Builds a self-contained HTML report from a DEprot or
DEprot.analyses object. The report always includes a quality-control
(QC) section (analysis parameters, value distributions, PCA of PC1/PC2/PC3
and sample correlation heatmaps) and, when differential analyses are present
in the object (DEprot.analyses), a results section reporting the
parameters used, a cross-contrast summary and, for each contrast, the volcano
plot, MA-plot and the top differential proteins. A final section lists the R
session and the versions of the packages used to generate the report.
The function writes a parameterised R Markdown document to a temporary file
and renders it with rmarkdown::render(); all plots are produced with
the native DEprot plotting functions (perform.PCA,
plot.PC.scatter.123, plot.PC.cumulative,
plot.correlation.heatmap, plot.volcano and
plot.MA) or the plots already stored inside the object.
export.report(
DEprot.object,
output.file = "DEprot.report.html",
report.title = "DEprot report",
author.name = "DEprot",
which.data = NULL,
correlation.method = c("pearson", "spearman"),
correlation.display.values = TRUE,
PCA.color.column = "column.id",
PCA.shape.column = NULL,
PCA.label.column = NULL,
protein.summary.group.column = "column.id",
volcano.use.uncorrected.pvalue = FALSE,
show.MA.plot = TRUE,
include.contrast.qc = TRUE,
top.n.proteins = 25,
plot.width = 8,
plot.height = 5.5,
self.contained = TRUE,
keep.Rmd = FALSE,
quiet = TRUE
)An object of class DEprot or DEprot.analyses.
String with the path (or file name) of the HTML file to create. A .html extension is added when missing. Default: "DEprot.report.html".
String used as the report title. Default: "DEprot report".
String used as the report author. Default: "DEprot".
String indicating which counts to use for the QC section.
One among 'raw', 'normalized'/'norm', 'randomized'/'random',
'imputed'/'imp'. Default: NULL, in which case the best available data
are chosen automatically (imputed > normalized > randomized > raw).
Character vector with the correlation method(s) to display in the QC section. Any of 'pearson', 'spearman', 'kendall'. Default: c("pearson", "spearman").
Logical; whether the correlation coefficient is printed inside each cell of the sample-correlation heatmaps. Default: TRUE.
String with the metadata column used to color the PCA points. Default: "column.id" (one color per sample).
String with the metadata column used for the PCA point shapes. Default: NULL.
String with the metadata column used to label the PCA points. Default: NULL.
String with the metadata column used to group samples in the protein-summary barplot (absolute protein counts). Default: "column.id" (one bar per sample).
Logical; if TRUE the volcano plots are regenerated using the uncorrected p-value. Default: FALSE.
Logical; whether to include the MA-plot for each contrast. Default: TRUE.
Logical indicating whether to additionally include the per-contrast PCA and correlation plots stored in the object. Default: TRUE.
Integer; number of top proteins shown in the per-contrast results table, ranked by a combined score -log10(padj) * abs(log2FC) (the score itself is not shown). Default: 25.
Numeric; default figure width and height (in inches) used in the report. Default: 8 and 5.5.
Logical indicating whether the HTML embeds all resources into a single portable file. Default: TRUE.
Logical; if TRUE the intermediate .Rmd source is copied next to the output file. Default: FALSE.
Logical indicating whether to suppress the rendering log. Default: TRUE.
Invisibly, the path to the generated HTML file.
if (FALSE) { # \dontrun{
# QC-only report (DEprot object)
export.report(DEprot.object = DEprot::test.toolbox$dpo.imp,
output.file = "QC.report.html",
report.title = "Proteomics QC",
author.name = "Jane Doe")
# Full report with differential analyses (DEprot.analyses object)
export.report(DEprot.object = DEprot::test.toolbox$diff.exp.limma,
output.file = "DE.report.html",
report.title = "FBS vs DCC differential analysis",
author.name = "Jane Doe",
PCA.color.column = "condition",
PCA.shape.column = "replicate")
} # }