biplot_pq {MiscMetabar}

Visualization of two samples for comparison

Description

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(s)

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")