Description Usage Arguments Value Examples
This function uses the colorgram
function from the package
squash to plot log-posterior probability for the tested combinations of
cellularity and ploidy
1 2 3 4 5 6 7 | cp.plot(cp.table, xlab = "Ploidy", ylab = "Cellularity",
zlab = "Scaled rank LPP",
colFn = colorRampPalette(c('white', 'lightblue')), ...)
cp.plot.contours(cp.table, likThresh = c(0.95), alternative = TRUE,
col = palette(), legend.pos = "bottomright", pch = 18,
alt.pch = 3, ...)
get.ci(cp.table, level = 0.95)
|
cp.table |
list, as output from |
xlab |
xlab parameter as in the function |
ylab |
ylab parameter as in the function |
zlab |
zlab parameter as in the function |
colFn |
colFn parameter as in the function |
likThresh |
vector of quantiles to define tresholds for the confindent regions. |
alternative |
boolean parameter, if |
col |
vector of colors. |
legend.pos |
position for placing the legend. |
pch |
character used to indicate the point estimate. |
alt.pch |
if |
... |
additional arguments accepted by the function |
level |
decimal value of the confidence interval |
The get.ci
function returns a list with 6 items:
values.ploidy |
matrix of ploidy values with respective posterior probability. |
confint.ploidy |
boundaries of the confidence interval of the estimated ploidy. |
max.ploidy |
point estimate of the ploidy value that has the maximum posterior probability. |
values.cellularity |
matrix of cellularity values with respective posterior probability. |
confint.cellularity |
boundaries of the confidence interval of the estimated cellularity. |
max.cellularity |
point estimate of the cellularity value that has the maximum posterior probability. |
1 2 3 4 5 6 7 8 9 10 11 | data(CP.example)
cp.plot(CP.example)
cp.plot.contours(CP.example, add = TRUE)
# Plot more contours
cp.plot(CP.example)
cp.plot.contours(CP.example, likThresh = c(0.95, 0.9999), add = TRUE)
# Return the 95% confidence interval
CP.example.ci <- get.ci(CP.example)
str(CP.example.ci)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.