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

Description Usage Arguments Value Examples

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