Cannot change point size by size= in plotEmbedding()

[jiangpuxuan]

I run plotEmbedding() to get the score of a gene in my dataset
Here is my code :

p1 <- plotEmbedding(
    ArchRProj = proj, 
    colorBy = "GeneScoreMatrix", 
    name = "mygene", 
    continuousSet = "horizonExtra",
    embedding = "Harmony_ATAC",
    imputeWeights = getImputeWeights(proj),
    size=0.4
)
p1

I changed size but nothing happened.

BTW, when I run the code below to display the clustering, the size parameter worked:

plotEmbedding(
proj, 
colorBy = "cellColData", 
name = "ClustersHarmonyATAC.0.4", 
embedding = "Harmony_ATAC",  
size = 0.25)

[rcorces]

Please read all function documentation before posting. Had you read the function documentation for the size parameter, you would see:

size	A number indicating the size of the points to plot if plotAs is set to "points".

Your problem is that the default for plotAs is hex for GeneScoreMatrix but points for cellColData

[jiangpuxuan]

plotEmbedding(

Actually I had noticed plotAs parameter but misunderstood it.
I am sorry about that and thank you for your help.