micro_heatmap: Create heatmaps of estiamted coefficients from negative...

In CharlieCarpenter/tidy.micro: A Pipeline For Microbiome Analysis And Visualization

Description

A function to create heatmaps of estimated beta coeffients from each model fit by nb_mods

Usage

micro_heatmap(
  modsum,
  low_grad,
  high_grad,
  mid_grad,
  midpoint = 0,
  top_taxa = 10,
  low_lim,
  high_lim,
  mute_cols = T,
  alpha = 0.05,
  dot_size = 2,
  dot_shape = 8,
  main = NULL,
  xlab = NULL,
  ylab = NULL,
  subtitle = NULL,
  xaxis = NULL,
  caption = latex2exp::TeX("'*' denotes significance at $\\alpha$ = 0.05")
)

Arguments

modsum	The output from nb_mods
low_grad	The low gradient colors for the coefficient magnitude. Will be fed into scale_fill_gradient
high_grad	The high gradient colors for the coefficient magnitude. Will be fed into scale_fill_gradient
mid_grad	The medium gradient colors for the coefficient magnitude. Will be fed into scale_fill_gradient
midpoint	Midpoint for coefficient magnitude in legend
top_taxa	Only plot X taxa with the largest magnitude beta coefficients
low_lim	Lower limits of the fill gradient. Will default to the largest magnitude effect size
high_lim	Upper limits of the fill gradient. Will default to the largest magnitude effect size
mute_cols	Mute the colors of the fill gradients
alpha	Mark beta coefficient cells with p-values below this cutoff
dot_size	size of marker in cells
main	Plot title
xlab	x-axis label
ylab	y-axis label
subtitle	Plot label
xaxis	Labels for the x-axis ticks
shape	shape of marker in cells
legend_title	Title for the legend

Details

The output will give gray columns if there are missing values in the supplied continuous variable

Value

Returns a ggplot that you can add geoms to if you'd like

Examples

data(phy); data(cla); data(ord); data(fam); data(met)

otu_tabs = list(Phylum = phy, Class = cla, Order = ord, Family = fam)
set <- tidy_micro(otu_tabs = otu_tabs, meta = met) \
filter(day == 7) ## Only including the first week

## Creating negative binomial models on filtered tidy_micro set
nb_fam <- set \
mutate(bpd1 = factor(bpd1)) \
otu_filter(ra_cutoff = 0.1, exclude_taxa = c("Unclassified", "Bacteria")) \
nb_mods(table = "Family", bpd1)

nb_fam \

CharlieCarpenter/tidy.micro documentation built on Jan. 19, 2020, 6:28 p.m.