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rezakj / iCellR

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)).
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Seeking help to create different types of plots #33

Closed Rashidul1990 closed 2 years ago

Rashidul1990 commented 2 years ago

I would be highly grateful if you can answer the following questions-

  1. How to make a vector for more than one gene and display it in DotPlot?
  2. How to do co-expression analysis of two markers and create bicolored co-marker gradients in FeaturePlot?
  3. I want to present the average gene expression of a specific in Violin plots?
  4. How to do RidgePlot in iCellR?
rezakj commented 2 years ago

Hi,

iCellR dose not make 2 color plots but you can use the command below to export the expression of the genes you like and use ggplot2 to plot with 2 colors.

gene.plot(my.obj, gene = "MS4A1", write.data = T, scaleValue = F, data.type = "main")

For co-expression use gene-gene correlation plots, example below:

gg.cor(my.obj, interactive = F, gene1 = "GNLY", gene2 = "NKG7", conds = NULL, clusts = NULL, data.type = "imputed")

Rashidul1990 commented 2 years ago

Thanks very much for your kind response.

1st command work perfectly fine but the second command for gene-gene correlation plots give erros as-

gg.cor(my.obj, interactive = F, gene1 = "CD3D", gene2 = "PTPRC", conds = NULL, clusts = NULL, data.type = "imputed")

Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 14555, 0

Would you please further suggest solving this error?

Many thanks and best regards, Rashidul

rezakj commented 2 years ago

Did you impute the data before running it and also ran clustering?