seqLogo               package:seqLogo               R Documentation

_P_l_o_t _a _s_e_q_u_e_n_c_e _l_o_g_o _f_o_r _a _g_i_v_e_n _p_o_s_i_t_i_o_n _w_e_i_g_h_t _m_a_t_r_i_x

_D_e_s_c_r_i_p_t_i_o_n:

     This function takes the 4xW position weight matrix of a DNA
     sequence motif and plots the corresponding sequence logo.

_U_s_a_g_e:

       seqLogo(pwm, ic.scale=TRUE, xaxis=TRUE, yaxis=TRUE, xfontsize=15, yfontsize=15)

_A_r_g_u_m_e_n_t_s:

     pwm: 'numeric' The 4xW position weight matrix.

ic.scale: 'logical' If TRUE, the height of each column is proportional
          to its information content. Otherwise, all columns have the
          same height.

   xaxis: 'logical' If TRUE, an X-axis will be plotted.

   yaxis: 'logical' If TRUE, a Y-axis will be plotted.

xfontsize: 'numeric' Font size to be used for the X-axis.

yfontsize: 'numeric' Font size to be used for the Y-axis.

_D_e_t_a_i_l_s:

     Within each column, the height of a given letter is proportional
     to its frequency at that position. If ic.scale is TRUE, the height
     of each column in the plot indicates the information content at
     that position of the motif. Otherwise, the height of all columns
     are identical.

_V_a_l_u_e:

     None.

_N_o_t_e:

_A_u_t_h_o_r(_s):

     Oliver Bembom, bembom@berkeley.edu

_R_e_f_e_r_e_n_c_e_s:

_S_e_e _A_l_s_o:

_E_x_a_m_p_l_e_s:

     mFile <- system.file("Exfiles/pwm1", package="seqLogo")
     m <- read.table(mFile)
     pwm <- makePWM(m)
     seqLogo(pwm)

