boxplot              package:maigesPack              R Documentation

_M_e_t_h_o_d _b_o_x_p_l_o_t _f_o_r _o_b_j_e_c_t_s _d_e_f_i_n_e_d _i_n _t_h_i_s _p_a_c_k_a_g_e

_D_e_s_c_r_i_p_t_i_o_n:

     Generic function 'boxplot' to display boxplots of the data.

_U_s_a_g_e:

     ## S3 method for class 'maigesRaw':
     boxplot(x, ...)

     ## S3 method for class 'maiges':
     boxplot(x, name=NULL, gLabelID=NULL, sLabelID=NULL, gSamples=NULL, ...)

     ## S3 method for class 'maigesANOVA':
     boxplot(x, name=NULL, gLabelID=NULL, sLabelID=NULL, gSamples=NULL, ...)

     ## S3 method for class 'maigesDEcluster':
     boxplot(x, name=NULL, gLabelID=NULL, sLabelID=NULL, gSamples=NULL, ...)

_A_r_g_u_m_e_n_t_s:

       x: an object of any class defined in this package

    name: character string specifying a gene to do boxplot of their
          expression values along the types specified by 'sLabelID'.

gLabelID: character value giving the name of gene label to be used to
          search for parameter 'name'.

sLabelID: idem to 'gLabelID', specifying the name of sample label to be
          used to separate the gene observations.

gSamples: a named list containing character vectors defining groups of
          samples from 'sLabelID'.

     ...: additional parameters to 'boxplot' method defined in
          _graphics_ package or to 'maBoxplot' method defined in
          _marray_ package (for 'maigesRaw', 'maiges' or 'maigesANOVA'
          classes), in this case the additional parameters must not be
          named, because these names conflict with the 'boxplot'
          generic function definition.

_D_e_t_a_i_l_s:

     This method uses the function 'maBoxplot' from marray package to
     show boxplots of the W values along all the slides of a dataset or
     along specific accessor methods to stratify the data in objects of
     class 'maigesRaw'. For objects of classes 'maiges' or
     'maigesANOVA' this is also done if the argument 'name' is NULL,
     else the method shows boxplots for the expression values of the
     gene specified by 'name' stratified by sample types from
     'sLabelID'. For objects of class 'maigesDEcluster' only boxplots
     of genes are produced and the argument 'name' may not be NULL.

     If you especify the 'y' parameter (but not named), defined for the
     method 'maBoxplot' in package _marray_, it will be displayed the M
     values instead of W.

_A_u_t_h_o_r(_s):

     Gustavo H. Esteves <gesteves@vision.ime.usp.br>

_S_e_e _A_l_s_o:

     'maBoxplot' in the _marray_ package and 'boxplot' in the
     _graphics_ package.

_E_x_a_m_p_l_e_s:

     ## Loading the dataset
     data(gastro)

     ## To see the boxplots for W values in all chips
     boxplot(gastro.raw)  ## maigesRaw class
     boxplot(gastro.norm) ## maigesNorm class
     boxplot(gastro.summ) ## summarized data (also maigesNorm class)

     ## To see the boxplots for W values in individual chips
     ## separating into print tips.
     boxplot(gastro.raw[,1])  ## maigesRaw class, first chip
     boxplot(gastro.norm[,8]) ## maigesNorm class, 8th chip
     boxplot(gastro.summ[,19]) ## summarized data (also maigesNorm class), 19th chip

     ## Boxplot for individual genes into ANOVA model fitting
     gastro.ANOVA = designANOVA(gastro.summ, factors="Tissue")
     gastro.ANOVAfit = deGenesANOVA(gastro.ANOVA, retF=TRUE)

     boxplot(gastro.ANOVAfit, name="KLK13", gLabelID="GeneName", 
     sLabelID="Tissue")

