When plotting flowFrames, I sometimes get the warning, "Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'.

I have a general sense of what this is telling me in terms of the density plot, but I cannot figure out how to set the gridsize from the high order plotting function. Can anyone help point me to the right documentation or a specific syntax / work-around?

fs1 = read.flowSet(path = path, pattern = '.fcs')

> plot(fs1[[1]])

There were 50 or more warnings (use warnings() to see the first 50)

> warnings()

Warning messages:

1: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

2: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

3: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

4: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

5: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

6: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

7: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

8: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

9: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

10: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

11: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

12: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

13: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

14: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

15: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

16: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

17: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

18: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

19: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

20: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

21: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

22: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

23: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

24: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

25: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

26: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

27: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

28: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

29: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

30: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

31: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

32: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

33: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

34: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

35: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

36: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

37: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

38: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

39: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

40: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

41: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

42: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

43: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

44: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

45: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

46: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

47: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

48: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

49: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

50: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth, ... :

Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'

>

Thanks as always for the quick feedback and suggestions.

Thanks also for mentioning the future of flowViz --> ggcyto transition. Somehow, I've missed ggcyto up until now. I'm trying to put so much information together (as someone completely new to flow optometry) that these sorts of tips are extremely valuable. I'm guessing the latter transitions from lattice to ggplot2 as an underlying framework from its name?. I'll be sure to give ggcyto a try.

Yes. Unless you are plotting large number of samples on the same page, `ggcyto` should be sufficient for the majority of visualization tasks (e.g. 1d density, 2d hexbin, gates)