plot.twilight            package:twilight            R Documentation

_P_l_o_t _f_u_n_c_t_i_o_n _f_o_r _t_w_i_l_i_g_h_t _o_b_j_e_c_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     Interface to plotting of 'twilight' objects. Produces one of five
     possible plots.

_U_s_a_g_e:

     ## S3 method for class 'twilight':
     plot(x, which = NULL, grayscale = FALSE, legend = TRUE, ...)

_A_r_g_u_m_e_n_t_s:

       x: An object of class twilight. 

   which: A character string specifying the plot to be made. 

grayscale: Logical value. Specifying whether plots should be colored or
          grayscaled. Only necessary for "scores" and "fdr". 

  legend: Logical value. Produces a legend for "scores" and
          "effectsize". A legend for "fdr" is only available if
          bootstrap estimates exist. 

     ...: Additional graphical arguments. 

_D_e_t_a_i_l_s:

     Option 'which="scores"' plots the expected versus the observed
     test statistics and draws confidence lines calculated from
     permutations. This plot is similar to plots in Tusher et al.
     (2001).

     Option 'which="qvalues"' plots q-values versus the number of
     rejected hypotheses.

     Option 'which="fdr"' plots p-values versus 1 - local false
     discovery rate, that is the conditional probability of being
     significant given the corresponding p-value, plus bootstrap
     estimates if computed. Bottom ticks are 1%-quantiles of p-values.

     Option 'which="volcano"' results in the volcano plot, that is
     observed score versus 1 - local false discovery rate. Bottom ticks
     are 1%-quantiles of scores.

     Option 'which="effectsize"' plots the observed fold change
     equivalent score distribution overlaid by the estimated effect
     size distribution, that is distribution of scores under the
     alternative. This plot is only available if function
     'twilight.pval' was applied with 'method="fc"' as fold change
     equivalent scores are computed from log ratios.

     Option 'which="table"' tabulates histogram '"effectsize"'.

_V_a_l_u_e:

     No value is returned except for "table".

_A_u_t_h_o_r(_s):

     Stefanie Scheid <URL: http://www.molgen.mpg.de/~scheid>

_R_e_f_e_r_e_n_c_e_s:

     Scheid S and Spang R (2004): A stochastic downhill search
     algorithm for estimating the local false discovery rate, _IEEE
     TCBB_ *1(3)*, 98-108.

     Scheid S and Spang R (2005): twilight; a Bioconductor package for
     estimating the local false discovery rate, _Bioinformatics_
     *21(12)*, 2921-2922. 

     Scheid S and Spang R (2006): Permutation filtering: A novel
     concept for significance analysis of large-scale genomic data, in:
     Apostolico A, Guerra C, Istrail S, Pevzner P, and Waterman M
     (Eds.): _Research in Computational Molecular Biology: 10th Annual
     International Conference, Proceedings of RECOMB 2006, Venice,
     Italy, April 2-5, 2006_. Lecture Notes in Computer Science vol.
     3909, Springer, Heidelberg, pp. 338-347.

     Tusher VG, Tibshirani R and Chu G (2001): Significance analysis of
     mircroarrays applied to the ionizing response, _PNAS_ *98(9)*,
     5116-5121.

_S_e_e _A_l_s_o:

     'twilight.pval', 'twilight'

_E_x_a_m_p_l_e_s:

     ### contains a twilight object created by function twilight
     data(exfdr)
     plot(exfdr)

