track_reads_dada2: track_reads_dada2

Description Usage Arguments Examples

View source: R/track_reads_dada2.R

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

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track_reads_dada2(reads_track, single_end = FALSE,
  relative_abundance = FALSE, 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 FALSE. 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

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track_reads_dada2(demo_dada2_result$reads_track, single_end = FALSE)

yeguanhuav/visual16S documentation built on Aug. 11, 2019, 8:51 a.m.