'Error in UseMethod("as.dendogram")' when running CALANGO

[flayner2]

Issue

When running CALANGO using either a Pfam or GO database to analyze a dataset, the package errors while generating the HTML report with the following message:

Tests

The issue doesn't happen when running KOMODO2 with exactly the same data and parameters, it only happens when I try to run CALANGO. It may be useful to have some sort of verbose error logging to a file inbuilt to help with bug reporting in the future.

Data

Those are the parameter used for testing with both KOMODO2 and CALANGO. All file paths specified in the parameters are relative paths. If you need access to the data, reach me in private.

GO

annotation.files.dir = "../../../work/komodo_inputs/gene2go/masters_paper_inputs_gene2go"

# output directories -> include date directory as well
#output.dir = "../../../results/komodo_results/gene2go/mag/" # Base 10 power
#output.dir = "../../../results/komodo_results/gene2go/max/" # Maximum number of individuals
output.dir = "../../../results/komodo_results/gene2go/2021-10-12/log_noroot" # log of maximum number of individuals
#output.dir = "../../../results/komodo_results/gene2go/levels/" # Sociality levels

dataset.info = "../../../data/metadata/masters_paper_metadata/metadata_gene2go_52hymenoptera_final.tsv" 

#x.column = 3 # n of individuals
x.column = 4 # log of number of individuals
#x.column = 5 # power
#x.column = 6 # sociality level

short.name.column = 7

group.column = 8

ontology = "GO"

dict.path = ""

column = "GO"

denominator.column = 2

# path to the tree
tree.path = "../../../data/trees/2021-10-12/hymenoptera_52_tree_not_rooted_ultrametric_times.nwk"
tree.type = "newick"

type = "correlation"

MHT.method = "BH"

cores = 50

#spearman.qvalue.cutoff = 0.05
spearman.qvalue.cutoff = 1
pearson.qvalue.cutoff = 1
kendall.qvalue.cutoff = 1
#linear_model.qvalue.cutoff = 0.5
linear_model.qvalue.cutoff = 1

spearman.cor.upper.cutoff = -1
spearman.cor.lower.cutoff = 1
pearson.cor.upper.cutoff = -1
pearson.cor.lower.cutoff = 1
kendall.cor.upper.cutoff = -1
kendall.cor.lower.cutoff = 1

sd.cutoff = 0
cv.cutoff = 0

annotation_size.cutoff = 51
#annotation_size.cutoff = 1

prevalence.cutoff = 0

heterogeneity.cutoff = 0

raw_data_sd_filter = TRUE

Pfam

annotation.files.dir = "../../../work/komodo_inputs/pfam/masters_paper_inputs_pfam/"

# output directories -> include date directory as well
#output.dir = "../../../results/komodo_results/pfam/mag/" # Base 10 power
#output.dir = "../../../results/komodo_results/pfam/max/" # Maximum number of individuals
output.dir = "../../../results/komodo_results/pfam/2021-11-02/log/" # log of maximum number of individuals
#output.dir = "../../../results/komodo_results/pfam/levels/" # Sociality levels

dataset.info = "../../../data/metadata/masters_paper_metadata/metadata_pfam_52hymenoptera_final.tsv"

#x.column = 3 # n of individuals
x.column = 4 # log of number of individuals
#x.column = 5 # power
#x.column = 6 # sociality level

short.name.column = 7

group.column = 8

ontology = "other"

dict.path = "../../../data/dicts/2021-10-12/pfam_dict.tsv"

column = "Pfam"

denominator.column = 2

# path to the tree
tree.path = "../../../data/trees/2021-11-01/hymenoptera_52_without_outgroup_ze.nwk"
tree.type = "newick"

type = "correlation"

MHT.method = "BH"

cores = 50

spearman.qvalue.cutoff = 0.05
#spearman.qvalue.cutoff = 1
pearson.qvalue.cutoff = 1
kendall.qvalue.cutoff = 1
linear_model.qvalue.cutoff = 0.5
#linear_model.qvalue.cutoff = 1

spearman.cor.upper.cutoff = -1
spearman.cor.lower.cutoff = 1
pearson.cor.upper.cutoff = -1
pearson.cor.lower.cutoff = 1
kendall.cor.upper.cutoff = -1
kendall.cor.lower.cutoff = 1

sd.cutoff = 0
cv.cutoff = 0

annotation_size.cutoff = 51
#annotation_size.cutoff = 1

prevalence.cutoff = 0

heterogeneity.cutoff = 0

raw_data_sd_filter = TRUE

Hit me up if you need any additional information.

[flayner2]

Found two links that might help solving this issue:

• https://stackoverflow.com/questions/24919413/selecting-number-of-leaf-nodes-of-dendrogram-in-heatmap-2-in-r
• https://stackoverflow.com/questions/31972832/r-hclust-dendrogram-phylo

[fcampelo]

Thank you, @flayner2 . Solved in latest commit in https://github.com/fcampelo/CALANGO (version 1.0.7). Please reinstall from that repo and test again.

@franciscolobo , I sent you PR #9 to sync that yo your repo.

Cheers, Felipe