community_plot {LorMe} | R Documentation |
Generate Community Composition Plot Based on Tax_summary Object
Description
Microbial community composition visualization in format of barplot, areaplot and alluvialplot
Usage
community_plot(
taxobj,
taxlevel,
n = 10,
palette = "Spectral",
nrow = NULL,
rmprefix = NULL
)
Arguments
taxobj |
Configured tax summary objects.See in |
taxlevel |
Character. taxonomy levels used for visualization.Must be one of c("Domain","Phylum","Class","Order","Family","Genus","Species","Base"). |
n |
Numeric. Top n taxa remained according to relative abundance. Default:10 |
palette |
Character. Palette for visualization,default:"Spectral",recommended to use "Paired" for more than 15 tax. |
nrow |
Numeric. Number of rows when wrap panels,default:NULL. |
rmprefix |
Numeric. Removed prefix character in taxonomy annotation.Default:NULL. See details in example. |
Value
community_plot2 returns three ggplot objects, two data frame used in visualization and one character of filled mapping colors
Author(s)
Wang Ningqi2434066068@qq.com
Examples
{
require(magrittr)
### Data preparation ###
data("Two_group")
## Use taxonomy summary objects
phylum10 <- community_plot(
taxobj = Two_group,
taxlevel = "Phylum",
n = 10,
rmprefix = "p__"
)
phylum10$barplot # Check bar plot
phylum10$areaplot # Check area plot
phylum10$alluvialplot # Check alluvial plot
phylum10$Top10Phylum %>% head(10) # Check top taxa data frame
phylum10$Grouped_Top10Phylum %>% head(10) # Check grouped top taxa data frame
print(phylum10$filled_color) # Check mapping colors
# Double facet
data("Facet_group")
# Using palette by default
phylum10 <- community_plot(
taxobj = Facet_group,
taxlevel = "Phylum",
n = 10,
rmprefix = " p__"
)
phylum10$barplot
phylum10$areaplot
phylum10$alluvialplot
# Another example
genus20 <- community_plot(
taxobj = Facet_group,
taxlevel = "Genus",
n = 20,
palette = "Paired",
rmprefix = " g__"
)
genus20$alluvialplot
}