david-barnett microViz issues

david-barnett / microViz

R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.

https://david-barnett.github.io/microViz/

GNU General Public License v3.0

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issues

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version 0.12.5 with small fixes

#178 david-barnett closed 2 months ago
0
Use scores to get ordination scores: summary.cca will fail in the next vegan release

#176 david-barnett opened 2 months ago
0
Change levels for LM modeling in tax_tree

#175 scilexenko closed 2 months ago
1
Composition barplot sorting by 1 taxon

#174 magibc closed 2 months ago
4
fix for cowplot get_legend warning issue with ggplot2 3.5

#171 david-barnett closed 4 months ago
0
ps_filter by group?

#170 antoine4ucsd closed 3 months ago
1
Better error message for UniFrac distances? - issue #53

#168 alejandrocs98 opened 5 months ago
2
comp_barplot reduce/remove space between axes and bars

#166 greboul closed 5 months ago
1
0.12.3 ord_plot fixes

#165 david-barnett closed 5 months ago
0
fix critical error in sampleAnnotation throwing package version checking error since R 4.4

#162 david-barnett closed 5 months ago
0
Can I make a correlation heatmap between taxa and categorical variable?

#161 timz0605 closed 5 months ago
1
Use of custom transofmration in linear models.

#160 SilasK opened 5 months ago
1
Labelling samples in ord_plot PCoA

#155 we32i225 closed 5 months ago
1
Tax_fix no non-unknown values

#153 luigallucci closed 5 months ago
1
[FR] Add sankey/alluvial plots to visualize abundances

#152 camilogarciabotero opened 6 months ago
2
tax.fix(), and "Problematic Genus values detected in tax_table"

#150 Nekovirus closed 5 months ago
3
Strange behaviour when using comp_barplot with facet_grid

#149 DanaBlu closed 7 months ago
2
Error in access(object, "otu_table", errorIfNULL) : otu_table slot is empty.

#148 chrstraub opened 7 months ago
2
comp_barplot seem to have issues with domain being unknown

#147 NeginValizadegan closed 5 months ago
2
cor_heatmap taxon_renamer or alternative option for labeling rows

#146 AngelicaMiraples closed 5 months ago
3
Taxa cannot be aggregated at rank: Genus

#145 bylam closed 5 months ago
2
Annotated heatmaps - error in sample_anno

#144 gaworj closed 8 months ago
4
phylogenetic tree disappeared after tax_transform() step

#143 Leran10 closed 5 months ago
2
dominant taxa in each sample

#141 momodiame21 closed 5 months ago
2
Cannot build PCoA plot using ord_plot

#140 LauGuaUuu closed 5 months ago
2
how can i order my samples and show their names?

#139 we32i225 closed 10 months ago
3
Logical variable becomes numeric when plotting CCA

#137 hkaspersen closed 10 months ago
2
corncob no longer exports ibd_phylo, so now microViz does

#136 david-barnett closed 10 months ago
1
0.12.0

#134 david-barnett closed 10 months ago
1
get corncob from github remote

#133 david-barnett closed 10 months ago
0
some GUSTAME site links have changed

#132 david-barnett closed 10 months ago
1
comp_barplot of raw abundances

#131 moyn413 closed 10 months ago
2
Correlation heat map issue assigning taxonomic rank

#130 jspychalla closed 10 months ago
5
interactive site inactive

#129 skose82 closed 10 months ago
2
The `tax_filter` argument `min_sample_abundance` does not recognise proportions

#128 hkaspersen closed 2 months ago
3
Documentation for taxatrees

#127 hkaspersen opened 1 year ago
1
Adding p values to cor_heatmap

#126 mradz19 closed 10 months ago
1
taxatree_models trans arg

#122 david-barnett closed 1 year ago
1
fix #119 and bump version to 0.10.11

#121 david-barnett closed 1 year ago
0
error in taxatree_stats_p_adjust when using grouping = c("rank","term")

#119 SilasK closed 1 year ago
1
Support for TreeSummarizedExperiment?

#117 antagomir closed 1 year ago
2
Sample Names for Heatmaps

#115 Drob84761 closed 1 year ago
1
fix: fixed erroneous taxon ordering that occurred if comp_barplot tax_level is set to "Taxon"

#114 david-barnett closed 1 year ago
1
0.10.9

#113 david-barnett closed 1 year ago
1
Example ordination plot workflow could be improved/simplified - currently shows 10% prevalence filtering of genera before CLR transform on families..

#112 david-barnett closed 10 months ago
1
0.10.8 bug fix

#110 david-barnett closed 1 year ago
0
Error: if (any(test_matrix < 1 & test_matrix != 0)) {: missing value where TRUE/FALSE needed

#109 david-barnett closed 1 year ago
1
mixed effect in dist_permanova

#106 jorondo1 closed 1 year ago
0
Subsetting aitchison distance

#105 jorondo1 closed 1 year ago
0
Output from taxatree_models not matching corncob::differentialTest()

#104 wilhelmsjoland closed 1 year ago
0