Visualization of two samples for comparison — biplot

Usage

biplot_pq(
  physeq,
  fact = NULL,
  merge_sample_by = NULL,
  rarefy_after_merging = FALSE,
  inverse_side = FALSE,
  left_name = NULL,
  left_name_col = "#4B3E1E",
  left_fill = "#4B3E1E",
  left_col = "#f3f2d9",
  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,
  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
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.
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.
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_rect()`).