mp_plot_alpha {MicrobiotaProcess} | R Documentation |
Plotting the alpha diversity between samples or groups.
mp_plot_alpha( .data, .group, .alpha = c("Observe", "Shannon"), test = "wilcox.test", comparisons = NULL, step_increase = 0.05, ... ) ## S4 method for signature 'MPSE' mp_plot_alpha( .data, .group, .alpha = c("Observe", "Shannon"), test = "wilcox.test", comparisons = NULL, step_increase = 0.05, ... ) ## S4 method for signature 'tbl_mpse' mp_plot_alpha( .data, .group, .alpha = c("Observe", "Shannon"), test = "wilcox.test", comparisons = NULL, step_increase = 0.05, ... ) ## S4 method for signature 'grouped_df_mpse' mp_plot_alpha( .data, .group, .alpha = c("Observe", "Shannon"), test = "wilcox.test", comparisons = NULL, step_increase = 0.05, ... )
.data |
MPSE or tbl_mpse object |
.group |
the column name of sample group information |
.alpha |
the column name of alpha index after run mp_cal_alpha |
test |
the name of the statistical test, default is 'wilcox.test' |
comparisons |
A list of length-2 vectors. The entries in the vector are either the names of 2 values on the x-axis or the 2 integers that correspond to the index of the columns of interest, default is NULL, meaning it will be calculated automatically with the names in the .group. |
step_increase |
numeric vector with the increase in fraction of total height for every additional comparison to minimize overlap, default is 0.05. |
... |
additional parameters, see also |
Shuangbin Xu
## Not run: data(mouse.time.mpse) mpse <- mouse.time.mpse %>% mp_rrarefy() %>% mp_cal_alpha(.abundance=RareAbundance) mpse p <- mpse %>% mp_plot_alpha(.group=time, .alpha=c(Observe, Shannon, J)) p ## End(Not run)