plotHistTwoClasses           package:puma           R Documentation

_S_t_a_c_k_e_d _h_i_s_t_o_g_r_a_m _p_l_o_t _o_f _t_w_o _d_i_f_f_e_r_e_n_t _c_l_a_s_s_e_s

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

     Stacked histogram plot of two different classes

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

     plotHistTwoClasses(
             scores
     ,       class1Elements
     ,       class2Elements
     ,       space=0
     ,       col=c("white", "grey40")
     ,       xlab="PPLR"
     ,       ylab="Number of genes"
     ,       ylim=NULL
     ,       las=0 # axis labels all perpendicular to axes
     ,       legend=c("non-spike-in genes", "spike-in genes")
     ,       inset=0.05
     ,       minScore=0
     ,       maxScore=1
     ,       numOfBars=20
     ,       main=NULL
     )

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

  scores: A numeric vector of scores (e.g. from the output of 'pumaDE') 

class1Elements: Boolean vector, TRUE if element is in first class 

class2Elements: Boolean vector, TRUE if element is in second class 

   space: Numeric. x-axis distance between bars 

     col: Colours for the two different classes 

    xlab: Title for the x-axis 

    ylab: Title for the y-axis 

    ylim: 2-element numeric vector showing minimum and maximum values
          for y-axis. 

     las: See 'par'. Default of 0 means axis labels all perpendicular
          to axes. 

  legend: 2-element string vector giving text to appear in legend for
          the two classes. 

   inset: See 'legend' 

minScore: Numeric. Minimum score to plot. 

maxScore: Numeric. Maximum score to plot. 

numOfBars: Integer. Number of bars to plot. 

    main: String. Main title for the plot. 

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

     This function has no return value. The output is the plot created.

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

     Richard D. Pearson

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

             class1 <- rnorm(1000,0.2,0.1)
             class2 <- rnorm(1000,0.6,0.2)
             class1[which(class1<0)] <- 0
             class1[which(class1>1)] <- 1
             class2[which(class2<0)] <- 0
             class2[which(class2>1)] <- 1
             scores <- c(class1, class2)
             class1elts <- c(rep(TRUE,1000), rep(FALSE,1000))
             class2elts <- c(rep(FALSE,1000), rep(TRUE,1000))
             plotHistTwoClasses(scores, class1elts, class2elts, ylim=c(0,300))

