thank you!

jarrodscott commented 4 years ago

hi @tbmonica84 Did you ever solve this issue?

antoine4ucsd commented 3 years ago

same error. anyone can help with that? my simper.results file looks ok with simper.pretty simper.pretty(OTU, meta, c("pid"), perc_cutoff=1, low_cutoff = 'y', low_val=0.001, "tryme")

but then I got:

simper.results = data.frame(read.csv("tryme_clean_simper.csv")) kruskal.pretty(OTU, meta, simper.results, c("pid"), "output_name_krustal") Error in `[<-.data.frame`(`*tmp*`, , 6, value = numeric(0)) : new columns would leave holes after existing columns Called from: `[<-.data.frame`(`*tmp*`, , 6, value = numeric(0)) I am attaching the simper.results if it helps.... tryme_clean_simper.txt

thank you in advance!

maryfraou commented 3 years ago

Hello everyone!

Thank you @asteinberger9 for sharing the seq_scripts and @kdillmcfarland for the micro_ecol scripts for amplicon microbiota data analysis.

I get the same error with kruskal_pretty function: Error in [<-.data.frame(*tmp*, , 11, value = NULL) : new columns would leave holes after existing columns.

Has anyone managed to resolve that issue or have an idea of what that implies?

Cheers

asteinberger9 commented 3 years ago

Hi all, apologies for those who did not email me directly for help. I just pushed an updated version of the script which should fix the [<-.data.frame(tmp error. Also check out the README.md for updated info on input formatting and some troubleshooting options.

Let me know if you run into any additional issues.

Best!

AbidHussainBhat commented 1 year ago

@asteinberger9 @jarrodscott @antoine4ucsd @tbmonica84 @maryfraouI am getting this error while running kruskal.pretty: kruskal.pretty(OTU.clean, meta, simper.results, c('Group'), 'Group', tax) Error in eval(predvars, data, env) : object 'listbact' not found Can you please solve this issue?