boxplot.FCS             package:rflowcyt             R Documentation

_C_r_e_a_t_e _b_o_x_p_l_o_t_s _o_n_e _p_a_r_a_m_e_t_e_r _o_f _o_n_e (_o_r _m_o_r_e) _F_C_S _o_b_j_e_c_t(_s)

_D_e_s_c_r_i_p_t_i_o_n:

     Produce box-and-whisker plot(s) of a single column variable
     specified from the data of one (or more) FCS object(s).

_U_s_a_g_e:

     boxplot.FCS(x, varpos=c(1),...)                      

_A_r_g_u_m_e_n_t_s:

       x: a list of  one (or more) FCS object(s) or a cytoSet object

  varpos: the numerical column variable position of the data of the FCS
          object

     ...: any other arguments are passed to the 'boxplot' function

_D_e_t_a_i_l_s:

     If several FCS objects are supplied parallel boxplots will be
     plotted. Other options from the functions 'plot', 'boxplot'.

_V_a_l_u_e:

     The 'boxplot' will output a list with the following components: 

   stats: 

       n: 

    conf: 

     out: 

   group: 

   names: 

     a vector of names for the groups

_A_u_t_h_o_r(_s):

     N. Le Meur

_S_e_e _A_l_s_o:

     'boxplot', 'boxplot.stats'

_E_x_a_m_p_l_e_s:

      ## Example I:
      require(rfcdmin)
      data(flowcyt.data)

      ## Draw a boxplot for the Foward SCatter parameter for the time points 1
      ## and 6 (in this experiment, each time point corresponds to a column of
      ## a 96 wells plates)
      mat <- matrix(c(1:2),1,2,byrow=TRUE)
      nf <- layout(mat,respect=TRUE)
      boxplot.FCS(flowcyt.data[1:8],varpos=c(1),col=c(1:8),main="FSC across stains time point 1",names=paste("stain",c(1:8),sep=""))
      boxplot.FCS(flowcyt.data[65:72],varpos=c(1),col=c(1:8),main="FSC across stains time point 9",names=paste("stain",c(1:8),sep=""))

      ##Example II:
      ## Read a serie of FCS files
      if (require(rfcdmin)) {

      ##obtaining the location of the fcs files in the data
       pathFiles<-system.file("bccrc", package="rfcdmin")
       drugFiles<-dir(pathFiles)

      ## reading in the FCS files
       drugData<-read.series.FCS(drugFiles,path=pathFiles,MY.DEBUG=FALSE)
       }

      ##Draw a boxplot for the Foward SCatter parameter
      ##for the differents aliquots (of the same cell line)
      ##tested with different compounds. 
      boxplot.FCS(drugData,varpos=c(1),col=c(1:8),main="FSC of differents aliquots from the same cell line treated with different compounds.")

      

