'Error in UseMethod("as.dendogram")' when running CALANGO #8
Description
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.