Description Usage Arguments Examples
View source: R/track_reads_dada2.R
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.
1 2 3 4 5 6 7 | track_reads_dada2(
reads_track,
single_end = FALSE,
relative_abundance = TRUE,
legend_position = "top",
add_lines = FALSE
)
|
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. |
1 | track_reads_dada2(demo_dada2_result$reads_track, single_end = FALSE)
|
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