track_reads_dada2: track_reads_dada2

In yeguanhuav/visualization416S: Visualization functions for 16S and Metagenomics analysis

track_reads_dada2

Description

track_reads_dada2 can track the reads count in a dada2 workflow result which created by Xbiome 16S pipeline. Xbiome 16S pipeline dada2 workflow will generate a list that contain sequence table, taxonomy table and reads track data frame. Input the reads track data frame and read type, this function can draw a line plot of reads track of every sample. X-axis will be every stage in dada2 workflow, Y-axis will be the reads counts.

Usage

track_reads_dada2(
  reads_track,
  single_end = FALSE,
  relative_abundance = TRUE,
  legend_position = "top",
  add_lines = FALSE
)

Arguments

reads_track	The reads track data frame from Xbiome 16S pipeline dada2 workflow result.
single_end	Default is FALSE. If single_end == TRUE, means the sequence files are single end, the x-axis will contain 'input', 'filtered', 'dereplicated', 'nonchim'. If single_end == FALSE, means the sequence files are paired end, the x-axis will contain 'input', 'filtered', 'denoisedF', 'denoisedR', 'merged', 'nonchim'.
relative_abundance	Default is TRUE. If TRUE, will turn values to relative abundance.
legend_position	Legend position. Default is top. One of c("none", "left", "right", "bottom", "top").
add_lines	Default FALSE. If TRUE, add lines to the plot, lines represent the nochim reads of each sample.

Examples

track_reads_dada2(demo_dada2_result$reads_track, single_end = FALSE)

yeguanhuav/visualization416S documentation built on March 22, 2022, 9:03 p.m.