How to remove zero value of gene on FeatureScatter plot using Seurat?
It will not improve your correlation most likely, unless the zeros are not missing at random:

library(Seurat)
data &lt;- pbmc_small
data[["percent.mt"]] &lt;- PercentageFeatureSet(data, pattern = "^MT-")
data &lt;- NormalizeData(data)
genes &lt;-c("HLA-DRA","LYZ")
countdata = pbmc_small[["RNA"]]@data
countdata &lt;- t(as.matrix(countdata)[genes,])
plot(countdata)




Now you need to subset the matrix, and remove the rows where at least one of the entries is 0, you can use rowSums(..==0)==0, meaning no zeros in the rows:

plot(countdata[rowSums(countdata==0)==0,])




cor(countdata[rowSums(countdata==0)==0,])
          HLA-DRA       LYZ
HLA-DRA 1.0000000 0.2338371
LYZ     0.2338371 1.0000000