I appreciate your efforts in developing such an effective tool for spatial transcriptomics analysis! As I explore the capabilities of stLearn with Xenium data, I have encountered a point of confusion that I hope you can help clarify.
I am currently utilizing stLearn for analyzing Xenium data and have a question regarding the visualization of cell-cell interactions. In my understanding, when using st.pl.ccinet_plot and st.pl.lr_cci_map, the arrowhead points to the receiver (receptor side), and the base indicates the sender (ligand side). However, the results from st.pl.cci_map with the same cell type pairings in the same dataset show the arrowhead as the sender and the base as the receiver, which seems to contradict the previous findings. This pattern is consistent with what is shown in the tutorials on stLearn documentation, where st.pl.lr_cci_map and st.pl.cci_map also depict the arrowhead as the sender. Could you confirm whether the directionality in st.pl.ccinet_plot and st.pl.lr_cci_map should indeed indicate the arrowhead as the sender and the base as the receiver?
Dear stLearn Team,
I appreciate your efforts in developing such an effective tool for spatial transcriptomics analysis! As I explore the capabilities of stLearn with Xenium data, I have encountered a point of confusion that I hope you can help clarify.
I am currently utilizing stLearn for analyzing Xenium data and have a question regarding the visualization of cell-cell interactions. In my understanding, when using st.pl.ccinet_plot and st.pl.lr_cci_map, the arrowhead points to the receiver (receptor side), and the base indicates the sender (ligand side). However, the results from st.pl.cci_map with the same cell type pairings in the same dataset show the arrowhead as the sender and the base as the receiver, which seems to contradict the previous findings. This pattern is consistent with what is shown in the tutorials on stLearn documentation, where st.pl.lr_cci_map and st.pl.cci_map also depict the arrowhead as the sender. Could you confirm whether the directionality in st.pl.ccinet_plot and st.pl.lr_cci_map should indeed indicate the arrowhead as the sender and the base as the receiver?