Using Monocle 2.0, how does one plot the cell pseudo-time trajectories for only the cell clusters which are classified by the marker expression, and ignore the ambiguous/unknown cells. I am attaching a plot for the trajectory, with 3 cell clusters and 2 additional classes i.e. ambiguous cells and unknown cells. I would like to next visualize the marker expression on the trajectory and it will be much clearer if the large no. of ambiguous cells can be removed. How to do this ?
Keywords: Monocle, scRNA-seq, Bioinformatics, pseudotime trajectories
Hi,
If you use monocle as an R package, you can pre-filter your cells with particular threshold on your marker genes before feeding the data to pseudotime.
If the graph is made using ggplot, it is quite easy to add the expression of markers as size of the dot, therefore increasing the information, given by the data point.
For example:
data[i,j] # "I" is for cells, "j" is for genes expressed
data_filteredthreshold),]
gglpot(data_filtered, aes(x=component_1, y=component_2, color=cluster, size=marker))+geom_point()
Best,
Michail
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