bic.plot.alignment.summary: Plot numbers of mapped and unmapped reads for each sample

In bic-mskcc/bicrnaseq: MSKCC Bioinformatics Core RNASeq

Description

Stacked bar chart showing either absolute values or percentages of mapped and unmapped reads for R1 and R2 of each sample. Takes in data frame containing PICARD AlignmentSummaryMetrics, or at minimum a data frame with columns: CATEGORY, PF_READS, PF_READS_ALIGNED, SAMPLE, where CATEGORY column contains at least categories FIRST_OF_PAIR and SECOND_OF_PAIR.

Stacked bar chart showing either absolute values or percentages of mapped and unmapped reads for R1 and R2 of each sample. Takes in data frame containing PICARD AlignmentSummaryMetrics, or at minimum a data frame with columns: CATEGORY, PF_READS, PF_READS_ALIGNED, SAMPLE, where CATEGORY column contains at least categories FIRST_OF_PAIR and SECOND_OF_PAIR.

Usage

bic.plot.alignment.summary(dat, position = "stack", pct = FALSE,
  col.pal = "Set3", file = NULL)

bic.plot.alignment.summary(dat, position = "stack", pct = FALSE,
  col.pal = "Set3", file = NULL)

Arguments

dat	data frame of PICARD AlignmentSummaryMetrics, or at least containing columns CATEGORY, PF_READS, PF_READS_ALIGNED and SAMPLE, where CATEGORY contains at least values FIRST_OF_PAIR and SECOND_OF_PAIR
position	position of grouped bars; Default: "stack", option: "dodge"
pct	logical indicating whether to show percentages rather than absolute read counts
col.pal	name of color palette; must be from list of RColorBrewer palettes Default: "Set3"
file	PDF file to which plot should be saved (optional)
dat	data frame of PICARD AlignmentSummaryMetrics, or at least containing columns CATEGORY, PF_READS, PF_READS_ALIGNED and SAMPLE, where CATEGORY contains at least values FIRST_OF_PAIR and SECOND_OF_PAIR
pct	logical indicating whether to show percentages rather than absolute read counts
col.pal	name of color palette; must be from list of RColorBrewer palettes Default: "Set3"
position	position of grouped bars; Default: "stack", option: "dodge"
file	PDF file to which plot should be saved (optional)

bic-mskcc/bicrnaseq documentation built on May 24, 2019, 3:04 a.m.