plot_seeds_methods: plot seeds utility methods
In scsR: SiRNA correction for seed mediated off-target effect

Description Usage Arguments Details Author(s) Examples

Plots informations about the effect of the seed on the screen

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plot_effective_seeds_head(screen, seedColName="seed7",  scoreColName="score", enhancer_analysis=FALSE, min_oligos_x_seed=10, number_of_seeds=20, output_file=NULL, color="#CCCCCC33", colorBG="#0000CC11", xlim=c(-4,4), title="")

plot_seeds_oligo_count(screen, seedColName="seed7", scoreColName="score", output_file=NULL)

`screen`	data frame containing the results of the siRNA experiment.
`seedColName`	name of the column that contains the seed of the siRNA oligo sequences of the screen (character vector) (the sequences have to be provided in the guide/antisense orientation and each sequence must be in the format of a character vector, i.e. a simple string)
`scoreColName`	name of the column that contains the score of the screen (character vector)
`enhancer_analysis`	if set to true plot the seeds that cause the oligos to have an higher score instead of a lower score. (boolean)
`min_oligos_x_seed`	minimum number of oligos that seed must have in order to be considered (integer)
`number_of_seeds`	maximum number of seeds to represent in the graph (by default the top 20 seeds are shown) (integer)
`output_file`	name of the pdf file where to store the graph (character vector)
`color`	color of the bars that represent the seeds (character vector)
`colorBG`	color of the bars that represent the noise (i.e. analysis executed on randomized data) (character vector)
`xlim`	xlim of the graph (number)
`title`	title of the graph (number)

The methods currently depend on the type of to:

plot_effective_seeds_head: barplot that represents the most effective seeds as bar (the length of the bars corresponds to the average score of the oligos that contain that seed). A background bar is shown under every seed. We obtain these bar simply randomizing the score column of the screen (and they well represent the noise level).
plot_seeds_oligo_count: For each seed that is found in the siRNA screen, plots the number of oligos that contain that seed.
plot_seed_score_sd: For each seed plot its average score and its standard deviation.
plot_screen_seeds_count: For each siRNA oligo, plot the number of the other oligos in the screen that share the same seed.

Andrea Franceschini

	data(uuk_screen)

	# to speed up the example we use only the first 2500 rows
	uuk_screen_reduced = uuk_screen[1:5000,]

	plot_effective_seeds_head(add_seed(uuk_screen_reduced))