writeQAReport             package:flowQ             R Documentation

_C_r_e_a_t_e _H_T_M_L _r_e_p_o_r_t _f_o_r (_l_i_s_t_s _o_f) _q_a_P_r_o_c_e_s_s _o_b_j_e_c_t_s

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

     This function combines all graphical output of multiple QA
     processes for one or several 'flowSet's in a single hyperlinked
     HTML document.

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

     writeQAReport(set, processes, outdir = "./qaReport", grouping = NULL,
     pagebreaks = TRUE)

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

     set: A 'flowSet' or a list of several 'flowSet's 

processes: A list of A 'qaProcess' objects or, in the case of multiple
          'flowSet's, a list of lists of 'qaProcess' objects.

  outdir: The directory to which the HTML report is to be saved. Make
          sure that each 'qaProcess' object was created in the same
          directory. 

grouping: A character scalar indicating a variable in the 'flowSet''s
          'phenoData' that is used as a grouping factor in the output.

pagebreaks: A logical indicating whether the output should be on one
          long page, or split on several pages.

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

     Both the information about graphical output and the results for a
     QA process are stored in objects of class 'qaProcess'. The
     creation of such objects is abstracted in dedicated functions and
     the user should call these functions directly rather than creating
     'qaProcess' manually. 'writeQAReport' takes lists of such objects
     and combines their information in a unified HTML document. A
     grouping factor can be specified to indicate subgroups of the
     data. In the case of multiple panels, a list of 'flowSet's can be
     given to 'writeQAReport', and the function expects a list of lists
     of processes, where each process list is specific to one panel.

     An entry point to the output of this function can be found at
     'outdir/index.html'.

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

     The function is called for it's side effects

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

     Florian Hahne

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

     'qaProcess.marginevents', 'qaReport', 'qaProcess',
     'qaProcess.timeline'

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

     ## Not run: 
     data(GvHD)
     GvHD <- transform(GvHD, "FL1-H"=asinh(`FL1-H`), "FL2-H"=asinh(`FL2-H`))
     dest <- tempdir()
     qp1 <- qaProcess.timeline(GvHD, channel="FL1-H", outdir=dest, cutoff=1)
     qp2 <- qaProcess.marginevents(GvHD, channels=c("FL1-H", "FL2-H"),
       outdir=dest, cFactor=4)
     writeQAReport(GvHD, processes=list(qp1, qp2), outdir=dest,
       grouping="Patient")
     browseURL(file.path(dest, "index.html"))
     ## End(Not run)

