decompose.gs.ind: Data-wise or PC-wise decomposition of gene set scores for a...

In mengchen18/mogsa: Multiple omics data integrative clustering and gene set analysis

Description

Barplot of decomposed gene set scores, either with respect to datasets or axes.

Usage

decompose.gs.ind(
  x,
  gs,
  obs,
  type = 3,
  nf = 2,
  plot = TRUE,
  col.data = NULL,
  col.pc = NULL,
  legend = TRUE
)

Arguments

x	An object of class mgsa-class or moa.sup-class
gs	The gene set want to exam.
obs	The observations want to exam.
type	Which type of plot. type=1 - the data-pc mode; type=2 - the pc-data mode; type=3 - both. See detail.
nf	The number of axes/PCs to be calculated and plotted.
plot	A logical indicates if a plot should be drawn
col.data	The bar color of datasets
col.pc	The bar color of PCs
legend	A logical if legend should be shown

Details

type=1 (the data-pc mode), the axes/PCs are represented as the narrow bars with different colors and the background wide bars behind narrow bars are gene set scores for datasets, which is calculated from the sum of all underlying individual axes/PC scores. When type=2 (the pc-data mode) the interpreation of narrow and wide bars are in the other way around. If type=3, both are shown.

This function could only be used to check the decomposition of gene set scores of a single observation. So the function is not efficent when the number of observation is large. Another function decompose.gs.group, could be used in this case, particularly when the cluster information of the observation panel is available.

Value

Return nothing or a matrix depends on how argument plot is set.

Author(s)

Chen Meng

References

TBA

See Also

See Also as decompose.gs.group

Examples

  # library(mogsa)
  # loading gene expression data and supplementary data
  data(NCI60_4array_supdata)
  data(NCI60_4arrays)
  mgsa <- mogsa(x = NCI60_4arrays, sup=NCI60_4array_supdata, nf=9,
                proc.row = "center_ssq1", w.data = "inertia", statis = TRUE)

  allgs <- colnames(NCI60_4array_supdata[[1]])
  # plot
  decompose.gs.ind(x=mgsa, gs=allgs[5], obs="BR.MDA_MB_231", type=2, nf=5)
  # or
  decompose.gs.ind(x=getmgsa(mgsa, "sup"), gs=allgs[5], obs="BR.MDA_MB_231", type=3, nf=5)

mengchen18/mogsa documentation built on June 7, 2020, 6:05 p.m.