viewPWM {KinSwingR} | R Documentation |
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.
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