plotDensities             package:limma             R Documentation

_S_i_n_g_l_e-_c_h_a_n_n_e_l _D_e_n_s_i_t_i_e_s _P_l_o_t

_D_e_s_c_r_i_p_t_i_o_n:

     Creates a plot of the densities of single-channels from two-color
     cDNA microarray data.

_U_s_a_g_e:

     plotDensities(object, log.transform=FALSE, arrays=NULL, singlechannels=NULL,
                   groups=NULL, col=NULL) 

_A_r_g_u_m_e_n_t_s:

  object: must be either a list with components 'M' containing
          log-ratios and 'A' containing average intensities or a list
          with components 'R' containing log2 red intensities and 'G'
          containing log2 green intensities.  If object is given as an
          'MAList' it is converted to an 'RGList'.

log.transform: logical which needs to be 'TRUE' if object supplied is
          an 'RGList' of unlogged intensities.

  arrays: vector of integers giving the arrays from which the
          single-channels will be selected to be plotted. Corresponds
          to columns of 'M' and 'A' (or 'R' of 'G')  If 'NULL' (which
          is the default), arrays is given by '1:ncol(object$R)'.

singlechannels: vector of integers indicating which single-channels
          will be selected to be plotted.  Values correspond to the
          columns of the matrix of 'cbind(R,G)' and range between
          '1:ncol(R)' for red single-channels and '(
          (ncol(R)+1):(ncol(R)+ncol(G)) )' for the green
          single-channels in 'object'.

  groups: vector of consecutive integers beginning at 1 indicating the
          groups of arrays or single-channels (depending on which of
          'arrays' or 'singlechannels' are non 'NULL').  This is used
          to color any groups of the single-channel densities. If
          'NULL' (default), 'groups' correspond to the red and green
          channels.  If both 'arrays' and 'singlechannels' are 'NULL'
          all arrays are selected and groups (if specified) must
          correspond to the arrays.

     col: vector of colors of the same length as the number of
          different groups. If 'NULL' (default) the 'col' equals
          'c("red","green")'.  See details for more specifications.

_D_e_t_a_i_l_s:

     This function is used as a data display technique associated with
     single-channel normalization. See the section on single-channel
     normalization in the LIMMA User's Guide.

     If no 'col' is specified, the default is to color singlechannels
     according to red and green. If both 'arrays' and 'groups' are
     non-'NULL', then the length of 'groups' must equal the length of
     'arrays' and the maximum of 'groups' (i.e. the number of groups)
     must equal the length of 'col' otherwise the default color of
     black will be used for all single-channels. If 'arrays' is 'NULL'
     and both 'singlechannels' and 'groups' are non-'NULL', then the
     length of 'groups' must equal the length of 'singlechannels' and
     the maximum of 'groups' (i.e. the number of groups) must equal the
     length of 'col' otherwise the default color of black will be used
     for all single-channels.

_V_a_l_u_e:

     A plot is created on the current graphics device.

_A_u_t_h_o_r(_s):

     Natalie Thorne

_S_e_e _A_l_s_o:

     An overview of diagnostic plots in LIMMA is given in
     6.Diagnostics. There is a section using 'plotDensities' in
     conjunction with single-channel normalization in the _LIMMA User's
     Guide_.

_E_x_a_m_p_l_e_s:

     library(sma)
     data(MouseArray)

     #  no normalization but background correction is done
     MA.n <- MA.RG(mouse.data)

     #  Default settings for plotDensities.
     plotDensities(MA.n)

     #  One can reproduce the default settings.
     plotDensities(MA.n,arrays=c(1:6),groups=c(rep(1,6),rep(2,6)),
     col=c("red","green"))

     #  Color R and G single-channels by blue and purple.
     plotDensities(MA.n,arrays=NULL,groups=NULL,col=c("blue","purple"))

     #  Indexing single-channels using singlechannels (arrays=NULL).
     plotDensities(MA.n,singlechannels=c(1,2,7))

     #  Change the default colors from c("red","green") to c("pink","purple")
     plotDensities(MA.n,singlechannels=c(1,2,7),col=c("pink","purple"))

     #  Specified too many colors since groups=NULL defaults to two groups.
     plotDensities(MA.n,singlechannels=c(1,2,7),col=c("pink","purple","blue"))

     #  Three single-channels, three groups, three colors.
     plotDensities(MA.n,singlechannels=c(1,2,7),groups=c(1,2,3),
     col=c("pink","purple","blue"))

     #  Three single-channels, one group, one color.
     plotDensities(MA.n,singlechannels=c(1,2,7),groups=c(1,1,1),
     col=c("purple"))

     #  All single-channels, three groups (ctl,tmt,reference), three colors.
     plotDensities(MA.n,singlechannels=c(1:12),
     groups=c(rep(1,3),rep(2,3),rep(3,6)),col=c("darkred","red","green"))

