diff --git a/NAMESPACE b/NAMESPACE index a6126d3..98064a9 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,140 +1,75 @@ # Generated by roxygen2: do not edit by hand -export(betadiv) -export(betatest) -export(biomarker) -export(buildTree) -export(difftest) -export(distcolor) -export(do_aov) -export(do_ttest) -export(do_wilcox) -export(ldamarker) -export(lightcolor) -export(normalize) -export(otu_table) -export(phy_tree) -export(plotLDA) -export(plotalpha) -export(plotbar) -export(plotbeta) -export(plotdiff) -export(plotmarker) -export(plotquality) -export(preRef) -export(prefilter) -export(processSeq) -export(richness) -export(sample_data) -export(subset_samples) -export(subset_taxa) -export(tax_table) -importFrom(Biostrings,DNAStringSet) -importFrom(DECIPHER,AlignSeqs) -importFrom(DESeq2,DESeq) -importFrom(DESeq2,DESeqDataSetFromMatrix) -importFrom(DESeq2,counts) -importFrom(DESeq2,estimateDispersions) -importFrom(DESeq2,estimateSizeFactors) -importFrom(DESeq2,results) -importFrom(DESeq2,varianceStabilizingTransformation) -importFrom(MASS,lda) -importFrom(S4Vectors,DataFrame) -importFrom(SummarizedExperiment,assay) +export(.setcolnames) +export(convertplot) +export(indocx) +export(infigure) +export(inoffice) +export(inpptx) +export(todocx) +export(toffice) +export(tofigure) +export(tohtml) +export(topptx) +export(totable) +export(toxlsx) +importFrom(R.devices,devEval) importFrom(broom,tidy) -importFrom(dada2,addSpecies) -importFrom(dada2,assignTaxonomy) -importFrom(dada2,dada) -importFrom(dada2,derepFastq) -importFrom(dada2,filterAndTrim) -importFrom(dada2,getSequences) -importFrom(dada2,getUniques) -importFrom(dada2,learnErrors) -importFrom(dada2,makeSequenceTable) -importFrom(dada2,mergePairs) -importFrom(dada2,plotQualityProfile) -importFrom(dada2,removeBimeraDenovo) -importFrom(dplyr,bind_rows) -importFrom(dplyr,do) -importFrom(dplyr,filter) -importFrom(dplyr,group_by) -importFrom(dplyr,group_by_at) -importFrom(dplyr,left_join) -importFrom(dplyr,mutate) -importFrom(dplyr,one_of) -importFrom(dplyr,pull) -importFrom(dplyr,select) -importFrom(dplyr,summarise) -importFrom(dplyr,summarize) -importFrom(dplyr,ungroup) -importFrom(dplyr,vars) -importFrom(edgeR,calcNormFactors) +importFrom(devEMF,emf) +importFrom(dplyr,filter_) +importFrom(dplyr,select_) +importFrom(flextable,align) +importFrom(flextable,autofit) +importFrom(flextable,body_add_flextable) +importFrom(flextable,bold) +importFrom(flextable,empty_blanks) +importFrom(flextable,flextable) +importFrom(flextable,font) +importFrom(flextable,hline) +importFrom(flextable,theme_booktabs) importFrom(ggplot2,aes) importFrom(ggplot2,aes_string) -importFrom(ggplot2,coord_flip) importFrom(ggplot2,element_blank) -importFrom(ggplot2,element_text) importFrom(ggplot2,geom_bar) -importFrom(ggplot2,geom_point) +importFrom(ggplot2,geom_text) importFrom(ggplot2,ggplot) -importFrom(ggplot2,scale_color_manual) +importFrom(ggplot2,last_plot) importFrom(ggplot2,scale_fill_manual) -importFrom(ggplot2,scale_y_continuous) -importFrom(ggplot2,stat_ellipse) importFrom(ggplot2,theme) -importFrom(ggplot2,theme_light) -importFrom(ggplot2,xlab) -importFrom(ggplot2,ylab) -importFrom(ggpubr,facet) -importFrom(ggpubr,ggboxplot) -importFrom(ggpubr,ggdotchart) -importFrom(ggpubr,ggdotplot) -importFrom(ggpubr,ggviolin) -importFrom(ggpubr,stat_pvalue_manual) +importFrom(ggplotify,as.ggplot) +importFrom(ggplotify,as.grob) +importFrom(grDevices,col2rgb) +importFrom(grDevices,dev.cur) +importFrom(grDevices,dev.off) +importFrom(grDevices,dev.size) +importFrom(grDevices,hcl) +importFrom(grDevices,recordPlot) +importFrom(grDevices,rgb) +importFrom(graphics,plot) +importFrom(htmlwidgets,saveWidget) +importFrom(magick,image_ggplot) +importFrom(magick,image_raster) +importFrom(magick,image_read) +importFrom(magick,image_read_pdf) +importFrom(magick,image_read_svg) +importFrom(magick,image_write) importFrom(magrittr,"%>%") -importFrom(phangorn,NJ) -importFrom(phangorn,dist.ml) -importFrom(phangorn,optim.pml) -importFrom(phangorn,phyDat) -importFrom(phangorn,pml) -importFrom(phangorn,pml.control) -importFrom(phyloseq,'tax_table<-') -importFrom(phyloseq,`otu_table<-`) -importFrom(phyloseq,distance) -importFrom(phyloseq,estimate_richness) -importFrom(phyloseq,get_taxa_unique) -importFrom(phyloseq,nsamples) -importFrom(phyloseq,ordinate) -importFrom(phyloseq,otu_table) -importFrom(phyloseq,phyloseq) -importFrom(phyloseq,prune_taxa) -importFrom(phyloseq,psmelt) -importFrom(phyloseq,sample_data) -importFrom(phyloseq,subset_taxa) -importFrom(phyloseq,t) -importFrom(phyloseq,tax_table) -importFrom(phyloseq,taxa_are_rows) -importFrom(phyloseq,taxa_sums) -importFrom(phyloseq,transform_sample_counts) -importFrom(plyr,ddply) -importFrom(randomForest,importance) -importFrom(randomForest,randomForest) -importFrom(rlang,`!!`) -importFrom(rstatix,anova_test) -importFrom(rstatix,t_test) -importFrom(rstatix,wilcox_test) -importFrom(stats,as.formula) -importFrom(stats,kruskal.test) -importFrom(stats,p.adjust) -importFrom(stats,reorder) -importFrom(stats,update) -importFrom(tidyr,gather) -importFrom(tidyr,spread) -importFrom(utils,download.file) -importFrom(utils,head) -importFrom(utils,read.delim) -importFrom(utils,write.table) -importFrom(vegan,adonis) -importFrom(vegan,diversity) -importFrom(vegan,rarefy) -importFrom(vegan,specnumber) +importFrom(officer,add_slide) +importFrom(officer,body_add_img) +importFrom(officer,body_add_par) +importFrom(officer,docx_summary) +importFrom(officer,fp_border) +importFrom(officer,ph_location) +importFrom(officer,ph_location_type) +importFrom(officer,ph_with) +importFrom(officer,pptx_summary) +importFrom(officer,read_docx) +importFrom(officer,read_pptx) +importFrom(officer,read_xlsx) +importFrom(officer,slide_size) +importFrom(plotly,as_widget) +importFrom(plotly,ggplotly) +importFrom(rvg,dml) +importFrom(rvg,xl_add_vg) +importFrom(stats,formula) +importFrom(utils,type.convert)