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Error in library(amplicon) : there is no package called ‘amplicon’
Dear EasyMicrobiome development team,
I already downloaded the source code of EasyMicrobiome v1.16 (2022.8). I want to visualise the kraken+bracken output using the script EasyMicrobiome/script/tax_stackplot.R. But, I am not sure no output generated.
Command lines
module load tools computerome_utils/2.0
module load gcc/7.4.0
module load intel/perflibs
module load R/4.2.0
module load ampliconsuite-pipeline/20221021
chmod +x /PATH/EasyMicrobiome/linux/*
export PATH=$PATH:pwd/PATH/EasyMicrobiome/linux:pwd/PATH/EasyMicrobiome/script"
/services/tools/R/4.2.0/bin/Rscript /PATH/EasyMicrobiome/script/tax_stackplot.R
--input /bracken/bracken_1_24/bracken_1/1_P_nt.bracken
--output //bracken/bracken_1_24/bracken_1/1_P_nt.bracken.stackplot
--legend 10 --width 89 --height 59
Error screenshot
Could you give me some suggestions?
Best,
Bing
Error in UseMethod("gather") : no applicable method for 'gather' applied to an object of class "factor" Calls: %>% -> summarise -> group_by -> gather Execution halted
pipeline.sh file
compare="NSP-SP"
Rscript ${db}/script/compare_stamp.R \
--input result/otutab.txt --metadata result/metadata.txt \
--group Group --compare ${compare} --threshold 0.1 \
--method "t.test" --pvalue 0.05 --fdr "none" \
--width 189 --height 159 \
--output result/stamp/${compare}
# output
# 9
# NSP1 NSP2 NSP3 NSP4 NSP5 SP1 SP2 SP3
# 87.76123 92.04876 95.23562 93.24942 93.14364 89.66851 91.11344 90.94894
# SP4
# 95.62645
# idx
# TRUE
# 9
# Error in UseMethod("gather") :
# no applicable method for 'gather' applied to an object of class "factor"
# Calls: %>% -> summarise -> group_by -> gather
# Execution halted
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