The given position weight matrix is plotted as a heatmap or sequence logo
viz_pwm( pwm_mat, method = "heatmap", pos_lab = NULL, pdf_name = NULL, fixed_coord = FALSE, bits_yax = "full" )
Matrix (usually a PWM, but can be any non-normalized matrix) to be visualized. Rownames must be letters.
Character. Set this to 'heatmap' when plotting a heatmap, else you can set it to either of 'custom', 'bits', or 'probability' when you wish to visualize it as a sequence logo. Default is 'heatmap'.
Labels for sequence positions, should be of same length as that of the sequences. Default value is NULL, when the positions are labeled from 1 to the length of the sequences.
Name of the file which will be saved as PDF.
Set this to TRUE to use a fixed aspect ratio for the plot. Default is FALSE.
Specify 'full' if the information content y-axis limits should be 0-2 or 'auto' for a suitable limit. The 'auto' setting adjusts the y-axis limits according to the maximum information content of the sequence logo. Default is 'full'.
A ggplot object so you can simply call
on it later. If
pdf_name is given, it is also saved and the
ggplot2 object returned.
res <- readRDS(system.file("extdata", "example_seqArchRresult.rds", package = "seqArchR", mustWork = TRUE)) pwm <- seqArchR::make_PWMs(get_clBasVec_m(res,iter=1)[,1], add_pseudo_counts = FALSE, sinuc = FALSE) viz_pwm(pwm_mat = pwm, method = "heatmap", fixed_coord = TRUE) viz_pwm(pwm_mat = pwm, method = "bits", fixed_coord = TRUE) #> Scale for x is already present. #> Adding another scale for x, which will replace the existing scale. #> Coordinate system already present. Adding new coordinate system, which will #> replace the existing one.