search

btmonier / vidger

Make rapid visualizations of RNA-seq data in R
GNU General Public License v3.0
18 stars 6 forks source link

How to use 4-way plot between separate group? #3

Closed wajm closed 5 years ago

wajm commented 5 years ago

Hi, I need help. I have 2 sets of group. (p21 [Ctl vs cKO] and p28 [Ctl vs cKO]) In this case how to use 4-way plot set-up? vsFourWay( x = 'p21', y = 'p28', control = '???????????', data = df.deseq, d.factor = NULL, type = 'cuffdiff', padj = 0.05, x.lim = NULL, y.lim = NULL, lfc = NULL, legend = TRUE, title = TRUE, grid = TRUE )

btmonier commented 5 years ago

Before I can assess your problem, could you give me some more background information about your experimental setup? I'm not sure what you mean by "(p21 [Ctl vs cKO] and p28 [Ctl vs cKO])"

wajm commented 5 years ago

Oh, I'm sorry. I have two data sets. (p21 control vs p21 mutant and p28 control vs p28 mutant) p21 and p28 means development stage (day21 and day28). So I want to make 4-way plot (x-axis is p21 control vs mutant and y-axis is p28 control vs mutant). Thanks.

btmonier commented 5 years ago

Thanks - I understand now. vsFourWay()'s functionality explicitly works only with one data set implemented as one of the three data set types (DESeq2, edgeR, or cuffdiff table outputs). Additionally, vsFourWay() works with 3 variables in one data set, hence, why there is a x, y, and control parameter. Both x and y variables are compared to one control variable. I believe with your data, other ViDGER functionalities where you compare only two variables may be more appropriate and faceted together as an A/B figure.