Plot SJD score — SJDScorePlotter • SJD

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
)
#> [1] "**********************************************************"
#> [1] "plotting scores for twoStageLCA anaysis."
#> [1] "*******************************"
#> [1] "dataset: Meissner.inVitro.bulk.Hs"
#> [1] "grouping: Shared.All.4"
#> [1] 1
#> [1] 2
#> [1] "grouping: Shared.bulk.2"
#> [1] 1
#> [1] 2
#> [1] "grouping: Shared.sc.2"
#> [1] "No SJD scores for grouping : Shared.sc.2, moving to the next SJD output for Meissner.inVitro.bulk.Hs"
#> [1] "grouping: Hs.Meisnr.1"
#> [1] 1
#> [1] 2
#> [1] "grouping: Hs.AZ.1"
#> [1] "No SJD scores for grouping : Hs.AZ.1, moving to the next SJD output for Meissner.inVitro.bulk.Hs"
#> [1] "grouping: Gesch.1"
#> [1] "No SJD scores for grouping : Gesch.1, moving to the next SJD output for Meissner.inVitro.bulk.Hs"
#> [1] "grouping: Telley.1"
#> [1] "No SJD scores for grouping : Telley.1, moving to the next SJD output for Meissner.inVitro.bulk.Hs"
#> [1] "*******************************"
#> [1] "dataset: LIBD.AZ.inVitro.bulk.Hs"
#> [1] "grouping: Shared.All.4"
#> [1] 1
#> [1] 2
#> [1] "grouping: Shared.bulk.2"
#> [1] 1
#> [1] 2
#> [1] "grouping: Shared.sc.2"
#> [1] "No SJD scores for grouping : Shared.sc.2, moving to the next SJD output for LIBD.AZ.inVitro.bulk.Hs"
#> [1] "grouping: Hs.Meisnr.1"
#> [1] "No SJD scores for grouping : Hs.Meisnr.1, moving to the next SJD output for LIBD.AZ.inVitro.bulk.Hs"
#> [1] "grouping: Hs.AZ.1"
#> [1] 1
#> [1] 2
#> [1] "grouping: Gesch.1"
#> [1] "No SJD scores for grouping : Gesch.1, moving to the next SJD output for LIBD.AZ.inVitro.bulk.Hs"
#> [1] "grouping: Telley.1"
#> [1] "No SJD scores for grouping : Telley.1, moving to the next SJD output for LIBD.AZ.inVitro.bulk.Hs"
#> [1] "*******************************"
#> [1] "dataset: Geschwind.inVivo.sc.Hs"
#> [1] "grouping: Shared.All.4"
#> [1] 1
#> [1] 2
#> [1] "grouping: Shared.bulk.2"
#> [1] "No SJD scores for grouping : Shared.bulk.2, moving to the next SJD output for Geschwind.inVivo.sc.Hs"
#> [1] "grouping: Shared.sc.2"
#> [1] 1
#> [1] 2
#> [1] "grouping: Hs.Meisnr.1"
#> [1] "No SJD scores for grouping : Hs.Meisnr.1, moving to the next SJD output for Geschwind.inVivo.sc.Hs"
#> [1] "grouping: Hs.AZ.1"
#> [1] "No SJD scores for grouping : Hs.AZ.1, moving to the next SJD output for Geschwind.inVivo.sc.Hs"
#> [1] "grouping: Gesch.1"
#> [1] 1
#> [1] 2
#> [1] "grouping: Telley.1"
#> [1] "No SJD scores for grouping : Telley.1, moving to the next SJD output for Geschwind.inVivo.sc.Hs"
#> [1] "*******************************"
#> [1] "dataset: Jabaudon.inVivo.sc.Mm"
#> [1] "grouping: Shared.All.4"
#> [1] 1
#> [1] 2
#> [1] "grouping: Shared.bulk.2"
#> [1] "No SJD scores for grouping : Shared.bulk.2, moving to the next SJD output for Jabaudon.inVivo.sc.Mm"
#> [1] "grouping: Shared.sc.2"
#> [1] 1
#> [1] 2
#> [1] "grouping: Hs.Meisnr.1"
#> [1] "No SJD scores for grouping : Hs.Meisnr.1, moving to the next SJD output for Jabaudon.inVivo.sc.Mm"
#> [1] "grouping: Hs.AZ.1"
#> [1] "No SJD scores for grouping : Hs.AZ.1, moving to the next SJD output for Jabaudon.inVivo.sc.Mm"
#> [1] "grouping: Gesch.1"
#> [1] "No SJD scores for grouping : Gesch.1, moving to the next SJD output for Jabaudon.inVivo.sc.Mm"
#> [1] "grouping: Telley.1"
#> [1] 1
#> [1] 2