lowess regression function on  (RStudio)

Journal: Nature Communications

Article Title: On-microscope staging of live cells reveals changes in the dynamics of transcriptional bursting during differentiation

doi: 10.1038/s41467-022-33977-4

Figure Lengend Snippet: a Relationship between ON duration and total transcriptional output (area below the curve and above ON threshold for entire imaging period for each cell). LOWESS regression outlines the local relationship between these variables. The inflection point marks a step-change in the gradient of the regression. Cells above the inflection point we call ‘High ON’ cells, while those below are ‘Low ON’. b Example spot intensity traces for individual cells marked by coloured circles in a . Below each panel, thick lines indicate when intensity traces for each cell are above ON threshold (dotted lines). The measured ON duration and output (shaded area) are given for each example cell. (i) ‘basal amplitude’ bursting; (ii) ‘high ON, high amplitude’ bursting; (iii) ‘low ON, high amplitude’ bursting. c Calculated proportions of cells with different bursting behaviours in b at each differentiation stage (defined in Supplementary Fig. ).

Article Snippet: We did this based on the relationship between the ON duration and transcriptional output, for which we used robust LOWESS local regression (‘rlowess’ in Matlab ‘smooth’ function) to model. A clear inflection point suggested differences in burst amplitude at high ON duration (see ), and we, therefore, categorised cells as ‘High ON’ or ‘Low ON’ according to whether their ON duration was above or below this inflection point, respectively (Fig. ).

Techniques: Imaging