How to set the aesthetic mapping of PCoA?

[BinhongLiu]

Hi Shuangbin, I'm wondering how to set the aesthetic mapping of PCoA use the mapping parameter in the ggordpoint function. It seems to be that I can change the shape, size, or alpha of the points using this function just like ggplot2. Could you provide some demo about this function? Thanks!

[BinhongLiu]

I tried this code with the demo data:

ggordpoint(obj=pcoares, biplot=TRUE, speciesannot=TRUE,
           mapping=aes(size="time"),
           factorNames=c("time"), ellipse=TRUE) +
           scale_color_manual(values=c("#2874C5", "#EABF00"))

It showed this error: 错误: stat_ord_ellipse requires the following missing aesthetics: x and y

After I added the x and y:

ggordpoint(obj=pcoares, biplot=TRUE, speciesannot=TRUE,
           mapping=aes(x=pcoares@pca$vectors[,1],y=pcoares@pca$vectors[,2],size="time"),
           factorNames=c("time"), ellipse=TRUE) +
           scale_size_manual(values = c("Early"=12,"Late"=1))

The plot was still the same. Could you provide some demo about this function? Many thanks!

[xiangpin]

When your want to set it by yourself, only alpha can be setted, the first element of factorNames has been setted to map color, and the second element of factorNames has been setted to map shape. Please reinstall github version and use the following codes.

p <- ggordpoint(obj=pcoares, biplot=TRUE, speciesannot=TRUE,
                            mapping=aes(alpha=time),
                            factorNames=c("time", "time"), ellipse=TRUE) +
           scale_color_manual(values=c("#2874C5", "#EABF00"))

The first time will be mapped to color of point, and second time (if you have other variable) will be mapped to shape of point. and third continuous variable can be mapped to alpha. Because I don't have the datasets contained three variable.

Note: The gg functions of MicrobiotaProcess are not general like ggplot2 or other ggplot2-extension, because I want them to plot the figures to reduce the amout of codes of users, and geneatare the publicaton figures. So I want to keep a balance between reducing the amount of codes of users and flexibility.

[BinhongLiu]

Thanks! That help me a lot!

[HolmesCloud]

Learned from your answer above, I have known that factorNames can set the alpha,shape and fill. but I just want to change the shape.and just want a figure plot with circle point and different color fill.how should I code?Thanks!

[xiangpin]

The previous version didn't export the starshape of ggstar. (the point layer is provided by ggstar since it can provide more shapes). I will set the default shape to the circle point. But I recommend you use mp_cal_pca or mp_cal_pcoa to perform the analysis of PCA or PCoA. I re-built the framework based on MPSE object inherited SummarizedExperiment object and tibble (need re-install via remotes::install_github("YuLab-SMU/MicrobiotaProcess")). I am rebuilding the vignettes, but, you can also follow the examples of them. And you can use mp_import_dada2, mp_import_qiime or mp_import_qiime2 to parse the output of upstream analysis.