Description Usage Arguments Details Value Note Author(s) Examples
You can also visualize the read depth of genes per sgRNA in order to check for sufficient sequencing depth using 'carpools.read.depth'. For further details see '?carpools.read.depth'. You can either plot single dat samples or all four data samples at once.
1 2 3 4 5 | carpools.read.depth(datasets, namecolumn=1, fullmatchcolumn=2, dataset.names=NULL,
extractpattern=expression("^(.+?)_.+"), col=rgb(0, 0, 0, alpha = 0.65), xlab="Genes",
ylab="Read Count per sgRNA", statistics=TRUE, labelgenes = NULL,
controls.target = controls.target,
controls.nontarget=controls.nontarget, labelcolor="orange", waterfall=FALSE)
|
datasets |
A list of data frames of read-count data as created by load.file(). *Default* none *Values* A list of data frames |
namecolumn |
In which column are the sgRNA identifiers? *Default* 1 *Values* column number (numeric) |
fullmatchcolumn |
In which column are the read counts? *Default* 2 *Values* column number (numeric) |
dataset.names |
A list of names that must be according to the list of data sets given in *dataset*. *Default* NULL *Value* NULL or list of data names (list) |
extractpattern |
PERL regular expression that is used to retrieve the gene identifier from the overall sgRNA identifier. e.g. in **AAK1_107_0** it will extract **AAK1**, since this is the gene identifier beloning to this sgRNA identifier. **Please see: Read-Count Data Files** *Default* expression("^(.+?)(_.+)"), will work for most available libraries. *Values* PERL regular expression with parenthesis indicating the gene identifier (expression) |
col |
The color of the plotted data. Can be any R color or RGB object. See ?rgb() for further information. *Default* rgb(0, 0, 0, alpha = 0.65) *Values* Any R color name or RGB color object (character OR color object) |
xlab |
Label of X-Axis *Default* "X-Axis" *Values* "Label of X-Axis" (character) |
ylab |
Label of Y-Axis *Default* "Y-Axis" *Values* "Label of Y-Axis" (character) |
statistics |
Whether basic stattistics will be shown in the plot. *Default* TRUE *Values* TRUE, FALSE (boolean) |
labelgenes |
You can highlight certain genes within the plot. This expects a gene identifier or a fector of gene identifiers. *Default* NULL *Values* A gene identifier or vector of gene identifiers (character) |
labelcolor |
Color to highlight genes stated in 'labelgenes'. *Default* "organge" *Values* Any R color or RGB color object. |
controls.target |
Highlights the positive control in red color. *Default* NULL *Value* Gene Identifier (character) |
controls.nontarget |
Highlights the non-targeting control in blue color. *Default* "random" *Value* Gene Identifier (character) |
waterfall |
You can either plot the read depth sorted by gene identifier (FALSE, default) or according to the read depth. *Default* FALSE *Values* TRUE, FALSE (boolean) s |
notes
plot.read.depth returns a generic plot.
none
Jan Winter
1 2 3 4 5 6 | data(caRpools)
carpools.read.depth(datasets = list(CONTROL1), namecolumn=1 ,fullmatchcolumn=2,
dataset.names=list(d.CONTROL1), extractpattern=expression("^(.+?)_.+"),
xlab="Genes", ylab="Read Count per sgRNA",statistics=TRUE, labelgenes = NULL,
controls.target = "CASP8", controls.nontarget="random", waterfall=FALSE)
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