ranomaly issueshttps://forgemia.inra.fr/umrf/ranomaly/-/issues2024-01-22T15:26:43+01:00https://forgemia.inra.fr/umrf/ranomaly/-/issues/22error in `dada2_fun` for ITS after filtering2024-01-22T15:26:43+01:00Philippe Ruizphilippe.ruiz@inrae.frerror in `dada2_fun` for ITS after filteringin ITS mode after filtering, line [282](https://forgemia.inra.fr/umrf/ranomaly/-/blob/master/R/dada2_fun.R#L282), objects `filtFs_out` and `filtRs_out` does not exist because not created.
teh object is probably in `out` object, line [20...in ITS mode after filtering, line [282](https://forgemia.inra.fr/umrf/ranomaly/-/blob/master/R/dada2_fun.R#L282), objects `filtFs_out` and `filtRs_out` does not exist because not created.
teh object is probably in `out` object, line [201](https://forgemia.inra.fr/umrf/ranomaly/-/blob/master/R/dada2_fun.R#L201).
error : «Erreur dans learnErrors(filtFs_out, multithread = TRUE) :
objet 'filtFs_out' introuvable »https://forgemia.inra.fr/umrf/ranomaly/-/issues/21aggregate_top_taxa doesn't exist in the last version2024-01-22T15:20:31+01:00Philippe Ruizphilippe.ruiz@inrae.fraggregate_top_taxa doesn't exist in the last version`aggregate_top_taxa` was replaced by `aggregate_taxa` in the new version of microbiome package.
[Line 48](https://forgemia.inra.fr/umrf/ranomaly/-/blob/master/R/heatmap_fun.R#L48)`aggregate_top_taxa` was replaced by `aggregate_taxa` in the new version of microbiome package.
[Line 48](https://forgemia.inra.fr/umrf/ranomaly/-/blob/master/R/heatmap_fun.R#L48)https://forgemia.inra.fr/umrf/ranomaly/-/issues/20`plotVar` on pls-da2024-01-22T16:35:29+01:00Philippe Ruizphilippe.ruiz@inrae.fr`plotVar` on pls-daCan we add the `plotVar` graphic in the `plsda_fun` for `plsda` - `splsda` ?Can we add the `plotVar` graphic in the `plsda_fun` for `plsda` - `splsda` ?https://forgemia.inra.fr/umrf/ranomaly/-/issues/19no tax.tabe after generate phyloseq object2021-09-14T16:30:04+02:00Philippe Ruizphilippe.ruiz@inrae.frno tax.tabe after generate phyloseq objectThe `tax_table` is not save in the phyloseq object probably because `tax_table(as.matrix(tax.table))`
is missing in [line 59](https://forgemia.inra.fr/umrf/ranomaly/-/blob/master/R/generate_phyloseq_fun.R#L59).
work if we do `physeq <...The `tax_table` is not save in the phyloseq object probably because `tax_table(as.matrix(tax.table))`
is missing in [line 59](https://forgemia.inra.fr/umrf/ranomaly/-/blob/master/R/generate_phyloseq_fun.R#L59).
work if we do `physeq <- generate_phyloseq_fun(dada_res = dada_res,
tax.table = tax_table(as.matrix(tax.tablecheck)),
tree = tree,
metadata = "./sample_metadata.csv")`https://forgemia.inra.fr/umrf/ranomaly/-/issues/18diversity beta light adonis....2024-01-22T15:21:25+01:00Philippe Ruizphilippe.ruiz@inrae.frdiversity beta light adonis....Something go wrong with [adonis](https://forgemia.inra.fr/umrf/ranomaly/-/blob/master/R/diversity_beta_light.R#L88):
`Erreur dans G * t(hat) : tableaux de tailles inadéquates`
do the same for [`else`](https://forgemia.inra.fr/umrf/ranoma...Something go wrong with [adonis](https://forgemia.inra.fr/umrf/ranomaly/-/blob/master/R/diversity_beta_light.R#L88):
`Erreur dans G * t(hat) : tableaux de tailles inadéquates`
do the same for [`else`](https://forgemia.inra.fr/umrf/ranomaly/-/blob/master/R/diversity_beta_light.R#L90)
probably error comes from `adonis`
I think `adonis` is deprecated now ... better to use `adonis2`
tested with `vegan 2.5-7`https://forgemia.inra.fr/umrf/ranomaly/-/issues/17add example dataset2021-09-15T10:57:12+02:00Philippe Ruizphilippe.ruiz@inrae.fradd example datasetthink to add an example dataset in the package. The same as the vignette.
Easy to check function...think to add an example dataset in the package. The same as the vignette.
Easy to check function...https://forgemia.inra.fr/umrf/ranomaly/-/issues/16beta diversity covar error2024-01-22T15:24:16+01:00Philippe Ruizphilippe.ruiz@inrae.frbeta diversity covar errorcan't find [parameter covar](https://forgemia.inra.fr/umrf/ranomaly/-/blob/master/R/diversity_beta_fun.R#L194) in `diversity_beta_fun` if set or not :
`Erreur dans h(simpleError(msg, call)) :
erreur d'�valuation de l'argument 'x' lo...can't find [parameter covar](https://forgemia.inra.fr/umrf/ranomaly/-/blob/master/R/diversity_beta_fun.R#L194) in `diversity_beta_fun` if set or not :
`Erreur dans h(simpleError(msg, call)) :
erreur d'�valuation de l'argument 'x' lors de la s�lection d'une m�thode pour la fonction 'strsplit' : objet 'covar' introuvable`
call : ` test <- diversity_beta_fun(physeq, column1 = "Day", column2 = "individu", covar = "Type")`https://forgemia.inra.fr/umrf/ranomaly/-/issues/15error in `plsda_fun` output2021-09-14T16:15:18+02:00Philippe Ruizphilippe.ruiz@inrae.frerror in `plsda_fun` outputLine [168](https://forgemia.inra.fr/umrf/ranomaly/-/blob/master/R/plsda_fun.r#L168),
`Error in recordPlot() : no current device to record from`
The function save plot correctly in the folder but not in an R object.Line [168](https://forgemia.inra.fr/umrf/ranomaly/-/blob/master/R/plsda_fun.r#L168),
`Error in recordPlot() : no current device to record from`
The function save plot correctly in the folder but not in an R object.https://forgemia.inra.fr/umrf/ranomaly/-/issues/14`data.glom` is called before is created2021-07-02T17:16:08+02:00Philippe Ruizphilippe.ruiz@inrae.fr`data.glom` is called before is createdIn `metagenome_seq` [Ligne 38](https://forgemia.inra.fr/umrf/ranomaly/-/blob/master/R/metagenomeseq_fun.R#L38), in the case where `comp == ''` and `rank = "ASV"`In `metagenome_seq` [Ligne 38](https://forgemia.inra.fr/umrf/ranomaly/-/blob/master/R/metagenomeseq_fun.R#L38), in the case where `comp == ''` and `rank = "ASV"`https://forgemia.inra.fr/umrf/ranomaly/-/issues/13deseq2_fun plot all taxa2021-09-15T12:06:15+02:00Philippe Ruizphilippe.ruiz@inrae.frdeseq2_fun plot all taxaline [150](https://forgemia.inra.fr/umrf/ranomaly/-/blob/master/R/deseq2_fun.R#L150) in `deseq2_fun.R` is commented, so the function plot all taxa and not only significante foldchange. Can we add an argument to chooseto plot everything o...line [150](https://forgemia.inra.fr/umrf/ranomaly/-/blob/master/R/deseq2_fun.R#L150) in `deseq2_fun.R` is commented, so the function plot all taxa and not only significante foldchange. Can we add an argument to chooseto plot everything or only significant ?Etienne RifaEtienne Rifahttps://forgemia.inra.fr/umrf/ranomaly/-/issues/11dada2_fun arg "dadapool"2021-07-02T15:35:55+02:00Philippe Ruizphilippe.ruiz@inrae.frdada2_fun arg "dadapool"the names of the arg `dadapool` is not the same in the documentation and in the function. `dadapool` -> `pool`the names of the arg `dadapool` is not the same in the documentation and in the function. `dadapool` -> `pool`https://forgemia.inra.fr/umrf/ranomaly/-/issues/9bars_fun split as facet_wrap()2021-02-09T16:10:37+01:00Philippe Ruizphilippe.ruiz@inrae.frbars_fun split as facet_wrap()Is there a way to integrate split `bar_fun` argument like `facet_wrap` ?
I have fund this exemple in [stackoverflow](https://stackoverflow.com/questions/58103196/how-to-facet-a-plot-ly-chart) :
`library(dplyr)
iris%>%
group_by(Species...Is there a way to integrate split `bar_fun` argument like `facet_wrap` ?
I have fund this exemple in [stackoverflow](https://stackoverflow.com/questions/58103196/how-to-facet-a-plot-ly-chart) :
`library(dplyr)
iris%>%
group_by(Species) %>%
group_map(~ plot_ly(data=., x = ~Sepal.Length, y = ~Sepal.Width, color = ~Species, type = "scatter", mode="markers"), keep=TRUE) %>%
subplot(nrows = 1, shareX = TRUE, shareY=TRUE)`Etienne RifaEtienne Rifahttps://forgemia.inra.fr/umrf/ranomaly/-/issues/8error in deseq2_fun2020-04-07T11:15:57+02:00Philippe Ruizphilippe.ruiz@inrae.frerror in deseq2_funtest with `deseq2_fun(data, column1 = "Inoculation")`
return
`Error in model.matrix.formula(design(object), colData(object)) :
data must be a data.frame`test with `deseq2_fun(data, column1 = "Inoculation")`
return
`Error in model.matrix.formula(design(object), colData(object)) :
data must be a data.frame`https://forgemia.inra.fr/umrf/ranomaly/-/issues/7error in metacoder_fun2020-04-07T11:16:59+02:00Philippe Ruizphilippe.ruiz@inrae.frerror in metacoder_funif `plottree = TRUE` its return `impossible de trouver la fonction "heat_tree"`.if `plottree = TRUE` its return `impossible de trouver la fonction "heat_tree"`.https://forgemia.inra.fr/umrf/ranomaly/-/issues/6agricolae required for alpha_div_fun2020-04-07T11:14:17+02:00Philippe Ruizphilippe.ruiz@inrae.fragricolae required for alpha_div_funthe package `agricolae`is required by the function `diversity_alpha_fun` but is not in the SPACENAME or DESCRIPTION filesthe package `agricolae`is required by the function `diversity_alpha_fun` but is not in the SPACENAME or DESCRIPTION fileshttps://forgemia.inra.fr/umrf/ranomaly/-/issues/5no load in generate_phyloseq_fun and genrate_tree_function2020-04-06T10:24:56+02:00Philippe Ruizphilippe.ruiz@inrae.frno load in generate_phyloseq_fun and genrate_tree_function```r
load(dada_res)
load(tax.table)
load(tree)
``````r
load(dada_res)
load(tax.table)
load(tree)
```https://forgemia.inra.fr/umrf/ranomaly/-/issues/4error in diversity_alpha_fun function2020-04-06T10:25:09+02:00Philippe Ruizphilippe.ruiz@inrae.frerror in diversity_alpha_fun function`diversity_alpha_fun("phyloseq/robjects.Rdata", column1 = "Groups")`
return
`Error in access(object, "sam_data", errorIfNULL) : sam_data slot is empty.`
tested with phyloseq dataset created with `generate_phyloseq_fun`.`diversity_alpha_fun("phyloseq/robjects.Rdata", column1 = "Groups")`
return
`Error in access(object, "sam_data", errorIfNULL) : sam_data slot is empty.`
tested with phyloseq dataset created with `generate_phyloseq_fun`.https://forgemia.inra.fr/umrf/ranomaly/-/issues/3error in bars_fun function2020-04-06T10:32:36+02:00Philippe Ruizphilippe.ruiz@inrae.frerror in bars_fun function`bars_fun("phyloseq/robjects.Rdata", column1 = "Groups")`
return
`Error in access(object, "sam_data", errorIfNULL) :
sam_data slot is empty. `
tested with phyloseq dataset created with `generate_phyloseq_fun`.`bars_fun("phyloseq/robjects.Rdata", column1 = "Groups")`
return
`Error in access(object, "sam_data", errorIfNULL) :
sam_data slot is empty. `
tested with phyloseq dataset created with `generate_phyloseq_fun`.https://forgemia.inra.fr/umrf/ranomaly/-/issues/2dada2 with pseudo option2020-04-06T11:07:39+02:00Philippe Ruizphilippe.ruiz@inrae.frdada2 with pseudo optionI think the `dada` function with argument `pool = pseudo` don't need to be in a loop.
https://benjjneb.github.io/dada2/pseudo.html#pseudo-pooling
but used like `pool = TRUE`. line 276.
https://benjjneb.github.io/dada2/pseudo.html#pseud...I think the `dada` function with argument `pool = pseudo` don't need to be in a loop.
https://benjjneb.github.io/dada2/pseudo.html#pseudo-pooling
but used like `pool = TRUE`. line 276.
https://benjjneb.github.io/dada2/pseudo.html#pseudo-poolinghttps://forgemia.inra.fr/umrf/ranomaly/-/issues/1Raw sequence names2020-04-06T10:33:17+02:00Philippe Ruizphilippe.ruiz@inrae.frRaw sequence namesSometimes Raw sequences filenames have format V4_515F_New_V4_806R_New-C14_GAGACTATGC_R2.fastq.
filformat for line 175 of `dada2_fun.R` probably needs to be clarified.
for example, in this case line 175 should be : `get.sample.name <- fun...Sometimes Raw sequences filenames have format V4_515F_New_V4_806R_New-C14_GAGACTATGC_R2.fastq.
filformat for line 175 of `dada2_fun.R` probably needs to be clarified.
for example, in this case line 175 should be : `get.sample.name <- function(fname) strsplit(basename(fname), "_")[[1]][6]`
and line 210 : sample.names <- sapply(strsplit(basename(fnFs), "_"), `[`, 6)
`Creating output directory: /media/pruiz/DATA/Philippe/Projets/Audrey/Anomaly/Bact/reads//filtered
Error in filterAndTrim(fnFs, filtFs, fnRs, filtRs, truncLen = c(f_trunclen, :
All output files must be distinct.`