plotFastqcPCA {ngsReports} | R Documentation |
Draw a PCA plot for Fast QC modules across multiple samples
plotFastqcPCA( x, module = "Per_sequence_GC_content", usePlotly = FALSE, labels, sz = 4, groups, ... ) ## S4 method for signature 'ANY' plotFastqcPCA( x, module = "Per_sequence_GC_content", usePlotly = FALSE, labels, sz = 4, groups, ... ) ## S4 method for signature 'character' plotFastqcPCA( x, module = "Per_sequence_GC_content", usePlotly = FALSE, labels, sz = 4, groups, ... ) ## S4 method for signature 'FastqcDataList' plotFastqcPCA( x, module = "Per_sequence_GC_content", usePlotly = FALSE, labels, sz = 4, groups, ... )
x |
Can be a |
module |
|
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 |
sz |
The size of the text labels |
groups |
Optional factor of the same length as x. If provided, the plot will be coloured using this factor as the defined groups. Ellipses will also be added to the final plot. |
... |
Used to pass additional attributes to theme() and between methods |
This carries out PCA on a single FastQC module and plots the output using either ggplot or plotly. Current modules for PCA are Per_base_sequence_quality, Per_sequence_quality_scores, Per_sequence_GC_content, Per_base_sequence_content, and Sequence_Length_Distribution.
If a factor is provided in the groups argument, this will be applied to the
plotting colours and ellipses will be drawn using these groups.
Only the labels will be plotted using geom_text()
A standard ggplot2 object, or an interactive 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) grp <- as.factor(gsub(".+(R[12]).*", "\\1", fqName(fdl))) plotFastqcPCA(fdl, module = "Per_sequence_GC_content", groups = grp)