plot-methods              package:puma              R Documentation

_P_l_o_t _m_e_t_h_o_d _f_o_r _p_u_m_a_P_C_A_R_e_s _o_b_j_e_c_t_s

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

     This is the method to plot objects of class pumaPCARes. It will
     produce a scatter plot of two of the principal components

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

     ## S4 method for signature 'pumaPCARes, missing':
     plot(..., firstComponent = 1, secondComponent = 2, useFilenames = FALSE, phenotype = pData(pumaPCARes@phenoData), legend1pos = "topright", legend2pos = "bottomright")

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

     ...: Optional graphical parameters to adjust different components
          of the plot

firstComponent: Integer identifying which principal component to plot
          on the x-axis

secondComponent: Integer identifying which principal component to plot
          on the x-axis

useFilenames: Boolean. If TRUE then use filenames as plot points.
          Otherwise just use points.

phenotype: Phenotype information

legend1pos: String indicating where to put legend for first factor

legend2pos: String indicating where to put legend for second factor

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

             library(puma)
             data(affybatch.example)
             pData(affybatch.example) <- data.frame("level"=c("twenty","twenty","ten")
                 , "batch"=c("A","B","A"), row.names=rownames(pData(affybatch.example)))
             eset_mmgmos <- mmgmos(affybatch.example)
             pumapca_mmgmos <- pumaPCA(eset_mmgmos)
             plot(pumapca_mmgmos)

