v2m                   package:OLIN                   R Documentation

_C_o_n_v_e_r_t_s  _v_e_c_t_o_r _t_o _m_a_t_r_i_x _b_a_s_e_d _o_n _s_p_o_t _l_a_y_o_u_t

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

     This functions converts a vector to a matrix based on a given spot
     layout. Optionally, it produces a 2D-plot.

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

     v2m(V,Ngc,Ngr,Nsc,Nsr,visu=FALSE,color.lim=c(-1,1),xlab="Columns",ylab="Rows",...) 

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

       V: vector of real values 

     Ngc: number of columns for the grid matrix

     Ngr: number of rows for the grid matrix

     Nsc: number of columns for the spot matrix

     Nsr: number of rows for the spot matrix

    visu: If FALSE, MXY plot is generated.

color.lim: Limits of color range for MXY plot

    xlab: label of x -axis of MXY plot

    ylab: label of y-axis of MXY plot

     ...: Further optional parameters  for the 'image' function
          generating the MXY plot

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

     The function 'v2m' converts a vector 'V' (as e.g. derived by
     'maM(object)[,index]') to a matrix representing the spatial
     distribution of the values of 'V' across the array.  Note that
     this function assumes a specific mapping between the data points
     and the location of spot (i.e. the same mapping rule that is used
     for marrayRaw/marrayNorm objects.) The validity of this mapping
     should be  carefully checked (see also the documentation of packet
     _marray_.)   The option for spatial visualisation is rather
     restricted to logged fold-changes as the corresponding colour
     range is centred around zero and follows the conventional
     colouring (green for negative, red for positive fold-changes). The
     MXY plot produced by 'v2n' does not include a colour bar. To have
     a colour included, you can use 'mxy.plot'.

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

     A 2D-matrix with '(Ngc*Nsc)' columns and '(Ngr*Nsr)' is produced.
     This matrix represents the spatial distribution of the values of
     vector 'V' given the print-layout.

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

     Matthias E. Futschik, <URL:
     http://itb.biologie.hu-berlin.de/~futschik>

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

     'mxy.plot', 'm2v', 'marrayRaw'

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

     # LOADING DATA NOT-NORMALISED
     data(sw.olin) 
     # CONVERSION FROM VECTOR TO MATRIX
     M <- v2m(maM(sw.olin)[,1],Ngc=maNgc(sw.olin),Ngr=maNgr(sw.olin),
              Nsc=maNsc(sw.olin),Nsr=maNsr(sw.olin),visu=TRUE)

     # BACK-CONVERSION FROM MATRIX TO VECTOR
     V <- m2v(M,Ngc=maNgc(sw.olin),Ngr=maNgr(sw.olin),
                  Nsc=maNsc(sw.olin),Nsr=maNsr(sw.olin),visu=TRUE)

