Error to executing the Tutorial: Integrating QIIME2 and R for data visualization and analysis using qiime2R

[Patricia_Azevedo]

Hello all,
I'm trying to follow the tutorial cited and I ran the first steps but I'm having problems running the command:
gplots::venn(list(metadata=metadata$SampleID, shannon=shannon$SampleID)) with the error:

Error in metadata$SampleID : object of type 'closure' is not subsettable

and the command:

metadata %>%

• filter(!is.na(shannon)) %>%
• ggplot(aes(x=TIME, y=shannon, color=SAMPLES)) +
• stat_summary(geom="errorbar", fun.data=mean_se, width=0) +
• stat_summary(geom="line", fun.data=mean_se) +
• stat_summary(geom="point", fun.data=mean_se) +
• xlab("TIME") +
• ylab("Shannon Diversity") +
• theme_q2r() +
• scale_color_viridis_d(name="TIME")

with the error Error in UseMethod("filter") :
no applicable method for 'filter' applied to an object of class "c('standardGeneric', 'genericFunction', 'function', 'OptionalFunction', 'PossibleMethod', 'expression_OR_function', 'optionalMethod')"

I'm not an expert in R, can anyone help me to fix that script?

Thank you!

[Oddant1]

@Patricia_Azevedo this issue goes in Community Plugin Support because qiime2R is not a part of the core QIIME 2 distribution (the core development team does not work on it).

[Patricia_Azevedo]

Thank you for your answer. Do you know any other tutorial I can follow for generating images from qiime analysis? I'm not very familiarized with R.

Thanks again!

[cherman2 (Chloe Herman)]

Hi @Patricia_Azevedo,
I am not super familar with R so I am not sure what is going on with your errors. However to answer your second question:

@Patricia_Azevedo

Do you know any other tutorial I can follow for generating images from qiime analysis?

You could follow the moving pictures tutorial in the terminal to generate a variety of visualizations.

Do you have any specific images you are trying to generate?