plot_seeds_methods {scsR} | R Documentation

## 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.

### Author(s)

Andrea Franceschini

### 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))

[Package scsR version 1.23.0 Index]