Dysbiosis Score Gradient Visualization

Arguments

df: The data frame output from different dysbiosis calculators provided by dysbiosisR package.
score: Variable to plot on x-axis.
colors: colors to use for plotting. Default is NULL.
show_points: Logical TRUE or FALSE.
jitter_width: Passed to geom_jitter.

Value

A ggplot2 object

Details

A wrapper for dysbiosis gradient visualization.

Author

Sudarshan A. Shetty

Examples

data("WirbelJ_2018")
library(RColorBrewer)
dist.mat <- phyloseq::distance(WirbelJ_2018, "bray")
# get reference samples
ref.samples <- sample_names(subset_samples(WirbelJ_2018,
                                           disease == "healthy"))

dysbiosis_1 <- dysbiosisMedianCLV(WirbelJ_2018,
                                  dist_mat = dist.mat,
                                  reference_samples = ref.samples)

# get dysbiosis and normobiosis thresholds
dysbiosis_thres <- quantile(subset(dysbiosis_1, disease == "CRC")$score, 0.9)
normobiosis_thres <- quantile(subset(dysbiosis_1, disease == "CRC")$score, 0.1)

plotDysbiosisGradient(df=dysbiosis_1,
                      score="score",
                      high_line = dysbiosis_thres,
                      low_line = normobiosis_thres,
                      group_var = "disease",
                      group_colors=c("healthy" = "steelblue", "CRC"= "brown3"),
                      point_size = 2,
                      bg_colors = rev(brewer.pal(9, "YlOrBr")))