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RiboRingsRiboRings
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Merge pull request #23 from microbiome/dbb
Improve and extend importers
2 parents 5d40986 + 60c3926 commit f2d53d6

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6 files changed

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‎DESCRIPTION‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
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Package: miaDash
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Version: 1.1.1
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Version: 1.1.2
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Authors@R:
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c(person(given = "Giulio", family = "Benedetti", role = c("aut", "cre"),
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email = "giulio.benedetti@utu.fi",
@@ -25,7 +25,6 @@ Depends:
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shiny
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Imports:
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ape,
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biomformat,
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htmltools,
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iSEEtree (>= 1.1.4),
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mia,

‎NAMESPACE‎

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Original file line numberDiff line numberDiff line change
@@ -8,7 +8,6 @@ importFrom(SummarizedExperiment,colData)
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importFrom(TreeSummarizedExperiment,TreeSummarizedExperiment)
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importFrom(TreeSummarizedExperiment,rowTree)
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importFrom(ape,read.tree)
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importFrom(biomformat,read_biom)
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importFrom(htmltools,HTML)
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importFrom(htmltools,br)
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importFrom(htmltools,div)
@@ -28,9 +27,12 @@ importFrom(iSEEtree,RowTreePlot)
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importFrom(iSEEtree,ScreePlot)
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importFrom(mia,addAlpha)
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importFrom(mia,agglomerateByRank)
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importFrom(mia,convertFromBIOM)
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importFrom(mia,getDissimilarity)
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importFrom(mia,importBIOM)
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importFrom(mia,importHUMAnN)
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importFrom(mia,importMetaPhlAn)
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importFrom(mia,importMothur)
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importFrom(mia,importQIIME2)
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importFrom(mia,runNMDS)
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importFrom(mia,runRDA)
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importFrom(mia,subsetByPrevalent)
@@ -51,4 +53,5 @@ importFrom(stats,as.formula)
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importFrom(utils,data)
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importFrom(utils,packageVersion)
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importFrom(utils,read.csv)
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importFrom(utils,read.table)
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importFrom(vegan,vegdist)

‎NEWS‎

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Original file line numberDiff line numberDiff line change
@@ -1,24 +1,28 @@
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Changes in version 0.1.0
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* Initialised app
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* Added import functionality
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Changes in version 1.1.2
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* Added importers for HUMAnN, QIIME2 and Mothur
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* Improved biom importer
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Changes in version 0.2.0
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* Added manipulate functionality
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* Added estimate functionality
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* Added panel layout customisation
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* Added unit testing
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Changes in version 0.99.12
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* Fixed tab title
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Changes in version 0.99.2
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* Moved to shinydashboard
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Changes in version 0.99.5
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* Implemented error check system
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* Added mia logo
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Changes in version 0.99.3
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* Added tree import option
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* Fixed bugs with RDS and unifrac
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* Added clickable title box
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19-
Changes in version 0.99.5
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* Implemented error check system
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* Added mia logo
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Changes in version 0.99.2
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* Moved to shinydashboard
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23-
Changes in version 0.99.12
24-
* Fixed tab title
20+
Changes in version 0.2.0
21+
* Added manipulate functionality
22+
* Added estimate functionality
23+
* Added panel layout customisation
24+
* Added unit testing
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26+
Changes in version 0.1.0
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* Initialised app
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* Added import functionality

‎R/landing_page.R‎

Lines changed: 38 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -73,36 +73,54 @@
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tabPanel(title = "Foreign", value = "foreign", br(),
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radioButtons(inputId = "ftype",
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label = "Type:", choices = list("biom", "QZA",
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"MetaPhlAn"), inline = TRUE),
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radioButtons(inputId = "ftype", label = "Type:",
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choices = list("biom", "HUMAnN", "MetaPhlAn",
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"Mothur", "QIIME2"), inline = TRUE),
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fileInput(inputId = "main.file",
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label = "Main file:", accept = c(".biom",
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".QZA", ".txt"),
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placeholder = "biom, QZA or txt"),
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".tsv", ".shared", ".QZA", ".txt"),
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placeholder = "biom, tsv, shared, QZA or txt"),
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div(style = "margin-top: -20px"),
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fileInput(inputId = "col.data", label = "colData:",
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accept = c(".tsv", ".design"),
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placeholder = "tsv or design"),
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div(style = "margin-top: -20px"),
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conditionalPanel(
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condition = "input.ftype == 'biom'",
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condition = "input.ftype == 'Mothur' | input.ftype == 'QIIME2'",
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fileInput(inputId = "f.rowdata",
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label = "rowData:", accept = c(".taxonomy",
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".qza"), placeholder = "taxonomy or qza"),
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div(style = "margin-top: -20px")),
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conditionalPanel(
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condition = "input.ftype == 'biom' | input.ftype == 'MetaPhlAn'",
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fileInput(inputId = "tree.file",
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label = "rowTree:", placeholder = "tree.tree",
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accept = c(".tree", ".tre", ".qza")),
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div(style = "margin-top: -20px")),
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conditionalPanel(
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condition = "input.ftype == 'biom' | input.ftype == 'HUMAnN'",
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89110
checkboxInput(inputId = "rm.tax.pref",
90-
label = "Remove taxa prefixes"),
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label = "Remove taxa prefixes")),
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conditionalPanel(
114+
condition = "input.ftype == 'biom'",
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92116
checkboxInput(inputId = "rank.from.pref",
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label = "Derive taxa from prefixes")),
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conditionalPanel(
96-
condition = "input.ftype == 'MetaPhlAn'",
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fileInput(inputId = "col.data",
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label = "colData:", accept = ".tsv",
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placeholder = "coldata.tsv"),
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div(style = "margin-top: -20px"),
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fileInput(inputId = "tree.file",
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label = "Tree:", placeholder = "tree.tree",
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accept = c(".tree", ".tre"))))),
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condition = "input.ftype == 'HUMAnN'",
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checkboxInput(inputId = "rm.hum.suf",
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label = "Remove sample suffix")))),
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actionButton("import", "Upload", class = "btn-primary")),
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‎R/observers.R‎

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Original file line numberDiff line numberDiff line change
@@ -17,11 +17,11 @@
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#' @importFrom utils read.csv
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#' @importFrom ape read.tree
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#' @importFrom S4Vectors DataFrame
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#' @importFrom biomformat read_biom
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#' @importFrom mia convertFromBIOM importMetaPhlAn
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#' @importFrom mia importHUMAnN importMetaPhlAn importQIIME2 importMothur
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#' addAlpha
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#' @importFrom TreeSummarizedExperiment TreeSummarizedExperiment
2323
.create_import_observers <- function(input, rObjects) {
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# nocov start
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observeEvent(input$import, {
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isolate({
7474
req(input$main.file)
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75+
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coldata <- .set_optarg(input$col.data$datapath,
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alternative = input$col.data$datapath)
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79+
treefile <- .set_optarg(input$tree.file$datapath,
80+
alternative = input$tree.file$datapath)
81+
7682
if( input$ftype == "biom" ){
7783

78-
biom_object <- read_biom(input$main.file$datapath)
79-
80-
fun_args <- list(x = biom_object,
84+
fun_args <- list(file = input$main.file$datapath,
85+
col.data = coldata, tree.file = treefile,
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removeTaxaPrefixes = input$rm.tax.pref,
8287
rankFromPrefix = input$rank.from.pref)
83-
88+
8489
rObjects$tse <- .update_tse(
85-
rObjects$tse, convertFromBIOM, fun_args
90+
rObjects$tse, .importBIOM, fun_args
8691
)
8792

88-
} else if( input$ftype == "MetaPhlAn" ){
89-
90-
coldata <- .set_optarg(input$col.data$datapath,
91-
alternative = input$col.data$datapath)
93+
}else if( input$ftype == "HUMAnN" ){
94+
95+
fun_args <- list(file = input$main.file$datapath,
96+
col.data = coldata,
97+
prefix.rm = input$rm.tax.pref,
98+
remove.suffix = input$rm.hum.suf)
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93-
treefile <- .set_optarg(input$tree.file$datapath)
94-
100+
rObjects$tse <- .update_tse(
101+
rObjects$tse, importHUMAnN, fun_args
102+
)
103+
104+
}else if( input$ftype == "MetaPhlAn" ){
105+
95106
fun_args <- list(file = input$main.file$datapath,
96107
col.data = coldata, tree.file = treefile)
97108

98109
rObjects$tse <- .update_tse(
99-
rObjects$tse, importMetaPhlAn, fun_args
100-
)
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110+
rObjects$tse, importMetaPhlAn, fun_args
111+
)
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113+
}else if( input$ftype %in% c("Mothur", "QIIME2") ){
114+
115+
imp_fun <- eval(parse(text = paste0("import", input$ftype)))
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117+
rowdata <- .set_optarg(input$f.rowdata$datapath,
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alternative = input$f.rowdata$datapath)
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120+
fun_args <- list(assay.file = input$main.file$datapath,
121+
row.file = input, col.file = rowdata)
122+
123+
rObjects$tse <- .update_tse(
124+
rObjects$tse, imp_fun, fun_args
125+
)
126+
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}
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104129
})

‎R/utils.R‎

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Original file line numberDiff line numberDiff line change
@@ -116,4 +116,25 @@ NULL
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117117
cond <- all(vars %in% names(colData(tse)))
118118
return(cond)
119+
}
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121+
#' @importFrom mia importBIOM
122+
#' @importFrom S4Vectors DataFrame
123+
#' @importFrom ape read.tree
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#' @importFrom utils read.table
125+
.importBIOM <- function(file, col.data = NULL, tree.file = NULL, ...){
126+
127+
tse <- importBIOM(file, ...)
128+
129+
if( !is.null(col.data) ){
130+
coldata <- read.table(file = col.data, header = TRUE, sep = "\t")
131+
rownames(coldata) <- colnames(tse)
132+
colData(tse) <- DataFrame(coldata)
133+
}
134+
135+
if( !is.null(tree.file) ){
136+
rowTree(tse) <- read.tree(tree.file)
137+
}
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return(tse)
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}

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