Hello,

I am entirely new to this list, and not very experienced with R yet (but very excited about it!!). I am struggling with a dataset of x and y coordinate points I am plotting as a density map as follows:

trial <- read.csv(file="F12.csv", sep=",", skip=32, head=TRUE)
trial.sub <- subset(trial, Seconds>=30)
trial.sub <- subset(trial.sub, Seconds<=1830)

d <- trial.sub
require(MASS)
dens <- kde2d(d$x, d$y, h=20, n=100)
color <- function(x)rev(heat.colors(x))
filled.contour(dens, color.palette = color)

Each file contains 53000 observations (29 per second), so 53000 x and y coordinates. I have posted a sample of my heat map here: 
https://picasaweb.google.com/neurosci.christine/Public?authkey=Gv1sRgCLO3m6Obpsr_sgE#5619604653154721794

My main question I can't seem to find an answer to is what the numbers in the legend mean. The heatmap is created for coordinate points of a location occupied by an animal, so the high density means the animal spent most of its time there, but what percentage of time? if is possible to get this out of the data and/or displayed more clearly in the legend?

I addition, I would like to quantify the area size of the highest density region. Alternatively or in addition to this, I wouldn't mind measuring how many 'zones' the highest density region occupies. This might be more difficult, unless I can overlay a grid overtop of the data and count the number of zones covered. I have tried different strategies for this, including creating subsets of the coordinate point ranges, but I couldn't get it to work and any input will be greatly appreciated. To see a sample of another heatmap where this would be very relevant is posted here:

https://picasaweb.google.com/neurosci.christine/Public?authkey=Gv1sRgCLO3m6Obpsr_sgE#5619604756338447826


I really appreciate any help I could get with this! I've been working on it for a week and not getting any further ahead. 
Christine


Below is some of the data posted in case it might be helpful:

Tracking	area	(x1																				
125	7	547	482																			
Zone1-1	(x1																					
127	3	273	130																			
Zone2-2	(x1																					
272	5	412	131																			
Zone3-3	(x1																					
413	7	556	128																			
Zone4-4	(x1																					
128	128	274	239																			
Zone5-5	(x1																					
273	128	415	245																			
Zone6-6	(x1																					
417	129	555	245																			
Zone7-7	(x1																					
127	239	272	348																			
Zone8-8	(x1																					
273	243	418	347																			
Zone9-9	(x1																					
416	243	554	347																			
Zone10-10	(x1																					
125	345	274	475																			
Zone11-11	(x1																					
273	346	419	474																			
Zone12-12	(x1																					
419	347	556	473																			
Ruler1-x	(x1																					
178	434	506	446	70																		
Ruler2-y	(x1																					
173	28	178	434	70																		
PointDist1-tankcenter	(centrex																					
347	234	338	27	35																		
Seconds	x	y	FishMovement	Confidence	Confidence>30	Zone1-1	Zone2-2	Zone3-3	Zone4-4	Zone5-5	Zone6-6	Zone7-7	Zone8-8	Zone9-9	Zone10-10	Zone11-11	Zone12-12	Ruler1-x	Ruler2-y	PointDist1-tankcenter	
17.283	336	244	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	32.1929	37.5818	2.51121		
17.317	309	217	37.6572	9.72	0	0	0	0	0	1	0	0	0	0	0	0	0	26.2279	32.87	7.03213		
17.35	282	191	37.6572	13.5066	0	0	0	0	0	1	0	0	0	0	0	0	0	20.2707	28.3306	13.1651		
17.383	255	165	37.6572	26.64	0	0	0	0	1	0	0	0	0	0	0	0	0	14.3135	23.7912	19.4261		
17.417	228	139	150.629	35.8	1	0	0	0	1	0	0	0	0	0	0	0	0	8.35623	19.2518	25.7218		
17.45	229	138	1.41421	37.6066	1	0	0	0	1	0	0	0	0	0	0	0	0	8.56156	19.0815	25.6962		
17.483	228	137	1.41421	36.9029	1	0	0	0	1	0	0	0	0	0	0	0	0	8.34064	18.907	25.9339		
17.517	227	136	1.41421	41.045	1	0	0	0	1	0	0	0	0	0	0	0	0	8.11971	18.7325	26.1715		
17.55	226	136	1	43.4089	1	0	0	0	1	0	0	0	0	0	0	0	0	7.90658	18.7304	26.3026		
17.583	224	137	2.23607	51.268	1	0	0	0	1	0	0	0	0	0	0	0	0	7.48812	18.8985	26.4611		
17.617	222	137	2	46.4509	1	0	0	0	1	0	0	0	0	0	0	0	0	7.06186	18.8943	26.7272		
17.65	222	137	0	44.01	1	0	0	0	1	0	0	0	0	0	0	0	0	7.06186	18.8943	26.7272		
17.684	220	138	2.23607	47.0277	1	0	0	0	1	0	0	0	0	0	0	0	0	6.6434	19.0624	26.8927		
17.717	219	138	1	54.1086	1	0	0	0	1	0	0	0	0	0	0	0	0	6.43027	19.0603	27.0276		
17.75	218	137	1.41421	43.4641	1	0	0	0	1	0	0	0	0	0	0	0	0	6.20934	18.8858	27.2641		
17.784	218	138	1	48.685	1	0	0	0	1	0	0	0	0	0	0	0	0	6.21714	19.0582	27.1629		
17.817	217	139	1.41421	51.76	1	0	0	0	1	0	0	0	0	0	0	0	0	6.01181	19.2284	27.1986		
17.85	215	141	2.82843	52.589	1	0	0	0	1	0	0	0	0	0	0	0	0	5.60114	19.569	27.2762		
17.884	215	142	1	48.4927	1	0	0	0	1	0	0	0	0	0	0	0	0	5.60894	19.7414	27.1792		
17.917	214	144	2.23607	49.7199	1	0	0	0	1	0	0	0	0	0	0	0	0	5.41141	20.084	27.1272		
17.951	212	145	2.23607	60.0076	1	0	0	0	1	0	0	0	0	0	0	0	0	4.99295	20.2522	27.3143		
17.984	211	147	2.23607	49.1309	1	0	0	0	1	0	0	0	0	0	0	0	0	4.79541	20.5948	27.272		
18.017	210	149	2.23607	50.4243	1	0	0	0	1	0	0	0	0	0	0	0	0	4.59788	20.9375	27.2348		
18.051	208	151	2.82843	54.3917	1	0	0	0	1	0	0	0	0	0	0	0	0	4.18721	21.278	27.3477		
18.084	207	153	2.23607	59.2032	1	0	0	0	1	0	0	0	0	0	0	0	0	3.98968	21.6206	27.3221		
18.117	206	155	2.23607	57.2786	1	0	0	0	1	0	0	0	0	0	0	0	0	3.79214	21.9633	27.3018		
18.151	206	154	1	55.5511	1	0	0	0	1	0	0	0	0	0	0	0	0	3.78435	21.7909	27.3847		
18.184	204	156	2.82843	57.7186	1	0	0	0	1	0	0	0	0	0	0	0	0	3.37368	22.1314	27.5157		
18.217	203	157	1.41421	45.8427	1	0	0	0	1	0	0	0	0	0	0	0	0	3.16835	22.3017	27.5841		
18.251	202	159	2.23607	51.1054	1	0	0	0	1	0	0	0	0	0	0	0	0	2.97082	22.6443	27.5763		
18.284	201	161	2.23607	57.2206	1	0	0	0	1	0	0	0	0	0	0	0	0	2.77328	22.987	27.5737		
18.318	199	163	2.82843	62.3262	1	0	0	0	1	0	0	0	0	0	0	0	0	2.36262	23.3275	27.7285		
18.351	198	164	1.41421	58.4776	1	0	0	0	1	0	0	0	0	0	0	0	0	2.15728	23.4978	27.8087		
18.384	197	165	1.41421	64.2789	1	0	0	0	1	0	0	0	0	0	0	0	0	1.95195	23.6681	27.8906		
18.418	197	166	1	64.3908	1	0	0	0	1	0	0	0	0	0	0	0	0	1.95975	23.8404	27.8205		
18.451	196	167	1.41421	61.3067	1	0	0	0	1	0	0	0	0	0	0	0	0	1.75442	24.0107	27.9055		
18.484	195	167	1	56.2617	1	0	0	0	1	0	0	0	0	0	0	0	0	1.54129	24.0086	28.06		
18.518	193	170	3.60555	55.5843	1	0	0	0	1	0	0	0	0	0	0	0	0	1.13842	24.5215	28.1711		
18.551	192	171	1.41421	53.9743	1	0	0	0	1	0	0	0	0	0	0	0	0	0.933091	24.6918	28.2631		
18.584	191	175	4.12311	55.793	1	0	0	0	1	0	0	0	0	0	0	0	0	0.751151	25.3792	28.1736		
18.618	191	178	3	60.9063	1	0	0	0	1	0	0	0	0	0	0	0	0	0.774543	25.8964	27.9984		
18.651	191	180	2	56.5543	1	0	0	0	1	0	0	0	0	0	0	0	0	0.790138	26.2411	27.886		
18.685	189	182	2.82843	53.4996	1	0	0	0	1	0	0	0	0	0	0	0	0	0.379474	26.5817	28.0981		
18.718	187	183	2.23607	56.7465	1	0	0	0	1	0	0	0	0	0	0	0	0	-0.0389871	26.7498	28.3674		
18.751	187	184	1	49.3128	1	0	0	0	1	0	0	0	0	0	0	0	0	-0.0311897	26.9222	28.3166		
18.785	186	187	3.16228	52.0791	1	0	0	0	1	0	0	0	0	0	0	0	0	-0.220927	27.4372	28.3317		
18.818	186	190	3	50.138	1	0	0	0	1	0	0	0	0	0	0	0	0	-0.197535	27.9544	28.1939		
18.851	186	191	1	59.6442	1	0	0	0	1	0	0	0	0	0	0	0	0	-0.189737	28.1268	28.1498		
18.885	186	193	2	49.6857	1	0	0	0	1	0	0	0	0	0	0	0	0	-0.174142	28.4716	28.0645		
18.918	188	195	2.82843	43.124	1	0	0	0	1	0	0	0	0	0	0	0	0	0.267711	28.8206	27.6548		
18.952	188	197	2	50.1387	1	0	0	0	1	0	0	0	0	0	0	0	0	0.283306	29.1654	27.5763		
18.985	188	199	2	57.1661	1	0	0	0	1	0	0	0	0	0	0	0	0	0.298901	29.5101	27.5017		
19.018	187	200	1.41421	54.397	1	0	0	0	1	0	0	0	0	0	0	0	0	0.093569	29.6804	27.6311		
19.052	187	202	2	53.8919	1	0	0	0	1	0	0	0	0	0	0	0	0	0.109164	30.0252	27.5629		
19.085	188	204	2.23607	51.2277	1	0	0	0	1	0	0	0	0	0	0	0	0	0.337888	30.3721	27.3326		
19.118	188	206	2	50.1443	1	0	0	0	1	0	0	0	0	0	0	0	0	0.353483	30.7168	27.272		
19.152	188	206	0	53.5088	1	0	0	0	1	0	0	0	0	0	0	0	0	0.353483	30.7168	27.272		
19.185	190	207	2.23607	50.202	1	0	0	0	1	0	0	0	0	0	0	0	0	0.787539	30.8935	26.9102		
19.218	192	209	2.82843	56.5734	1	0	0	0	1	0	0	0	0	0	0	0	0	1.22939	31.2425	26.5214		
19.252	193	210	1.41421	59.6725	1	0	0	0	1	0	0	0	0	0	0	0	0	1.45032	31.417	26.3281		
19.285	195	211	2.23607	54.0302	1	0	0	0	1	0	0	0	0	0	0	0	0	1.88438	31.5936	25.9685		
19.319	196	213	2.23607	60.698	1	0	0	0	1	0	0	0	0	0	0	0	0	2.1131	31.9405	25.7528		
19.352	197	215	2.23607	63.1126	1	0	0	0	1	0	0	0	0	0	0	0	0	2.34182	32.2874	25.5408		
19.385	197	216	1	60.0831	1	0	0	0	1	0	0	0	0	0	0	0	0	2.34962	32.4598	25.5202		
19.419	197	216	0	63.885	1	0	0	0	1	0	0	0	0	0	0	0	0	2.34962	32.4598	25.5202		
19.452	198	217	1.41421	62.8781	1	0	0	0	1	0	0	0	0	0	0	0	0	2.57055	32.6343	25.3328		
19.485	199	218	1.41421	64.7832	1	0	0	0	1	0	0	0	0	0	0	0	0	2.79147	32.8088	25.1462		



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