smcPlot                package:PGSEA                R Documentation

_P_l_o_t _P_G_S_E_A _r_e_s_u_l_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     This basic function will plot results from PGSEA with easy
     altering of margins, colors, and text.

_U_s_a_g_e:

     smcPlot(m, ff = NULL, skip = "NO", scale = c(-3, 3), na.color = par("bg"), margins = NULL, r.cex = NULL, c.cex = NULL, show.grid = F, cnames = TRUE, rnames = TRUE, ...)

_A_r_g_u_m_e_n_t_s:

       m: matrix - your results from PGSEA (or any other numeric matrix
          of data)

      ff: factor - this factor corresponds to the subtypes of your
          samples and will control the column names

    skip: character - which subtype(s) to skip from"ff"

   scale: vector, length 2 - this vector sets the minimum and maximum
          values for the graph scale (at bottom of plot)

na.color: character - color to display in the result of an NA

 margins: vector, length 4 - this vector gives the expansion values for
          the margins

   r.cex: numeric - number giving the amount by which row names should
          be scaled relative to the default

   c.cex: numeric - number giving the amount by which column names
          should be scaled relative to the default 

show.grid: boolean - show grid outlines within plot?

  cnames: boolean or character - vector of alternatvie column names 

  rnames: boolean or character - vector of alternative row names

     ...: additional graphical parameters passed along to the plotting
          function 

_A_u_t_h_o_r(_s):

     Karl Dykema <karl.dykema@vai.org>

_E_x_a_m_p_l_e_s:

     library(PGSEA)
     datadir <- system.file("data", package = "PGSEA")
     sample <- readGmt(file.path(datadir, "sample.gmt"))
     data(nbEset)

     pg <- PGSEA(nbEset@exprs,cl=sample,ref=1:5)
     sub <- factor(c(rep(NA,5),rep("NeuroB",5),rep("NeuroB_MYC+",5)))

     smcPlot(pg,sub,scale=c(-10,10),col=.rwb,margins=c(1,1,8,13))

