SJDScorePlotter: Plot SJD score

In CHuanSite/SJD: Structured Joint Decomposition (SJD)

Plot SJD score

Description

plot dimensionality reduction scores for each SJD algorithm for dataset analyzed by SJD

Usage

SJDScorePlotter(
  SJDalg,
  scores,
  lbb,
  info,
  SampleMetaNamesTable,
  clrs2end = c("plum", "purple", "blue", "blue4", "black", "darkred", "red", "orange",
    "yellow"),
  clrs1end = c("black", "black", "black", "darkred", "red", "orange", "yellow")
)

Arguments

SJDalg	SJD algorithm to plot i.e 'twoStageLCA'
scores	score list of the SJD algorithm i.e twoStageLCA$score_list
lbb	dataset label i.e 'NeuroGenesis4'
info	list of sample meta data matrices
SampleMetaNamesTable	dataframe containing column information of each sample meta data matrices
clrs2end	color scale for result scores from other algorithms. Default: c("plum","purple","blue","blue4","black","darkred","red","orange","yellow")
clrs1end	color scale for result scores from sepNMF, concatNMF and jointNMF algorithms. Default: c("black","black","black","darkred","red","orange","yellow")

Value

A list containing ggplot object

Examples

library(ggplot2)

data(NeuroGenesis4.afterWrap)
data(NeuroGenesis4.info)

SampleMetaNamesTable = data.frame(
   row.names = names(NeuroGenesis4),
   Type = c('Yaxis','Yaxis','2Dscatter','2Dscatter'),
   XaxisColumn = c("X","DAYx","tSNE_1","tsne1:ch1"),
   YaxisColumn = c("PJDscores","PJDscores","tSNE_2","tsne2:ch1"),
   COLaxisColumn = c("color","colorBYlabelsX","PJDscores","PJDscores"),
   PCHColumn = c("","","",""),
   inset = c(TRUE, TRUE, TRUE, TRUE),
   insetLOC = c("topright", "topright", "topright", "topright"),
   insetZoom = c(0.3, 0.3, 0.3, 0.3),
   ordDECREASE=c(FALSE, FALSE, FALSE, FALSE),
   CLRfoldPRB=c(0.5, 0.5, 0.5, 0.5)
)

grp = list(
Shared.All.4 = c(1 : 4),
Shared.bulk.2 = c(1, 2),
Shared.sc.2 = c(3, 4),
Hs.Meisnr.1 = c(1),
Hs.AZ.1 = c(2),
Gesch.1 = c(3),
Telley.1 = c(4)
)

dims = c(2, 2, 2, 2, 2, 2, 2)

twoStageLCA.out = twoStageLCA(dataset = NeuroGenesis4.afterWrap, group = grp, comp_num = dims)

SJDScorePlotter.obj = SJDScorePlotter(
    SJDalg = "twoStageLCA",
    scores = twoStageLCA.out$score_list,
    lbb = "NeuroGenesis4.p2",
    info = NeuroGenesis4.info,
    SampleMetaNamesTable = SampleMetaNamesTable
)

CHuanSite/SJD documentation built on Nov. 29, 2024, 5:52 a.m.