Description Usage Arguments Details Examples
The GOHeat function generates a heatmap of the relationship
between genes and terms. Biological processes are displayed in rows and
genes in columns. In addition genes are clustered to highlight groups of
genes with similar annotated functions. The input can be generated with the
chord_dat
function.
1 |
data |
The matrix represents the binary relation (1= is related to, 0= is not related to) between a set of genes (rows) and processes (columns) |
nlfc |
Defines the number of logFC columns (default = 0) |
fill.col |
Defines the color scale break points |
The heatmap has in general two modes which depend on the nlfc
argument. If nlfc = 0
, so no logFC values are available, the
coloring encodes for the overall number of processes the respective gene is
assigned to. In case of nlfc = 1
the color corresponds to the logFC
of the gene.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ## Not run:
# Load the included dataset
data(EC)
# Generate the circ object
circ <- circle_dat(EC$david, EC$genelist)
# Generate the chord object
chord <- chord_dat(circ, EC$genes, EC$process)
# Create the plot with user-defined colors
GOHeat(chord, nlfc = 1, fill.col = c('red', 'yellow', 'green'))
## End(Not run)
|
Loading required package: ggplot2
Loading required package: ggdendro
Loading required package: gridExtra
Loading required package: RColorBrewer
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