pamr.plotcen              package:pamr              R Documentation

_A _f_u_n_c_t_i_o_n _t_o _p_l_o_t _t_h_e _s_h_r_u_n_k_e_n _c_l_a_s_s _c_e_n_t_r_o_i_d_s, _f_r_o_m _t_h_e _n_e_a_r_e_s_t _s_h_r_u_n_k_e_n _c_e_n_t_r_o_i_d _c_l_a_s_s_i_f_i_e_r

_D_e_s_c_r_i_p_t_i_o_n:

     A function to plot the shrunken class centroids, from the nearest
     shrunken centroid classifier produced by pamr.train

_U_s_a_g_e:

     pamr.plotcen(fit, data,  threshold)

_A_r_g_u_m_e_n_t_s:

     fit: The result of a call to pamr.train

    data: The input data, in the same form as that used by pamr.train

threshold: The desired threshold value

_D_e_t_a_i_l_s:

     'pamr.plotcen' plots the shrunken class centroids for each class,
     for genes surviving the threshold for at least once class. If
     genenames are included in "data", they are added to the plot.
     Note: for many classes and long gene names, this plot may need
     some manual prettying.

_A_u_t_h_o_r(_s):

     Trevor Hastie, Robert Tibshirani, Balasubramanian Narasimhan, and
     Gilbert Chu

_R_e_f_e_r_e_n_c_e_s:

_E_x_a_m_p_l_e_s:

     set.seed(120)
     x <- matrix(rnorm(1000*20),ncol=20)
     y <- sample(c(1:4),size=20,replace=TRUE)
     mydata <- list(x=x,y=y,genenames=as.character(1:1000))
     mytrain <-   pamr.train(mydata)
     mycv <- pamr.cv(mytrain,mydata)
     pamr.plotcen(mytrain, mydata,threshold=1.6)
      

