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, pdf=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. See below
          for further details.

  outdir: The directory to which the HTML report is to be saved. Each
          'qaProcess' object should have been 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 over several pages. 

     pdf: A logical indicating whether vectorized versions of the
          images should be included. Setting this to 'TRUE' implies
          that the individual QA processes have also been created with
          setting 'pdf=TRUE'. 

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

     Both the information about graphical output generated as part of a
     QA process as well as the qunatitative or qualitative results are
     stored in objects of class 'qaProcess'. The creation of such
     objects is abstracted in dedicated constructor function 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 mostly called for it's side effects, that is, the
     generation of a HTML quality report in 'outdir'. A URL to an entry
     point for browsing of the report is returned.

_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)
     url <- writeQAReport(GvHD, processes=list(qp1, qp2), outdir=dest,
       grouping="Patient")
     browseURL(url)
     ## End(Not run)

