image.stamPrediction          package:stam          R Documentation

_M_o_l_e_c_u_l_a_r _S_y_m_p_t_o_m_s _I_m_a_g_e _o_n _S_t_A_M _P_r_e_d_i_c_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     Shows prediction results for each sample of the class of interest
     and for all nodes of  a StAM model fit as a color coded image.

_U_s_a_g_e:

     ## S3 method for class 'stamPrediction':
     image(x, aclass = NULL, main = NULL, 
                          xlab = NULL, show.graph = TRUE, 
                          max.label.length = 40, 
                          sample.labels = FALSE, full.names = TRUE, 
                          outfile = NULL, ps = FALSE, res = 72, 
                          pointsize = 10, width = 11, 
                          minspec = NULL, minsens = 0.1, 
                          maxsens = 1, invert = FALSE, 
                          col = stam.rgb.colors(r0 = 0), 
                          bin.thresh = NULL, ...)

_A_r_g_u_m_e_n_t_s:

       x: stamPrediction object to be illustrated

  aclass: the name of the phenotype class of interest, usually  the
          disease class. If set to NULL the first class in
          lexicographical order is chosen

    main: the main title of the plot, generated automatically if  left
          blank

    xlab: the label of the x-axis

show.graph: (default is T) whether or not to show GO relations between
          the nodes

max.label.length: the maximum string length for a GO term

sample.labels: whether or not to show sample names on the x-axis

full.names: whether or not to show GO terms instead of GO IDs

 outfile: name of output file if postscript or PNG graphics is  to be
          generated. The extension of the file is chosen automatically
          according to the  'ps' argument. If no outfile is specified,
          an interactive plot is attempted

     res: resolution in points per inch

      ps: if set to TRUE postscript output is generated

pointsize: the standard fontsize

   width: width of image in inches (the height is computed according to
          the number of nodes to be shown and the 'pointsize')

 minspec: nodes to be shown must be at least this specific. If  set to
          NULL this is chosen such that no more than 50 nodes are
          shown.

 minsens: nodes to be shown must be at least this sensitive

 maxsens: nodes to be shown must be at most this sensitive

  invert: whether or not to invert background and foreground colors

     col: the color gradient to code classifier output

bin.thresh: threshold for binary color coding, if left at the  default
          NULL, classifier outputs are coded on a continuous scale.

     ...: additional options passed to 'image'

_D_e_t_a_i_l_s:

     This image illustrates classifier outputs generated during a
     structured analysis of  microarrays (StAM). The centralpart of the
     image shows the color coded classifier  outputs for each sample in
     the class of interest (columns) and each nodes from StAM's  model
     fit (rows). Nodes can be restricted to those of minimal
     sensitivity or  specificity. Also nodes with particularly high
     sensitivity can be excluded. The color  code for the classifier
     outputs is shown in a color bar on the right hand side if a 
     continuous is used. If a testset is specified only these samples
     are used to compute  sensitivity and specificity. If the sample
     names are not displayed on the x-axis, the test samples are marked
     with capital letters or just vertical bars (bars if there are  too
     many test samples). Sensitivity and specificity is shown to the
     left of the figure  together with the relations between the GO
     nodes from the Gene Ontology. GO terms are  printed on the right
     of the image and may be used for a clickable map in HTML.

_V_a_l_u_e:

     A string to be used on an HTML page to provide a clickable map for
     the GO terms.

_A_u_t_h_o_r(_s):

     Claudio Lottaz

_S_e_e _A_l_s_o:

     'stam.predict'

