Figure legend in lefserPlotClad output

[shbrief]

Why are there only two circle sizes in the figure legend?

> library(lefser)
> ## Old cMD data in the lefser package
> data(zeller14)
> zeller14 <- zeller14[, zeller14$study_condition != "adenoma"]
> zeller14$study_condition <- factor(zeller14$study_condition,
+                                    levels = c("CRC", "control")) # re-levels
> tn <- get_terminal_nodes(rownames(zeller14))
> zeller14_tn <- zeller14[tn,]
> zeller14_tn_ra <- relativeAb(zeller14_tn)
> zeller14_input <- rowNames2RowData(zeller14_tn_ra)
> resAll <- lefserClades(zeller14_input, classCol = "study_condition")
18 features don't have species information.
96 features don't have strain information.
Dropped 96 features without full taxonomy information.
lefser will be run at the phylum, class, order, family, genus, species, strain level.

>>>> Running lefser at the phylum level. <<<<
The outcome variable is specified as 'study_condition' and the reference category is 'CRC'.
 See `?factor` or `?relevel` to change the reference category.

>>>> Running lefser at the class level. <<<<
The outcome variable is specified as 'study_condition' and the reference category is 'CRC'.
 See `?factor` or `?relevel` to change the reference category.

>>>> Running lefser at the order level. <<<<
The outcome variable is specified as 'study_condition' and the reference category is 'CRC'.
 See `?factor` or `?relevel` to change the reference category.

>>>> Running lefser at the family level. <<<<
The outcome variable is specified as 'study_condition' and the reference category is 'CRC'.
 See `?factor` or `?relevel` to change the reference category.

>>>> Running lefser at the genus level. <<<<
The outcome variable is specified as 'study_condition' and the reference category is 'CRC'.
 See `?factor` or `?relevel` to change the reference category.

>>>> Running lefser at the species level. <<<<
The outcome variable is specified as 'study_condition' and the reference category is 'CRC'.
 See `?factor` or `?relevel` to change the reference category.

>>>> Running lefser at the strain level. <<<<
The outcome variable is specified as 'study_condition' and the reference category is 'CRC'.
 See `?factor` or `?relevel` to change the reference category.
> lefserPlotClad(resAll) 
Using palette: colorblind

[shbrief]

@sdgamboa Just double-checking: the circle size is 'LDA score' but not 'relative abundance'?

[sdgamboa]

Yeah. It's the absolute LDA score. I think the scores are higher and more stable because the features abundance is agglomerated by clade.