viewPWM: View motif
In KinSwingR: KinSwingR: network-based kinase activity prediction

Description Usage Arguments Value Examples

View source: R/view_pwm.r

View information content for each position of the PWM. Information content is modelled using Shannon's Entropy Model. The maximum information content is therefore log2(n), where n is the number of amino acids. Colors of Amino Acids are in accordance with the Lesk scheme.

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viewPWM(pwm_in = NULL, which_pwm = NULL, fontsize = 10,
  view_pwm = FALSE, pseudo = 0.01, convert_PWM = FALSE,
  color_scheme = "shapely", correction_factor = NULL)

`pwm_in`	View a PWM provided using the buildPWM. Default = NULL
`which_pwm`	If pwms are input (outputs of buildPWM), a kinase name must match a name in pwms$kinase$kinase list of names. Default = NULL
`fontsize`	Font size to use on x and y axis. Default = 10
`view_pwm`	View the PWM. Default = FALSE
`pseudo`	Small amount added to the PWM model, where zero's exist, to avoid log zero. Default = 0.01
`convert_PWM`	pwm_in is a matrix of counts at position. TRUE will convert this matrix to a PWM. Default = FALSE
`color_scheme`	Which color scheme to use for Amino Acid Groups. Options are "lesk" or "shapely". Default = "shapely"
`correction_factor`	Number of sequences used to infer the PWM. This can be used where a small number of sequences were used to build the model and included as E_n in the Shannon's Entropy Model. Default = NULL

Visualisation of a motif, scaled on bits and two tables. 1) pwm: corresponding to the PWM from pwm and 2) pwm_bits: corresponding to the conversion to bits.

## Build PWM models from phosphositeplus data with default of minimum
## of 10 substrate sequences for building a PWM model.
data(phosphositeplus_human)
##randomly sample 1000 substrates for demonstration.
set.seed(1)
sample_pwm <- phosphositeplus_human[sample(nrow(phosphositeplus_human), 
1000),]
pwms <- buildPWM(sample_pwm)

## Data frame of models built and number of sequences used to build each
## PWM model:
head(pwms$kinase)
## Will not visualise the motif
CAMK2A_motif <- viewPWM(pwm_in = pwms, 
                        which_pwm = "CAMK2A",
                        view_pwm = FALSE)
# Use view_pwm = TRUE to view the motif