Usage
carpools.read.count.vs(dataset, namecolumn=1, fullmatchcolumn=2, title="Read Count",
dataset.names = NULL, xlab="Readcount Dataset1", ylab="Readcount Dataset2", xlim=NULL,
ylim=NULL, pch=16, col = rgb(0, 0, 0, alpha = 0.65), labelgenes=NULL, labelcolor="red",
extractpattern=expression("^(.+?)_.+"), plotline=TRUE, normalize=TRUE,
norm.function=median, offsetplot=1.2, center=FALSE, aggregated=FALSE,
pairs=FALSE, type=NULL, plot.identify=FALSE, plot.log=TRUE)
Arguments
dataset
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)
title
The title of the plot.
*Default* "Read Count"
*Values* "Any title" (character)
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)
xlab
Label of X-Axis, only if `pairs=FALSE`
*Default* "X-Axis"
*Values* "Label of X-Axis" (character)
ylab
Label of Y-Axism only if `pairs=FALSE`
*Default* "Y-Axis"
*Values* "Label of Y-Axis" (character)
xlim
You can define the x-axis range being plotted, e.g. `c(0,1)`.
*Default* empty
*Values* empty or a vector with the lower and upper limit.
ylim
You can define the y-axis range being plotted, e.g. `c(0,1)`.
*Default* empty
*Values* empty or a vector with the lower and upper limit.
pch
The type of point used in the plot. See `?par()`.
*Default* 16
*Values* Any number describing the point, e.g. 16 (numeric)
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)
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.
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)
plotline
You can draw additional lines indicating a fold change of 0, 2, 4.
*Default* TRUE
*Values** TRUE, FALSE (boolean)
normalize
Whether you would like to normalize read-counts first. Recommended if not done already.
*Default* TRUE
*Values* TRUE, FALSE (boolean)
norm.function
The mathematical function to normalize data if `normalize=TRUE`. By default, the median is used.
*Default* median
*Values* Any mathematical function of R (function)
offsetplot
Offetplot is used to stretch the x- and y-axis for nicer graphs. This will extend plotting area by offsetplot.
*Default* 1.2 (Plotting area is streched to 1.2 times)
*Values* any number (numeric)
center
If you like you can center your data within the plot.
*Default* FALSE
*Values* TRUE, FALSE (boolean)
aggregated
If you want to highlight genes, set this to true if you provide already aggregated gene read count instead of sgRNA read counts.
*Default* FALSE
*Values* TRUE, FALSE (boolean)
pairs
In the case of plotting all four data sets at once, you can use a pairs plot for easier overview (see `?pairs()`).
*Default* FALSE
*Values* TRUE, FALSE (boolean)
type
This indicates whether you would like to color all highlighted genes in either red ("enriched") or blue ("depleted") color according to the standrds in caRpools for plotting enriched or depleted genes after analysis.
*Default* NULL
*Values* NULL, "enriched", "depleted"
plot.identify
You can ask R to let you identify genes by clikcing on the dots in the graph. This only works if `pairs=FALSE`.
*Default* FALSE
*Values* TRUE, FALSE (boolean)
plot.log
If all plots are created using log-transformed data.
*Default* TRUE
*Values* TRUE, FALSE (boolean)