| xHeatmap | R Documentation |
xHeatmap is supposed to draw heatmap using ggplot2.
xHeatmap(
data,
reorder = c("none", "row", "col", "both"),
colormap = "spectral",
ncolors = 64,
zlim = NULL,
barwidth = 0.3,
barheight = NULL,
nbin = 64,
legend.title = "",
x.rotate = 45,
x.text.size = 6,
x.text.hjust = 0,
y.text.size = 6,
legend.text.size = 4,
legend.title.size = 6,
shape = 19,
size = 2,
plot.margin = unit(c(5.5, 5.5, 5.5, 5.5), "pt"),
font.family = "sans",
na.color = "transparent",
data.label = NULL,
label.size = 1,
label.color = "black",
...
)
data |
a data frame/matrix for coloring. The coloring can be continuous (numeric matrix) or discrete (factor matrix) |
reorder |
how to reorder rows and columns. It can be "none" for no reordering, "row" for reordering rows according to number of sharings (by default), "col" for reordering columns, and "both" for reordering rows and columns |
colormap |
short name for the colormap. It can be one of "jet" (jet colormap), "bwr" (blue-white-red colormap), "gbr" (green-black-red colormap), "wyr" (white-yellow-red colormap), "br" (black-red colormap), "yr" (yellow-red colormap), "wb" (white-black colormap), and "rainbow" (rainbow colormap, that is, red-yellow-green-cyan-blue-magenta). Alternatively, any hyphen-separated HTML color names, e.g. "blue-black-yellow", "royalblue-white-sandybrown", "darkgreen-white-darkviolet". A list of standard color names can be found in http://html-color-codes.info/color-names |
ncolors |
the number of colors specified over the colormap |
zlim |
the minimum and maximum z values for which colors should be plotted, defaulting to the range of the finite values of displayed matrix |
barwidth |
the width of the colorbar. Default value is 'legend.key.width' or 'legend.key.size' in 'theme' or theme |
barheight |
the height of the colorbar. Default value is 'legend.key.height' or 'legend.key.size' in 'theme' or theme |
nbin |
the number of bins for drawing colorbar |
legend.title |
the title of the colorbar. By default, it is ” |
x.rotate |
the angle to rotate the x tick labelings. By default, it is 60 |
x.text.size |
the text size of the x tick labelings. By default, it is 6 |
x.text.hjust |
the hjust of the x tick labelings. By default, it is 0.5 |
y.text.size |
the text size of the y tick labelings. By default, it is 6 |
legend.text.size |
the text size of the legend tick labelings. By default, it is 5 |
legend.title.size |
the text size of the legend titles. By default, it is 6 |
shape |
the number specifying the shape. By default, it is 19 |
size |
the number specifying the shape size. By default, it is 2 |
plot.margin |
the margin (t, r, b, l) around plot. By default, it is unit(c(5.5,5.5,5.5,5.5),"pt") |
font.family |
the font family for texts |
na.color |
the color for NAs. By default, it is 'transparent' |
data.label |
a data frame/matrix used for the labelling |
label.size |
the label size |
label.color |
the label color |
... |
additional graphic parameters for supraHex::visTreeBootstrap |
a ggplot2 object
none
xHeatmap
RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
## Not run:
data(mtcars)
gp <- xHeatmap(mtcars, reorder="none", colormap='jet.top', x.rotate=45,
shape=19, size=3, x.text.size=8,y.text.size=8, legend.title='mtcars')
gp + theme(legend.position="bottom",legend.direction="horizontal") +
guides(color=guide_colorbar(title="mtcars",title.position="top",barwidth=5,barheight=0.3))
gp + theme(legend.position="bottom",legend.direction="horizontal") +
guides(color=guide_legend(title="mtcars",title.position="top",barwidth=5,barheight=0.3))
gp + geom_text(aes(x, y,
label=val),size=1.8,color='black',fontface='bold',na.rm=TRUE,angle=45)
## End(Not run)