Occupancy plot

[nickloman]

To show which pores active and when

[arq5x]

Ha we were just discussing the same thing.

[nickloman]

I made a start here: https://github.com/arq5x/poretools/blob/master/poretools/occupancy.py

[nickloman]

woops!

[arq5x]

Nice. Would be interesting to visualize this using circle heatmaps as below (first answer methinks): http://stackoverflow.com/questions/13983225/plot-plate-layout-heatmap-in-r

Would love to organize the flow according to the flowcell layout such that bubbles or other structural effects are made apparent.

Ideas:

1. Color of circle is on a gradient to depict fraction of run time that it was active?
2. (optional) Size depicts log10 of the total yield of the pore?

[nickloman]

Ah OK, I was also thinking about a time-series style plot a la:

The other would be a flow cell style heatmap.

It seems like the pore IDs are arranged slightly oddly (but regularly) judged from the MinKNOW screen.

No idea if there is any run-to-run variation in this?

[nickloman]

Should also spit out some stats, e.g. total channels seen, % occupancy (over time)

[arq5x]

This is a useful visualization as well. Perhaps we could offer two viz. options? I am happy to hack the heatmap style. They appear to use a reproducible 4 row wrapping algorithm for the layout. Upper right is the origin. The first block of 128 pores is found in the first 4 rows by 32 columns, the next 128 in the next 4 x 32, etc.

[nickloman]

If you wanna take this on I'd be more than happy!

[arq5x]

Will do. By the time you post the first method, I should be able to free up some fun time to work on this.

[arq5x]

First pass of the ggplot code. Need to solve the layout issue:

library(ggplot2)
set.seed (123)
platelay <- data.frame (rown = rep (letters[1:16], 32), coln = rep (1:32, each = 16),
                    colorvar = rnorm (512, 0.3, 0.2))

ggplot(platelay, aes(y = factor(rown, rev(levels(rown))),x = factor(coln))) + 
  geom_point(aes(colour = colorvar), size =12)  +theme_bw() +
  geom_text(aes(label = 1:512), colour="white") +
  labs(x=NULL, y = NULL)

[arq5x]

Boom. Layout unlocked.

Code:

# generate from the following Python code:
# seeds = [125,121,117,113,109,105,101,97,93,89,85,81,77,73,69,65,61,57,53,49,45,41,37,33,29,25,21,17,13,9,5,1]
#for s in seeds:
#  for block in range(4):
#      for row in range(4):
#          print str(s + 128*block + row) + ",",
labels = c(125, 126, 127, 128, 253, 254, 255, 256, 381, 382, 383, 384, 509, 510, 511, 512, 
           121, 122, 123, 124, 249, 250, 251, 252, 377, 378, 379, 380, 505, 506, 507, 508, 
           117, 118, 119, 120, 245, 246, 247, 248, 373, 374, 375, 376, 501, 502, 503, 504, 
           113, 114, 115, 116, 241, 242, 243, 244, 369, 370, 371, 372, 497, 498, 499, 500, 
           109, 110, 111, 112, 237, 238, 239, 240, 365, 366, 367, 368, 493, 494, 495, 496, 
           105, 106, 107, 108, 233, 234, 235, 236, 361, 362, 363, 364, 489, 490, 491, 492, 
           101, 102, 103, 104, 229, 230, 231, 232, 357, 358, 359, 360, 485, 486, 487, 488, 
           97, 98, 99, 100, 225, 226, 227, 228, 353, 354, 355, 356, 481, 482, 483, 484, 
           93, 94, 95, 96, 221, 222, 223, 224, 349, 350, 351, 352, 477, 478, 479, 480, 
           89, 90, 91, 92, 217, 218, 219, 220, 345, 346, 347, 348, 473, 474, 475, 476, 
           85, 86, 87, 88, 213, 214, 215, 216, 341, 342, 343, 344, 469, 470, 471, 472, 
           81, 82, 83, 84, 209, 210, 211, 212, 337, 338, 339, 340, 465, 466, 467, 468, 
           77, 78, 79, 80, 205, 206, 207, 208, 333, 334, 335, 336, 461, 462, 463, 464, 
           73, 74, 75, 76, 201, 202, 203, 204, 329, 330, 331, 332, 457, 458, 459, 460, 
           69, 70, 71, 72, 197, 198, 199, 200, 325, 326, 327, 328, 453, 454, 455, 456, 
           65, 66, 67, 68, 193, 194, 195, 196, 321, 322, 323, 324, 449, 450, 451, 452, 
           61, 62, 63, 64, 189, 190, 191, 192, 317, 318, 319, 320, 445, 446, 447, 448, 
           57, 58, 59, 60, 185, 186, 187, 188, 313, 314, 315, 316, 441, 442, 443, 444, 
           53, 54, 55, 56, 181, 182, 183, 184, 309, 310, 311, 312, 437, 438, 439, 440, 
           49, 50, 51, 52, 177, 178, 179, 180, 305, 306, 307, 308, 433, 434, 435, 436, 
           45, 46, 47, 48, 173, 174, 175, 176, 301, 302, 303, 304, 429, 430, 431, 432, 
           41, 42, 43, 44, 169, 170, 171, 172, 297, 298, 299, 300, 425, 426, 427, 428, 
           37, 38, 39, 40, 165, 166, 167, 168, 293, 294, 295, 296, 421, 422, 423, 424, 
           33, 34, 35, 36, 161, 162, 163, 164, 289, 290, 291, 292, 417, 418, 419, 420, 
           29, 30, 31, 32, 157, 158, 159, 160, 285, 286, 287, 288, 413, 414, 415, 416, 
           25, 26, 27, 28, 153, 154, 155, 156, 281, 282, 283, 284, 409, 410, 411, 412, 
           21, 22, 23, 24, 149, 150, 151, 152, 277, 278, 279, 280, 405, 406, 407, 408, 
           17, 18, 19, 20, 145, 146, 147, 148, 273, 274, 275, 276, 401, 402, 403, 404, 
           13, 14, 15, 16, 141, 142, 143, 144, 269, 270, 271, 272, 397, 398, 399, 400, 
           9, 10, 11, 12, 137, 138, 139, 140, 265, 266, 267, 268, 393, 394, 395, 396, 
           5, 6, 7, 8, 133, 134, 135, 136, 261, 262, 263, 264, 389, 390, 391, 392, 
           1, 2, 3, 4, 129, 130, 131, 132, 257, 258, 259, 260, 385, 386, 387, 388)

library(ggplot2)
set.seed (123)
platelay <- data.frame (rown = rep (letters[1:16], 32), coln = rep (1:32, each = 16),
                        colorvar = rnorm (512, 0.3, 0.2))

ggplot(platelay, aes(y = factor(rown, rev(levels(rown))),x = factor(coln))) + 
  geom_point(aes(colour = colorvar), size =12)  +theme_bw() +
  geom_text(aes(label = labels), colour="white") +
  labs(x=NULL, y = NULL)

[nickloman]

schweeet

[arq5x]

Would be neat to use color to depict occupied versus unoccupied and make a time lapse movie of these plots over time

[timp0]

Also - a suggestion would be to add channel to the poretools times function - though easy to regexp, it might make it easier for people to generate their own occupancy plots.

[arq5x]

Great suggestion. Just added it to the repo.

[timp0]

This pore layout plot (i have my own version by stealing your R code) - is globally useful for more than occupied - I suggest also allowing pore yield to be plotting in this way?

[timp0]

Also, may want a plot of (length of time empty) as a function of run time - I found (plot below) - with orange empty duration and blue occupied duration - can you guess when we added more library?