In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

knitr::opts_chunk$set(echo = TRUE,warning=FALSE, message=FALSE, out.width = "49%")
## This report requires summary files form mothur
debug <- FALSE

  ### create plots:5. pheatmap
  show_pHeatmap <- heatmapForPhylotseqPlotPheatmap(inputData,designMatrix)

Started on r format(Sys.time(), "%Y-%m-%d %H:%M:%S")

Data pre-processing {.tabset}

Mothur data analysis: summary of the reads filtered by mapping

kable(finalListOfSummaryTables["MapFiltSummary"]$MapFiltSummary$mergedTable, escape=TRUE, row.names=FALSE, format="html") %>%
  kable_styling(bootstrap_options = c("striped", "bordered"),
                full_width = T) %>%
  group_rows(index = finalListOfSummaryTables["MapFiltSummary"]$MapFiltSummary$aboveHeader) %>%
  scroll_box(width = "100%", height = "600px")

Mothur data analysis: summary of the reads preclustered and filtered for chimeras

  plot(chimeraPlotsToReport)

Mothur data analysis: OTUs convergence summary

kable(convStepTableToReport["stepConvergenceSummary"]$stepConvergenceSummary$mergedTable, escape=TRUE, row.names=FALSE, format="html") %>%
  kable_styling(bootstrap_options = c("striped", "bordered"),
                full_width = T) %>%
  group_rows(index = convStepTableToReport["stepConvergenceSummary"]$stepConvergenceSummary$aboveHeader) %>%
  scroll_box(width = "100%", height = "600px")

Mothur data analysis: OTUs saturation plots

  plot(otuSaturPlotToReport)

Phyloseq analysis: abundance barplots

If samples are grouped, the second plot is more informative

plot(abundPlot)

Phyloseq analysis: richness plots

plot(plotRichness)

Phyloseq analysis:rarefaction plots

par(mfrow=c(1,2), las=1)
for (RarPlot in rarefPlot){
plot(RarPlot)
}

SessionInfo

sessionInfo()

uzh/ezRun documentation built on May 4, 2024, 3:23 p.m.