plotSampleRelation           package:lumi           R Documentation

_v_i_s_u_a_l_i_z_e _t_h_e _s_a_m_p_l_e _r_e_l_a_t_i_o_n_s

_D_e_s_c_r_i_p_t_i_o_n:

     plot the sample relations based on MDS or hierarchical clustering

_U_s_a_g_e:

     plotSampleRelation(x, selProbe = NULL, cv.Th = 0.1, standardize = TRUE, method = c("cluster", "mds"), dimension = c(1, 2), color = NULL, ...)

_A_r_g_u_m_e_n_t_s:

       x: a LumiBatch object, ExpressionSet object or a matrix with
          each column corresponding to a sample

selProbe: the selected probes used to determine the sample relations.
          If not provide, all the probes will be used. 

   cv.Th: the threshold of the coefficient of variance of probes used
          to select probes to estimate sample relations 

standardize: standardize the expression profiles or not 

  method: "MDS" or "hierarchical clustering" 

dimension: the principle components to visualize the MDS plot 

   color: the color for each sample during plot. Only support the "mds"
          method 

     ...: Other parameters used by plot function. 

_D_e_t_a_i_l_s:

     Estimate the sample relations based on selected probes (based on
     large coefficient of variance (mean / standard variance)). Two
     methods can be used: MDS (Multi-Dimensional Scaling) or
     hierarchical clustering methods.

_V_a_l_u_e:

     Plot the results or return the distance matrix.

_A_u_t_h_o_r(_s):

     Pan Du

_S_e_e _A_l_s_o:

     'lumiQ', 'LumiBatch', , 'plot.LumiBatch'

_E_x_a_m_p_l_e_s:

     ## load example data
     data(example.lumi)

     ## plot the sample relations with MDS
     ## the color of sample is automatically set based on the sample type
     plotSampleRelation(example.lumi, col=c('100US', '95US:5P', '100US', '95US:5P'))

     ## plot the sample relations with hierarchical clustering
     plotSampleRelation(example.lumi, method='cluster')

