scsR (version 1.8.0)

plot_seeds_methods: plot seeds utility methods

Description

Plots informations about the effect of the seed on the screen

Usage

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)

Arguments

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)

Details

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.

Examples

	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))