runPathoStat {PathoStat} | R Documentation |
Statistical Microbiome Analysis on the pathostat input and generates a html report and produces interactive shiny app plots
runPathoStat(pstat = NULL, report_file = "PathoStat_report.html", report_dir = ".", report_option_binary = "111111111", view_report = FALSE, interactive = TRUE)
pstat |
phyloseq extension pathostat object |
report_file |
Output report file name |
report_dir |
Output report directory path |
report_option_binary |
9 bits Binary String representing the plots to display and hide in the report |
view_report |
when TRUE, opens the report in a browser |
interactive |
when TRUE, opens the interactive shinyApp |
outputfile The output file with all the statistical plots
runPathoStat(interactive = FALSE)