micro_heatmap: Create heatmaps of estiamted coefficients from negative...
In tidyMicro: A Pipeline for Microbiome Analysis and Visualization

Description Usage Arguments Details Value Examples

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

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,
  legend_title = NULL,
  caption = NULL
)

`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
`dot_shape`	shape 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
`legend_title`	Title of figure legend
`caption`	plot caption to be displayed at the bottom of plot

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

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

data(bpd_phy); data(bpd_cla); data(bpd_ord); data(bpd_fam); data(bpd_clin)

otu_tabs <- list(Phylum = bpd_phy, Class = bpd_cla,
Order = bpd_ord, Family = bpd_fam)
set <- tidy_micro(otu_tabs = otu_tabs, clinical = bpd_clin) %>%
filter(day == 7) ## Only including the first week

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

nb_fam %>% micro_heatmap