Description Usage Arguments Examples
Plot extracted components
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | plot_comp_size(hdpsample, legend = TRUE, col_a = "hotpink",
col_b = "skyblue3", xlab = "Component", ylab = "Number of data items",
...)
plot_comp_distn(hdpsample, comp = NULL, cat_names = NULL, grouping = NULL,
col = "grey70", col_nonsig = NULL, show_group_labels = FALSE,
cred_int = TRUE, weights = NULL, plot_title = NULL,
group_label_height = 1.05, cex.cat = 0.7, ...)
plot_dp_comp_exposure(hdpsample, dpindices, col_comp, dpnames = NULL,
main_text = NULL, incl_numdata_plot = TRUE, incl_nonsig = TRUE,
incl_comp0 = TRUE, ylab_numdata = "Number of data items",
ylab_exp = "Component exposure", leg.title = "Component",
cex.names = 0.6, cex.axis = 0.7, mar = c(1, 4, 2, 0.5), oma = c(1.5,
1.5, 1, 1), ...)
|
hdpsample |
A hdpSampleChain or hdpSampleMulti object including output
from |
legend |
Logical - should a legend be included? (default TRUE) |
col_a |
Color ramp side for early posterior samples (if hdpSampleChain) or first chain (if hdpSampleMulti) |
col_b |
Color ramp side for late posterior samples (if hdpSampleChain) or last chain (if hdpSampleMulti) |
xlab |
Horizontal axis label |
ylab |
Vertical axis label |
... |
Other arguments to plot |
comp |
(Optional) Number(s) of the component(s) to plot (from 0 to the max component number). The default is to plot all components. |
cat_names |
(Optional) Data category names to label the horizontal axis |
grouping |
(Optional) A factor indicating data category groups. |
col |
Either a single colour for all data categories, or a vector of colours for each group (in the same order as the levels of the grouping factor) |
col_nonsig |
(Optional) Colour for any data category whose 95% credibility interval overlaps with zero (if set, overrides col argument) |
show_group_labels |
Logical - should group labels be added to the top horizontal axis? (default FALSE) (only works if categories alreayd come in orders) |
cred_int |
Logical - should 95% credibility intervals be plotted? (default TRUE) |
weights |
(Optional) Weights over the data categories to adjust their relative contribution (multiplicative) |
plot_title |
(Optional) Character vector of custom plot titles (one for each component plotted) |
group_label_height |
Multiplicative factor from top of plot for group label placement |
cex.cat |
Expansion factor for the (optional) cat_names |
dpindices |
Indices of DP nodes to plot |
col_comp |
Colours of each component, from 0 to the max number |
dpnames |
(Optional) Names of the DP nodes |
main_text |
(Optional) Text at top of plot |
incl_numdata_plot |
Logical - should an upper barplot indicating the number of data items per DP be included? (Default TRUE) |
incl_nonsig |
Logical - should components whose credibility intervals include 0 be included (per DP)? (Default TRUE) |
incl_comp0 |
Logical - should component zero be plotted? (Default TRUE) |
ylab_numdata |
Vertical axis label for numdata plot |
ylab_exp |
Vertical exis label for exposure plot |
leg.title |
Legend title |
cex.names |
Expansion factor for bar labels (dpnames) in exposure plot |
cex.axis |
Expansion factor for vertical-axis annotation |
mar |
See ?par |
oma |
See ?par |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | mut_example_multi <- hdp_extract_components(mut_example_multi)
plot_comp_size(mut_example_multi, bty="L")
bases <- c("A", "C", "G", "T")
trinuc_context <- paste0(rep(rep(bases, times=6), each=4),
rep(c("C", "T"), each=48),
rep(bases, times=24))
group_factor <- as.factor(rep(c("C>A", "C>G", "C>T", "T>A", "T>C", "T>G"),
each=16))
plot_comp_distn(mut_example_multi, cat_names=trinuc_context,
grouping=group_factor, col=RColorBrewer::brewer.pal(6, "Set2"),
col_nonsig="grey80", show_group_labels=TRUE)
plot_dp_comp_exposure(mut_example_multi, 5:30,
RColorBrewer::brewer.pal(12, "Set3"))
plot_dp_comp_exposure(mut_example_multi, 5:30,
RColorBrewer::brewer.pal(12, "Set3"),
incl_numdata_plot=FALSE, incl_nonsig=FALSE)
|
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