| Title: | Creating Composite Plots using 'aplot' |
| Version: | 0.0.4 |
| Description: | Many complex plots are actually composite plots, such as 'oncoplot', 'funkyheatmap', 'upsetplot', etc. We can produce subplots using 'ggplot2' and combine them to create composite plots using 'aplot'. In this way, it is easy to customize these complex plots, by adding, deleting or modifying subplots in the final plot. This package provides a set of utilities to help users to create subplots and complex plots. |
| Depends: | R (≥ 4.1.0) |
| Imports: | aplot (≥ 0.2.3), dplyr, forcats, ggfun (≥ 0.1.1), ggplot2, grid, maftools, purrr, rlang, stats, tibble, tidyr, utils, ggstar, yulab.utils (≥ 0.0.8) |
| Suggests: | ggtree, data.table, RColorBrewer, R.utils |
| URL: | https://github.com/YuLab-SMU/aplotExtra |
| License: | Artistic-2.0 |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.2 |
| NeedsCompilation: | no |
| Packaged: | 2025-06-12 02:36:09 UTC; HUAWEI |
| Author: | Guangchuang Yu 
[aut, cre],
Shuangbin Xu
[ctb],
Chun-Hui Gao
[ctb],
Shensuo Li [ctb] |
| Maintainer: | Guangchuang Yu <guangchuangyu@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2025-06-12 04:20:02 UTC |
aplotExtra: Creating Composite Plots using 'aplot'
Description
Many complex plots are actually composite plots, such as 'oncoplot', 'funkyheatmap', 'upsetplot', etc. We can produce subplots using 'ggplot2' and combine them to create composite plots using 'aplot'. In this way, it is easy to customize these complex plots, by adding, deleting or modifying subplots in the final plot. This package provides a set of utilities to help users to create subplots and complex plots.
Author(s)
Maintainer: Guangchuang Yu guangchuangyu@gmail.com (ORCID)
Other contributors:
Shuangbin Xu xshuangbin@163.com (ORCID) [contributor]
Chun-Hui Gao gaospecial@gmail.com (ORCID) [contributor]
Shensuo Li lishensuo@163.com (ORCID) [contributor]
See Also
Useful links:
funky_bar
Description
create bar plot for funkyheatmap
Usage
funky_bar(data, cols)
Arguments
data |
data frame |
cols |
selected columns |
Value
ggplot object
Author(s)
Guangchuang Yu
funky_heatmap
Description
create a funkyheatmap
Usage
funky_heatmap(..., data = NULL, widths = NULL, options = NULL)
Arguments
... |
funky plots (e.g., outputs of |
data |
If data is provided, create a funkyheatmap from it. Otherwise, create composite plot from |
widths |
relative widths of the plots |
options |
any ggplot component that can be added to the plots |
Value
gglist object
Author(s)
Guangchuang Yu
funky_point
Description
create dot plot for funkyheatmap
Usage
funky_point(data, cols, cols2 = NULL, ...)
Arguments
data |
data frame |
cols |
selected columns |
cols2 |
selected columns to keep names |
... |
additional parameters, passing to |
Value
ggplot object
Author(s)
Guangchuang Yu
funky_text
Description
create text plot (i.e., rownames) for funkyheatmap
Usage
funky_text(data, cols = 1, hjust = 0)
Arguments
data |
data frame |
cols |
selected column |
hjust |
text alignment adjustment |
Value
ggplot object
Author(s)
Guangchuang Yu
Get the items/names/ids of subsets from a named list
Description
Get the items/names/ids of subsets from a named list
Usage
get_all_subsets(list, name_separator = "/")
Arguments
list |
a named list |
name_separator |
default is / |
Value
a tibble
Examples
list = list(A = sample(LETTERS, 20),
B = sample(LETTERS, 22),
C = sample(LETTERS, 24),
D = sample(LETTERS, 30, replace = TRUE))
get_all_subsets(list)
ploting oncoplot with aplot
Description
ploting oncoplot with aplot
Usage
oncoplot(maf, genes = 20)
Arguments
maf |
MAF object. |
genes |
the gene names or the number, default is 20. |
Value
oncoplot object, which is also a aplot object
Examples
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml.clin <- system.file('extdata', 'tcga_laml_annot.tsv', package = 'maftools')
laml <- maftools::read.maf(maf = laml.maf, clinicalData = laml.clin)
oncoplot(maf = laml, genes = 20)
upsetplot2
Description
Plot a upset plot
Usage
upset_plot(
list,
nintersects = NULL,
order.intersect.by = c("size", "name"),
order.set.by = c("size", "name"),
color.intersect.by = "none",
color.set.by = "none",
remove_empty_intersects = TRUE
)
Arguments
list |
a list of sets |
nintersects |
number of intersects. If NULL, all intersections will show. |
order.intersect.by |
one of 'size' or 'name' |
order.set.by |
one of 'size' or 'name' |
color.intersect.by |
color scheme for 'intersect' bars (e.g., "Set2"), default is "none" |
color.set.by |
color scheme for 'set' bars (e.g., "Set3"), default is "none" |
remove_empty_intersects |
remove the intersects which have zero elements. Default is TRUE. |
Details
This function generate a upset plot by creating a composite plot which contains subplots generated by ggplot2.
Value
an upset plot
Examples
list = list(A = sample(LETTERS, 20),
B = sample(LETTERS, 22),
C = sample(LETTERS, 14),
D = sample(LETTERS, 30, replace = TRUE))
upset_plot(list)
upset_plot(list, remove_empty_intersects = TRUE)
upset_plot(list, order.intersect.by = "name")
upset_plot(list, order.set.by = "name")
upset_plot(list, nintersects = 6)