Clarification on compute_sc_flux Output and Heatmap Column Interpretation

[xukun-zhang]

Clarification on compute_sc_flux Output and Heatmap Column Interpretation

Dear KChen-lab,

I hope this message finds you well. I am currently working with the compute_sc_flux function and have encountered some confusion regarding the output and its subsequent use in heatmap visualization. I would appreciate your assistance in clarifying the following:

1. Regarding the compute_sc_flux function:

After running the following code:

flux <- compute_sc_flux(num_cell = num_cell, fraction = fractions, fluxscore = scores, medium = human_blood)

I noticed that the resulting flux object does not seem to have columns equal to the num_cell value as expected. Could you kindly explain what the rows and columns in the returned result represent?

2. Regarding the heatmap generation:

Based on the tutorial code provided, I am generating a heatmap:

mapal <- colorRampPalette(RColorBrewer::brewer.pal(11,"RdBu"))(256)
pheatmap::pheatmap(all_pathway_score, cluster_cols = F, color = rev(mapal), scale = "row")

However, I am unsure about the meaning of the columns in the generated heatmap (e.g., V1, V2, V3, etc.). These columns do not seem to represent the cell types as I initially expected. Could you please clarify what these columns represent in the heatmap?

I would greatly appreciate your insights on these questions.

Thank you for your time and support.

Best regards,
Xukun Zhang