Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST)).
I am trying to look at gene expression of a specific condition in my UMAP from a converted Seurat object, however, whenever I try to specify the condition this plot comes up blank. I've checked to make sure the names of the conditions when I initially aggregated the data match the name that I specify in the command, however that does not seem to be the issue. When I try to plot without conds.to.plot it works, however when I add the command back in I receive the blank image. Any suggestions?
Here is the code I used when aggregating the data:
my.data <- data.aggregation(samples = c("sample1","sample2", "sample3", "sample4", "sample5"), condition.names = c("S1","S2", "S3", "S4", "S5"))
and here is the code I used to call the plot, which comes out blank
Hi Reza,
I am trying to look at gene expression of a specific condition in my UMAP from a converted Seurat object, however, whenever I try to specify the condition this plot comes up blank. I've checked to make sure the names of the conditions when I initially aggregated the data match the name that I specify in the command, however that does not seem to be the issue. When I try to plot without conds.to.plot it works, however when I add the command back in I receive the blank image. Any suggestions?
Here is the code I used when aggregating the data:
my.data <- data.aggregation(samples = c("sample1","sample2", "sample3", "sample4", "sample5"), condition.names = c("S1","S2", "S3", "S4", "S5"))and here is the code I used to call the plot, which comes out blank
C <- gene.plot(my.obj, gene = "NFIB", plot.type = "scatterplot", conds.to.plot = "S2", interactive = F, out.name = "scatter_plot", plot.data.type = "umap")