Making a plot cleaner By this code I produced this tSNE

&gt; length(expr)
[1]  1 209
&gt; aaa=as.matrix(signif(expr,digits=1))
&gt; colnames(aaa)="value"
&gt; aaa=as.data.frame(aaa)
&gt; cc &lt;- AddMetaData(object = seurat, metadata = aaa)
&gt; cc &lt;- SetAllIdent(object = cc, id = "value")
&gt; head(as.matrix(cc@meta.data))
     nGene  nUMI      orig.ident      res.0.7 CELL   STAGE GENO dataset
s1.1 "4331" " 373762" "SeuratProject" "0"     "s1.1" "H16" "WT" "1"    
s1.2 "5603" "1074639" "SeuratProject" "0"     "s1.2" "H16" "WT" "1"    
s1.3 "2064" "  49544" "SeuratProject" "0"     "s1.3" "H16" "WT" "1"    
s1.4 "4680" " 772399" "SeuratProject" "1"     "s1.4" "H16" "WT" "1"    
s1.5 "3876" " 272356" "SeuratProject" "1"     "s1.5" "H16" "WT" "1"    
s1.6 "2557" " 122314" "SeuratProject" "0"     "s1.6" "H16" "WT" "1"    
     stage.nice celltype value   
s1.1 "H16"      "0"      "-2e-01"
s1.2 "H16"      "0"      " 3e-02"
s1.3 "H16"      "0"      "-1e-01"
s1.4 "H16"      "1"      "-4e-02"
s1.5 "H16"      "1"      " 2e-01"
s1.6 "H16"      "0"      "-8e-02"
&gt; TSNEPlot(object = cc)




As you are seeing the range of expression still is very sporadic or when simply use seurat featueplot, again plot is not informative



&gt; feature.plot(seurat,features.plot ="DDB_G0267412")


I fed my scaled data from seurat to single cell orange software, when I plotted one gene on tSNE gave me this 



You are considering how much the plot is clean

How can I  have such a clean plot please? I mean how I can obtain such a range in colouring my cells 

&gt; head(cc@meta.data)
     nGene    nUMI    orig.ident res.0.7 CELL STAGE GENO dataset stage.nice
s1.1  4331  373762 SeuratProject       0 s1.1   H16   WT       1        H16
s1.2  5603 1074639 SeuratProject       0 s1.2   H16   WT       1        H16
s1.3  2064   49544 SeuratProject       0 s1.3   H16   WT       1        H16
s1.4  4680  772399 SeuratProject       1 s1.4   H16   WT       1        H16
s1.5  3876  272356 SeuratProject       1 s1.5   H16   WT       1        H16
s1.6  2557  122314 SeuratProject       0 s1.6   H16   WT       1        H16
     celltype  value
s1.1        0  0.080
s1.2        0  0.100
s1.3        0 -0.060
s1.4        1  0.007
s1.5        1 -0.060
s1.6        0  0.010
&gt;
It doesn't look like this data has been clustered, and you are plotting the 'value', rather than the cluster. If you want to represent values on a tSNE using Seurat, a better function to use is the FeaturePlot, which will colour the points in a more meaningful colour gradient based on their value.
[It's possible this function wasn't available at the time this question was written]
If, instead, you want to plot clusters, then you should carry out some clustering on the data first using FindNeighbors/FindClusters.
There's a great introductory tutorial to guide you into using Seurat on the Satija lab page:
https://satijalab.org/seurat/articles/pbmc3k_tutorial.html