plotQA.FCS             package:rflowcyt             R Documentation

_C_r_e_a_t_e _a _s_c_a_t_t_e_r_p_l_o_t _s_u_m_m_a_r_y_z_i_n_g _o_n_e (_o_r _t_w_o) _p_a_r_a_m_e_t_e_r(_s)
_f_o_r _s_e_v_e_r_a_l _F_C_S _o_b_j_e_c_t_s _s_t_o_r_e_d _i_n _a  _p_l_a_t_e

_D_e_s_c_r_i_p_t_i_o_n:

     Create a scatterplot summaryzing one (or two) parameter(s) for
     several FCS objects stored in a  plate. The points are colored
     according to their position in the plate (row or column number.)

_U_s_a_g_e:

     plotQA.FCS(data,varpos=c(1,2),FUN1=IQR,FUN2=NULL,col="row",nrow=8,ncol=12,ind=c(1:96),labeling=TRUE,...)                      

_A_r_g_u_m_e_n_t_s:

    data: a list of fluorescent data from one (or more) FCS object(s)
          or a cytoset

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

    FUN1: function to summaryze the distribution of the data, e.g.
          mean, median, IQR, MODE

    FUN2: function to summaryze the distribution of the  data e.g.
          mean, median, IQR, MODE

     col: 

    nrow: numeric, number of rows per plate

    ncol: numeric, number of columns per plate

     ind: numeric vector, index of the wells to be plotted

labeling: logical, draw plate position (default=TRUE)

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

_V_a_l_u_e:

     None.

_A_u_t_h_o_r(_s):

     Nolwenn Le Meur

_S_e_e _A_l_s_o:

     'plot'

_E_x_a_m_p_l_e_s:

       ##Example I:
      data(flowcyt.data)

      ##Draw a scatterplot of the median values
      ##of the Foward scatter and the Side scatter parameters
      ##of each FCS file. The files correspond to samples store in a 96 well plate.
      plotQA.FCS(flowcyt.data,varpos=c(1,2),FUN1=median,nrow=8,ncol=10,ind=c(1:80),col="row",pch="*",labeling=FALSE,xlim=c(0,300),ylim=c(0,300),main="FSCmedian vs.SSCmedian by row",xlab="SSC median",ylab="FSC median")

      ##Example II:
      ##Draw a a scatterplot of the mode and IQR values for the Foward scatter
      ##of each FCS file. 
      plotQA.FCS(flowcyt.data,varpos=c(1),FUN1=IQR,FUN2=MODE,nrow=8,ncol=10,ind=c(1:80),col="col",pch="*",labeling=TRUE,xlim=c(0,300),ylim=c(0,300),xlab="FSC mode",ylab="FSC IQR",main="FSC IQR vs.FSC mode by column")
      

