plotMdGsa {mdgsa} | R Documentation |
Plots confidence region for a Gene Set in a two dimensional space.
plotMdGsa(index, block, cr = 0.95, pch = ".", pch.block = 20, lwd = 2, col.all = "blue", col.block = "red", project = FALSE, col.proj = "green", diagonals = FALSE, col.diag = "gray", ...)
index |
matrix or data frame with the two columns of ranking statistics. |
block |
matrix or data frame with gene ids in the first column and gene set ids in the second column. |
cr |
level of the confidence region. |
pch |
plotting character for all genes. |
pch.block |
plotting character for the genes in the gene set or functional block. |
lwd |
line width. Used when drawing ellipses and other lines. |
col.all |
color used to represent all genes. |
col.block |
color used to represent the genes in the gene set being plotted. |
project |
if TRUE projection over the axis are displayed for the genes of the gene set. |
col.proj |
color used to plot the projection. |
diagonals |
if TRUE diagonals are plotted. |
col.diag |
color used to plot the diagonals. |
... |
arguments to be passed to plot |
Black dots show all genes in the dataset. Red stars show the genes in the Gene Set. Blue axis show the "center" of the distribution of all genes; blue ellipse shows the confidence region for all genes. Red axis show the "center" of the distribution of the genes in the Gene Set; red ellipse shows the confidence region for genes in the Gene Set.
A plot.
David Montaner dmontaner@cipf.es
mdGsa
, mdPat
, mdPat
,
ellipsoidPoints
## Not run: res <- mdGsa (rindexMat, annotList) plotMdGsa (rindexMat, block = annotList[["GO:0006915"]]) ## End(Not run)