Plot LOGO of the pssm result from the regression

Usage

plot_pssm_logo(
  pssm,
  title = "Sequence model",
  subtitle = ggplot2::waiver(),
  pos_bits_thresh = NULL,
  revcomp = FALSE,
  method = "bits"
)

Arguments

pssm: PSSM matrix or data frame
title: title of the plot
subtitle: subtitle of the plot
pos_bits_thresh: Positions with bits above this threshold would be highlighted in red. If NULL, no positions would be highlighted.
revcomp: whether to plot the reverse complement of the PSSM
method: Height method, can be one of "bits" or "probability" (default:"bits")

Value

a ggplot object

Examples

pssm <- data.frame(
    pos = seq(0, 9, by = 1),
    A = c(
        0.16252439817826936, 0.4519127838188067, 0, 1, 0, 0.9789171974522293,
        0.9743866100297978, 0.013113942843003835, 0.3734676916683981,
        0.32658771473191045
    ),
    C = c(
        0.43038386467143785, 0.13116231900388756, 0, 0, 0, 0, 0, 0.46975132995175056,
        0.1669956368169541, 0.29795679333680375
    ),
    G = c(
        0.22999349381912818, 0.002929742520705392, 1, 0, 0, 0, 0.012679896024852597,
        0.4808858097241123, 0.4248389777685435, 0.20458094742321709
    ),
    T = c(
        0.1770982433311646, 0.41399515465660036, 0, 0, 1, 0.0210828025477707,
        0.012933493945349648, 0.03624891748113324, 0.0346976937461043,
        0.17087454450806872
    )
)
plot_pssm_logo(pssm)

if (FALSE) { # \dontrun{
res <- regress_pwm(sequences_example, response_mat_example)
plot_pssm_logo(res$pssm)
} # }