Man pages for microresearcher/MicroVis
Microbiome Analysis and Visualization
| activate | Activate Dataset |
| addGrps | Add Groups |
| addSamples | Add Samples |
| adiv | Alpha Diversity Calculation |
| agglomTaxa | Agglomerate taxa into parent taxa |
| ASVtoTaxa | Translate ASV Numbers to Taxa Names |
| autonametoggle | Automatically Name Results |
| bdiv | Beta Diversity Analysis |
| calcUniVar | Core Univariate Analysis Function |
| capitalize | Capitalize a Single-Word String |
| changeFactor | Switch to a Different Factor |
| changerank | Change the active rank of a dataset |
| checkColors | Check Colors of Groups in a Dataset |
| checkFormula | Check that a formula is valid for a dataset |
| checkGroups | Check that each group has at least a certain number of... |
| chooseFactors | Choose Factors for the Dataset |
| chooseGrps | Choose Groups to be Analyzed in Each Factor |
| chooseSamples | Select specific samples to analyze |
| cleanASVs | Clean ASVs in ASV Dataframe |
| cleanData | Clean up a metadata factor column in a merged data table |
| cleanGroups | Clean Metadata Factors |
| cleanUnkTaxa | Rename Taxa with NA and at Species Level |
| clearFeatureFilt | Clear Feature Filtering |
| clearNormalization | Clear Normalization |
| clearProcessing | Clear Normalization and Feature Filtering |
| clr | Centered log-ratio functions |
| clusterSamples | Cluster samples |
| colorGrps | Color Groups |
| combineDupeASVs | Combine Identical ASVs |
| cor2cov | Convert a symmetric correlation matrix to a covariance matrix... |
| countFeatures | Get Number of Included Samples in a Dataset |
| countSamples | Get Number of Included Samples in a Dataset |
| countSamples.base | Core function for calculating sample sizes |
| excludeFeatures | Exclude specific features at a specified taxonomic rank. Only... |
| filterLowAbun | Filter Low Abundance Features |
| filterLowPrev | Filter Low Prevalence Features |
| filterLowRelAbun | Filter Low Relative Abundance Features |
| filterLowTotAbun | Filter Low Total Abundance Features |
| filterLowVar | Filter Low Variance Features |
| filterNAs | Filter Unassigned Taxa |
| findSigFisher | Run Fisher Test on Features |
| foldChange | Calculate Fold Change |
| ftcor | Compute feature correlation matrices for each group and all... |
| ftRatio | Calculate ratio between two features |
| ftRatiostab | Generate a table of feature ratios |
| getdata | Get Data with/without Attached Metadata |
| getDiscriminatingFeatures | Get features that uniquely identify one group from other... |
| getFeatures | Get list of features in a dataset |
| getFormulaVars | Extract Variables from a Formula |
| getFtStats | Get Feature Statistics for Filtering |
| getLowestRank | Get Lowest Rank in a Dataset |
| getNetwork | Get the co-occurence network for a dataset |
| getParentTaxa | Get parent taxa |
| getRanks | Get All Ranks of a Dataset |
| getSamples | Get samples with certain metadata characteristics from a... |
| ggcorrplot | Visualization of a correlation matrix using ggplot2 |
| glog | Generalized Log |
| keepSigFisher | Function for setting whether or not to run Fisher tests to... |
| listsigs | List Significant Features of a Dataset in Current State |
| listUniques | List features uniquely over/under-expressed in a specified... |
| loadFxnlFile | Load pathways file |
| loadMDFile | Load metadata file |
| loadTaxaFile | Load Taxonomy File |
| makeAldex | Make an ALDEx2 CLR Object |
| makeASVtab | Make ASV Table |
| makeDeseq | Make a DESeq object from a MicroVis dataset |
| makePS | Make a phyloseq object from a MicroVis dataset |
| makeRankTabs | Make Abundance Tables at Each Rank |
| makeTaxMap | Make a taxmap object from a MicroVis dataset |
| multisave | Determine how to save multiple figures |
| mvaldex | ALDEx2 Differential Abundance Analysis |
| mvCClasso | CClasso Network Analysis |
| mvcombine | Merge Two Datasets with Different Sample Sets |
| mvdeseq | DESeq2 Analysis |
| mvdist | Distance Calculation |
| mvhelp | List available functions |
| mvlefse | LEfSe Analysis |
| mvLMEM | Linear Mixed Effects Model Discriminant Analysis |
| mvload | MicroVis Data Loading |
| mvmelt | Melt the metadata and abundance table at a given rank for the... |
| mvmerge | Merge Two Datasets with Overlapping Samples |
| mvNetwork | Construct an association network between features |
| mvsave | Save Dataset in its Current State |
| mvstratify | Make a melted data table grouped by strata |
| mvunifrac | Unifrac Distance Calculation |
| nameAnalysis | Automatically name the analysis based on factors and the... |
| nameStratification | Standardized naming of the stratification of an analysis |
| networkClusters | Get feature clusters determined by network analysis |
| normalizer | Normalizing Function |
| normalizeTable | Normalize a Standalone Abundance Table |
| norm_to_total | Total Sum Normalize |
| orderGroups | Order Groups |
| pairedCor | Correlate abundance of features between paired samples |
| parseStratifiers | Parse Stratifiers |
| phyloDiversity | Faith's Phylogenetic Diversity Index |
| pipe | Pipe operator |
| plotAlphaDiv | Plot Alpha Diversity |
| plotBetaDiv | Plot Beta Diversity |
| plotClad | Plot Cladogram |
| plotDeseq | Plot DESeq Results |
| plotFeatureDensity | Plot distribution curves of abundances of each feature across... |
| plotFtCorlines | Plot correlation trendlines between different features |
| plotFtCormat | Plot feature correlation matrix |
| plotGroupedBars | Plot grouped bar plot of significant taxa at each rank of all... |
| plotHeatmap | Plot Heatmap of Data |
| plotHeatTree | Plot Heat Tree |
| plotLEFSE | Plot LEfSe analysis (not cladogram plot) |
| plotLMEM | Plot Volcano Plots of LMEM Log2FC Results |
| plotNetwork | Plot Feature Network |
| plotPairedCor | Correlate abundance of features between paired samples |
| plotRareCurves | Plot rarefaction curves |
| plotRFImp | Plot random forest important features |
| plotSampleDensity | Plot distribution curves of feature abundances in each sample |
| plotSimilarity | Plot similarity matrix between samples |
| plotStackedBars | Plot stacked abundace barplots |
| plotUnivar | Plot box-plots of univariate analysis |
| pnova | PERMANOVA Analysis |
| poolGroups | Pool groups of a factor into fewer, larger groups |
| posthoctoggle | Switch between Tukey/Games-Howell or T-test/Wilcox for... |
| print.mvdata | Print function for mvdata (MicroVis dataset) objects |
| print.mvmerged | Print function for mvmerged (merged MicroVis dataset) objects |
| processDataset | Process Dataset for Analysis |
| pval.sparccboot | SparCC p-vals |
| rangetotext | Translate Range Factor Levels into Interpretable Text |
| rarefySamples | Data Rarefaction |
| readdepth | Get read depth summary statistics for each group or for all... |
| removeGrps | Remove Groups |
| removeLowQuality | Remove Low Quality Samples |
| removePool | Remove a factor of pooled groups |
| removeSamples | Remove Specific Samples |
| resetResDir | Reset the Results Directory |
| rfboruta | Perform random forest Boruta analysis |
| runFeatureFilter | Feature Filter |
| runFeatureRemover | Feature Remover |
| runNormalization | Data Normalization |
| runRarefaction | Rarefy Dataset |
| runSampleFilter | Sample Filter |
| sampleFreq | Frequency table of samples |
| samplesWith | Filter a datatable to only samples with certain metadata... |
| saveResults | Save figure and statistics results |
| savetoggle | Switch Saving Mode |
| scaleFeatures | Scale Features |
| scaleSamples | Scale Samples |
| selectFeatures | Select Specific Features |
| setFVar | Set Factor Variable |
| sliceCormats | Select only significant and/or high-correlation values from... |
| sparcc | Sparcc wrapper |
| sparccboot | Bootstrap SparCC |
| summarizeTaxa | Get mean and SE of features |
| TaxatoASV | Translate Taxa Names to ASV Numbers |
| theme_mv | MicroVis ggplot theme |
| transData | Data Transformation |
| univar | Perform Univariate Analysis |
| unselectFeatures | Undo Feature Selection |
| validFactor | Factor Validation |
| viewactive | View the active dataset in RStudio Viewer |
| viewstats | View Statistics of All Features |
| viewtable | View Abundance Table |
| zeroReplace | Replace Zeros with Non-Zero Value |
| zerostoggle | Switch Method for Replacing Zeros |
