Visualization of two samples for comparison — biplot

Graphical representation of distribution of taxa across two samples.

Usage

biplot_pq(
  physeq,
  fact = NULL,
  merge_sample_by = NULL,
  rarefy_after_merging = FALSE,
  rngseed = FALSE,
  verbose = TRUE,
  inverse_side = FALSE,
  left_name = NULL,
  left_name_col = "#4B3E1E",
  left_fill = "#4B3E1E",
  left_col = "#4B3E1E",
  right_name = NULL,
  right_name_col = "#1d2949",
  right_fill = "#1d2949",
  right_col = "#1d2949",
  log10trans = TRUE,
  nudge_y = c(0.3, 0.3),
  geom_label = FALSE,
  text_size = 3,
  size_names = 5,
  y_names = NA,
  ylim_modif = c(1, 1),
  nb_samples_info = TRUE,
  split_by_sample = FALSE,
  sample_border_col = "#d4d0acff",
  sample_border_width = 0.3,
  color_rank = NULL,
  taxa_names_rank = NULL,
  plotly_version = FALSE,
  ...
)

Arguments

physeq: (required) a phyloseq-class object obtained using the phyloseq package.
fact: (default: NULL) Name of the factor in physeq@sam_data. If left to NULL use the left_name and right_name parameter as modality.
merge_sample_by: (default: NULL) if not NULL samples of physeq are merged using the vector set by merge_sample_by. This merging used the merge_samples2(). In the case of biplot_pq() this must be a factor with two levels only.
rarefy_after_merging: Rarefy each sample after merging by the modalities merge_sample_by
rngseed: (Optional). A single integer value passed to phyloseq::rarefy_even_depth(), which is used to fix a seed for reproducibly random number generation (in this case, reproducibly random subsampling). If set to FALSE, then no fiddling with the RNG seed is performed, and it is up to the user to appropriately call set.seed beforehand to achieve reproducible results. Default is FALSE.
verbose: (logical). If TRUE, print additional information.
inverse_side: Inverse the side (put the right modality in the left side).
left_name: Name fo the left sample.
left_name_col: Color for the left name
left_fill: Fill fo the left sample.
left_col: Color fo the left sample.
right_name: Name fo the right sample.
right_name_col: Color for the right name
right_fill: Fill fo the right sample.
right_col: Color fo the right sample.
log10trans: (logical) Does abundancy is log10 transformed ?
nudge_y: A parameter to control the y position of abundancy values. If a vector of two values are set. The first value is for the left side. and the second value for the right one. If one value is set, this value is used for both side.
geom_label: (default: FALSE, logical) if TRUE use the ggplot2::geom_label() function instead of ggplot2::geom_text() to indicate the numbers of sequences.
text_size: size for the number of sequences
size_names: size for the names of the 2 samples
y_names: y position for the names of the 2 samples. If NA (default), computed using the maximum abundances values.
ylim_modif: vector of two values. Modificator (by a multiplication) of ylim. If one value is set, this value is used for both limits.
nb_samples_info: (default: TRUE, logical) if TRUE and merge_sample_by is set, add the number of samples merged for both levels.
split_by_sample: (default: FALSE, logical) if TRUE and merge_sample_by is set, the bars are not merged but stacked by sample, with borders between segments so that the distribution of sequences across samples is visible. The border color and width are controlled by sample_border_col and sample_border_width.
sample_border_col: (default: "white") Color of the border between sample segments when split_by_sample = TRUE.
sample_border_width: (default: 0.3) Width of the border between sample segments when split_by_sample = TRUE.
color_rank: (default: NULL) Name of a taxonomic rank in tax_table(physeq) to use for coloring bars. When NULL (default), bars are colored by sample modality using left_fill and right_fill. When set (e.g. "Class"), each bar is colored according to its taxonomic assignment at that rank and the left_fill/right_fill color parameters are ignored.
taxa_names_rank: (default: NULL) Name of a taxonomic rank in tax_table(physeq) to use as labels on the taxa axis instead of taxa_names(). When NULL (default), taxa_names() are used. When set (e.g. "Genus"), the genus name is displayed. OTUs sharing the same label at this rank will appear as a single merged bar.
plotly_version: If TRUE, use plotly::ggplotly() to return a interactive ggplot.
...: Other arguments for the ggplot function

Value

A plot

Author

Adrien Taudière

Examples

data_fungi_2Height <- subset_samples(data_fungi_mini, Height %in% c("Low", "High"))
biplot_pq(data_fungi_2Height, "Height", merge_sample_by = "Height")
#> Cleaning suppress 5 taxa and 0 samples.
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.

biplot_pq(data_fungi_2Height, "Height",
  merge_sample_by = "Height",
  split_by_sample = TRUE
)
#> The two modalities differ greatly (more than x2) in their number of sequences (1885 vs 10201). You may be interested by the parameter rarefy_after_merging
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.

biplot_pq(data_fungi_2Height, "Height",
  merge_sample_by = "Height",
  color_rank = "Order",
  taxa_names_rank = "Genus"
)
#> Cleaning suppress 5 taxa and 0 samples.
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.