show_sig_feature_corrplot() error

ShixiangWang / sigminer

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html

https://shixiangwang.github.io/sigminer/

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show_sig_feature_corrplot() error #376

Closed xiw588 closed 3 years ago

xiw588 commented 3 years ago

Hi shixiang,

I applied show_sig_feature_corrplot() to the output of get_tidy_association(p_adjust = TRUE) as below but got the following error message. Do you know what's wrong with this? Thank you.

Error in gglist[[1]] : subscript out of bounds

ShixiangWang commented 3 years ago

I need the data to check why it doesn't work. Could send me by email w_shixiang@163.com or upload your data here?

ShixiangWang commented 3 years ago

@xiw588 Hi Ann, please reinstall the sigminer from GitHub and try the following commands.

data = readr::read_csv("C:/Users/Administrator/Downloads/test_show_sig_feature_cor.csv")

show_sig_feature_corrplot(
   data, p_val = 1,  breaks_count = NULL
)

show_sig_feature_corrplot(
   data, p_val = 1,  breaks_count = NA 
)

Your data has no association with p < 0.05, so you need to reset the p value threshold.

Best,

Shixiang

xiw588 commented 3 years ago

Hi Shixiang,

Thank you very much for your help! I somehow fixed the issue with the correlation plot although it still has some warning messages. I will try as what you suggested here and rerun the analysis.

Thanks!

ShixiangWang commented 3 years ago

The warning messages in this plot function mainly can be ignored.