arrayPlot                package:GLAD                R Documentation

_S_p_a_t_i_a_l _i_m_a_g_e _o_f _m_i_c_r_o_a_r_r_a_y _s_p_o_t_s _s_t_a_t_i_s_t_i_c

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

     The function 'arrayPlot' creates spatial images of shades of gray
     or colors that correspond to the values of a statistic for each
     spot on the array. The statistic can be the intensity log-ratio, a
     spot quality measure (e.g. spot size or shape), or a test
     statistic. This function can be used to explore whether there are
     any spatial effects in the data, for example, print-tip or
     cover-slip effects.

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

     arrayPlot.default(Statistic, Col, Row,
                       ArrCol, ArrRow, SpotCol, SpotRow,
                       mediancenter=FALSE,
                       col=myPalette("green", "red", "yellow"),
                       contour=FALSE, nlevels=5,
                       zlim=NULL, bar=c("none", "horizontal", "vertical"),
                       layout=TRUE, ...) 

     arrayPlot.arrayCGH(arrayCGH, variable,
                        mediancenter=FALSE,
                        col=myPalette("green", "red", "yellow"),
                        contour=FALSE, nlevels=5,
                        zlim=NULL, bar=c("none", "horizontal", "vertical"),
                        layout=TRUE, ...)

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

arrayCGH: Object of class 'arrayCGH'.

variable: Variable to be plotted

Statistic: Statistic to be plotted.

     Col: Vector of columns coordinates.

     Row: Vector of rows coordinates.

  ArrCol: Number of columns for the blocs.

  ArrRow: Number of rows for the blocs.

 SpotCol: Number of column for each bloc.

 SpotRow: Number of rows for each bloc.

mediancenter: If 'mediancenter=TRUE', values of 'Statistic' are
          median-centered.

     col: List of colors such as that generated by 'Palettes'. In
          addition to these color palettes functions, a new function
          'myPalette' was defined to generate color palettes from user
          supplied low, middle, and high color values. 

 contour: If 'contour=TRUE', contour are plotted, otherwise they are
          not shown.

 nlevels: Numbers of levels added by 'contour' if 'contour=TRUE'.

    zlim: Numerical vector of length 2 giving the extreme values of 'z'
          to associate with colors 'low' and 'high' of 'myPalette'. By
          default 'zlim' is the range of 'z'.  Any values of 'z'
          outside the interval 'zlim' will be truncated to the relevant
          limit.

     bar: If 'bar=='horizontal'' (resp. ''vertical''), an horizontal
          (resp. vertical) calibration color bar is shown to the right
          of the image.

  layout: If 'layout==TRUE' plot layout is automatically set when a
          color bar is asked for

     ...: Graphical parameters can be given as arguments to function
          'image'.


     N.B. : Col takes the values in 1:arrayRow*SpotRow and Row takes
     the values in 1:arrayCol*SpotCol

_D_e_t_a_i_l_s:

     This function is very similar to the 'maImage' written by Sandrine
     Dudoit with added options 'zlim', 'mediancenter' and 'layout'.

_V_a_l_u_e:

     An image is created on the current graphics device.

_N_o_t_e:

     People interested in tools dealing with array CGH analysis can
     visit our web-page <URL: http://bioinfo.curie.fr>.

_A_u_t_h_o_r(_s):

     Philippe Hup, glad@curie.fr.

_S_e_e _A_l_s_o:

     'image', 'contour', 'arrayPersp', 'myPalette'.

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

     data(arrayCGH)

     pdf(file="arrayCGH.pdf",height=21/cm(1),width=29.7/cm(1))
     arrayPlot(array2$Log2Rat, array2$Col, array2$Row, 4,4,21,22, main="Spatial Image of array CGH")
     dev.off()

     # object of class arrayCGH

     array <- list(arrayValues=array2, arrayDesign=c(4,4,21,22))
     class(array) <- "arrayCGH"

     arrayPlot(array,"Log2Rat", main="Spatial Image of array CGH")

