plotGcContent {ngsReports} | R Documentation |
Plot the Per Sequence GC Content for a set of FASTQC files
plotGcContent(x, usePlotly = FALSE, labels, theoreticalGC = TRUE, gcType = c("Genome", "Transcriptome"), species = "Hsapiens", GCobject, Fastafile, n = 1e+06, ...) ## S4 method for signature 'ANY' plotGcContent(x, usePlotly = FALSE, labels, theoreticalGC = TRUE, gcType = c("Genome", "Transcriptome"), species = "Hsapiens", GCobject, Fastafile, n = 1e+06, ...) ## S4 method for signature 'character' plotGcContent(x, usePlotly = FALSE, labels, theoreticalGC = TRUE, gcType = c("Genome", "Transcriptome"), species = "Hsapiens", GCobject, Fastafile, n = 1e+06, ...) ## S4 method for signature 'FastqcData' plotGcContent(x, usePlotly = FALSE, labels, theoreticalGC = TRUE, gcType = c("Genome", "Transcriptome"), species = "Hsapiens", GCobject, Fastafile, n = 1e+06, counts = FALSE, lineCols = c("red", "blue"), ...) ## S4 method for signature 'FastqcDataList' plotGcContent(x, usePlotly = FALSE, labels, theoreticalGC = TRUE, gcType = c("Genome", "Transcriptome"), species = "Hsapiens", GCobject, Fastafile, n = 1e+06, plotType = c("heatmap", "line"), pwfCols, cluster = FALSE, dendrogram = FALSE, ...)
x |
Can be a |
usePlotly |
|
labels |
An optional named vector of labels for the file names. All filenames must be present in the names. File extensions are dropped by default. |
theoreticalGC |
|
gcType |
|
species |
|
GCobject |
an object of class GCTheoretical. Defaults to the gcTheoretical object supplied with the package |
Fastafile |
a fasta file contains DNA sequences to generate theoretical GC content |
n |
number of simulated reads to generate theoretical GC content from
|
... |
Used to pass various potting parameters to theme. |
counts |
|
lineCols |
Colors for observed and theoretical GC lines in single plots |
plotType |
Takes values "line" or "heatmap" |
pwfCols |
Object of class |
cluster |
|
dendrogram |
|
Makes plots for GC_Content. When applied to a single FastqcData object a simple line plot will be drawn, with Theoretical GC content overlaid if desired.
When applied to multiple FastQC reports, the density at each GC content bin
can be shown as a heatmap by setting theoreticalGC = FALSE
. By
default the difference in observed and expected theoretical GC is shown.
Species and genome/transcriptome should also be set if utilising the
theoretical GC content.
As an alternative to a heatmap, a series of overlaid distributions can be
shown by setting plotType = "line"
.
Can produce a static ggplot2 object or an interactive plotly object.
A ggplot2 or plotly object
# Get the files included with the package packageDir <- system.file("extdata", package = "ngsReports") fl <- list.files(packageDir, pattern = "fastqc.zip", full.names = TRUE) # Load the FASTQC data as a FastqcDataList object fdl <- FastqcDataList(fl) # The default plot for a FastqcDataList plotGcContent(fdl) # Plot a single FastqcData object plotGcContent(fdl[[1]])