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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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Error: plotFunctions with metadata_groups parameter #657

Closed flsaravia closed 1 year ago

flsaravia commented 1 year ago

Hello, I am trying to enter my own metadata groups list and samples character vector for the plot. However, I am running into an error. I would appreciate any input. Thank you!

Samples List

sqm_samples <- c('EM7222022LRM15R1','EM7222022LRM15R2','EM7222022LRM15R3','EM7222022OP15R1','EM7222022OP15R2','EM7222022OP15R3','EM7222022YX15R1','EM7222022YX15R2','EM7222022YX15R3','EM7222022LRM4R1','EM7222022LRM4R2','EM7222022LRM4R3','EM7222022OP4R1','EM7222022OP4R2','EM7222022OP4R3','EM7222022YX4R1','EM7222022YX4R2','EM7222022YX4R3','EM7222022LRM8R1','EM7222022LRM8R2','EM7222022LRM8R3','EM7222022OP8R1','EM7222022OP8R2','EM7222022OP8R3','EM7222022YX8R1','EM7222022YX8R2','EM7222022YX8R3','EM7222022LRMUB1','EM7222022LRMUB2','EM7222022LRMUB3','EM7222022OPUB1','EM7222022OPUB2','EM7222022OPUB3','EM7222022YXUB1','EM7222022YXUB1','EM7222022YXUB3','EM7222022LRMUT1','EM7222022LRMUT2','EM7222022LRMUT3','EM7222022OPUT1','EM7222022OPUT2','EM7222022OPUT3','EM7222022YXUT1','EM7222022YXUT2','EM7222022YXUT3','EM7222022LRM24hrUT1','EM7222022LRM24hrUT2','EM7222022LRM24hrUT3','EM7222022OP24hrUT1','EM7222022OP24hrUT2','EM7222022OP24hrUT3','EM7222022YX24hrUT1','EM7222022YX24hrUT2','EM7222022YX24hrUT3', 'EM7222022LRMSaliva','EM7222022OMSaliva','EM7222022YXSaliva','EM7222022LRMPlaMW1','EM7222022LRMPlaMW2','EM7222022LRMPlaMW3','EM7222022OPPlaMW1','EM7222022OPPlaMW2','EM7222022OPPlaMW3','EM7222022YXPlaMW1','EM7222022YXPlaMW2','EM7222022YXPlaMW3','EM7222022LRM08RMW1','EM7222022LRM08RMW2','EM7222022LRM08RMW3','EM7222022OP08RMW1','EM7222022OP08RMW2','EM7222022OP08RMW3','EM7222022YX08MW1','EM7222022YX08RMW2','EM7222022YX08RMW3')

Metadata Groups

sqm_groups <- list('ArgTP15' = c('EM7222022LRM15R1','EM7222022LRM15R2','EM7222022LRM15R3','EM7222022OP15R1','EM7222022OP15R2','EM7222022OP15R3','EM7222022YX15R1','EM7222022YX15R2','EM7222022YX15R3'),'ArgTP4' = c('EM7222022LRM4R1','EM7222022LRM4R2','EM7222022LRM4R3','EM7222022OP4R1','EM7222022OP4R2','EM7222022OP4R3','EM7222022YX4R1','EM7222022YX4R2','EM7222022YX4R3'),'ArgTP8' = c('EM7222022LRM8R1','EM7222022LRM8R2','EM7222022LRM8R3','EM7222022OP8R1','EM7222022OP8R2','EM7222022OP8R3','EM7222022YX8R1','EM7222022YX8R2','EM7222022YX8R3'),'Ultrabrite' = c('EM7222022LRMUB1','EM7222022LRMUB2','EM7222022LRMUB3','EM7222022OPUB1','EM7222022OPUB2','EM7222022OPUB3','EM7222022YXUB1','EM7222022YXUB1','EM7222022YXUB3'),'Untreated' = c('EM7222022LRMUT1','EM7222022LRMUT2','EM7222022LRMUT3','EM7222022OPUT1','EM7222022OPUT2','EM7222022OPUT3','EM7222022YXUT1','EM7222022YXUT2','EM7222022YXUT3'),'Untreated24hr' = c('EM7222022LRM24hrUT1','EM7222022LRM24hrUT2','EM7222022LRM24hrUT3','EM7222022OP24hrUT1','EM7222022OP24hrUT2','EM7222022OP24hrUT3','EM7222022YX24hrUT1','EM7222022YX24hrUT2','EM7222022YX24hrUT3'),'Pellet' = c('EM7222022LRMSaliva','EM7222022OMSaliva','EM7222022YXSaliva'),'PlaceboMW' = c('EM7222022LRMPlaMW1','EM7222022LRMPlaMW2','EM7222022LRMPlaMW3','EM7222022OPPlaMW1','EM7222022OPPlaMW2','EM7222022OPPlaMW3','EM7222022YXPlaMW1','EM7222022YXPlaMW2','EM7222022YXPlaMW3'),'ArgMW08' = c('EM7222022LRM08RMW1','EM7222022LRM08RMW2','EM7222022LRM08RMW3','EM7222022OP08RMW1','EM7222022OP08RMW2','EM7222022OP08RMW3','EM7222022YX08MW1','EM7222022YX08RMW2','EM7222022YX08RMW3'))

Plot Functions

plotFunctions(sqm_arcGenes, fun_level = 'KEGG', count = 'tpm', base_size = 7, N = 3, gradient_col = c( "#FAEFD1", "#02401B"), metadata_groups = sqm_groups, samples = sqm_samples)

Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) : 'x' must be atomic

flsaravia commented 1 year ago

Error has been fixed. There is an error in samples listed within metadata groups.