Create diagnostic plot for understanding the Roleswitch model outputs.

Description

Create diagnostic plot for understanding the roleswitch outputs. Create a 2 by 4 panels of plots. From left to right, the top panel displays the observed N mRNA and M miRNA expression (x.o and z.o), the N by M seed-match matrix (c), and the inferred total mRNA expression; the bottom panel displays the inferred probability of the M miRNAs targeting the N mRNA (miRNA-mRNA; p.x), the probability of the N mRNA "targeting" the M miRNAs (mRNA-miRNA; p.z), the dot product of the above two matrices (Joint) and the convergence rate (delta.p.all).

Usage

diagnosticPlot(pred)

Arguments

Author(s)

Yue Li

References

Li, Y., ..., Zhang, Z., Inference of personalized miRNA-mRNA interactions toward redefining cancer signatures (in preparation).

See Also

roleswitch

Examples

x.o <- matrix(abs(rnorm(10, mean=3)), 
  dimnames=list(c(1:10),"mRNA")) # mRNA expression
  
z.o <- matrix(abs(rnorm(4, mean=3)),
  dimnames=list(c(1:4),"miRNA"))  # miRNA expression
  
c <- matrix(rpois(40, lambda=3),nrow=nrow(x.o), 
  dimnames=list(c(1:10),c(1:4))) # seed match matrix

rs.pred <- roleswitch(x.o, z.o, c)

diagnosticPlot(rs.pred)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(Roleswitch)
Loading required package: pracma
Loading required package: reshape
Loading required package: plotrix
Loading required package: microRNA
Loading required package: biomaRt
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:reshape':

    expand, rename

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DBI
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Roleswitch/diagnosticPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: diagnosticPlot
> ### Title: Create diagnostic plot for understanding the Roleswitch model
> ###   outputs.
> ### Aliases: diagnosticPlot
> ### Keywords: plot
> 
> ### ** Examples
> 
> x.o <- matrix(abs(rnorm(10, mean=3)), 
+   dimnames=list(c(1:10),"mRNA")) # mRNA expression
>   
> z.o <- matrix(abs(rnorm(4, mean=3)),
+   dimnames=list(c(1:4),"miRNA"))  # miRNA expression
>   
> c <- matrix(rpois(40, lambda=3),nrow=nrow(x.o), 
+   dimnames=list(c(1:10),c(1:4))) # seed match matrix
> 
> rs.pred <- roleswitch(x.o, z.o, c)

Start roleswitch with 4 miRNA and 10 mRNA
1: max(p.x-p.x.prev)=0.86294
2: max(p.x-p.x.prev)=0.00019
3: max(p.x-p.x.prev)=0.00006
4: max(p.x-p.x.prev)=0.00000
> 
> diagnosticPlot(rs.pred)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>