knitr::opts_chunk$set(echo = TRUE,warning=FALSE, message=FALSE, out.width = "49%") ## This report requires summary files form mothur debug <- FALSE
### create plots:5. pheatmap show_pHeatmap <- heatmapForPhylotseqPlotPheatmap(inputData,designMatrix)
Started on r format(Sys.time(), "%Y-%m-%d %H:%M:%S")
kable(finalListOfSummaryTables["MapFiltSummary"]$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$aboveHeader) %>% scroll_box(width = "100%", height = "600px")
plot(chimeraPlotsToReport)
kable(convStepTableToReport["stepConvergenceSummary"]$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$aboveHeader) %>% scroll_box(width = "100%", height = "600px")
plot(otuSaturPlotToReport)
par(mfrow=c(1,2), las=1) plot(abundPlot) plot(abundPlotGroup)
par(mfrow=c(1,2), las=1) plot(plotOrdTaxa) plot(plotOrdSamples)
plot(plotRichness)
plot(plotTree)
par(mfrow=c(1,2), las=1) for (RarPlot in rarefPlot){ plot(RarPlot) }
show_pHeatmap()
par(mfrow=c(1,3), las=1) plot(deseqResults$vPlot) plot(deseqResults$logPlot) plot(deseqResults$pieChart)
kable(deseqResults$table, escape=TRUE, row.names=FALSE, format="html") %>% kable_styling(bootstrap_options = c("striped", "bordered"), full_width = T) %>% scroll_box(width = "100%", height = "600px")
sessionInfo()
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