[R-sig-Geo] Plotting a tif file
Paul Hiemstra
p.hiemstra at geo.uu.nl
Sun Nov 7 21:14:01 CET 2010
Then take a better look at the export function of QGIS and see what it
spits out. If you do not know what is in the data, how can we help you in
which column to plot. My guess is that the first column is the kriging
prediction, the second the kriging variance and the third the kriging
standard deviation. Primarily because the third column is the square root
of the second.
You could also import the point data into R and do the interpolation
there, which gives you more control over what is happening. It might even
be that QGis uses R (packages gstat+automap) under the hood.
good luck,
Paul
> Honestly Paul, I don't know. The tif is a result from the kriging in
> Quantum GIS.
> Is very strange, right?
>
> Manuel
>
> On 07/11/2010 07:03 a.m., Paul Hiemstra wrote:
>> So what is in the three bands?
>>
>> Paul
>>
>> On 11/07/2010 02:06 PM, Manuel Spínola wrote:
>>> Species richness (from 3 to 20 more or less)
>>>
>>> On 07/11/2010 06:46 a.m., Paul Hiemstra wrote:
>>>> What is the data captured by the tif file?
>>>>
>>>> Paul
>>>>
>>>> On 11/07/2010 12:45 PM, Manuel Spínola wrote:
>>>>> Thank you very much Paul.
>>>>>
>>>>> This is the data frame that I created
>>>>>
>>>>> > head(riquezakrig_df)
>>>>> band1 band2 band3 x y
>>>>> 269 1.760396 1.620212 1.272875 460590.1 1216391
>>>>> 1686 1.760396 1.620212 1.272875 460540.1 1216341
>>>>> 1687 1.760396 1.620212 1.272875 460590.1 1216341
>>>>> 3103 1.760396 1.620212 1.272875 460490.1 1216291
>>>>> 3104 1.760396 1.620212 1.272875 460540.1 1216291
>>>>> 3105 1.760396 1.620212 1.272875 460590.1 1216291
>>>>>
>>>>>
>>>>> You suggest to make a new column with the color, but I don't
>>>>> understand which information should I provide to the new column.
>>>>>
>>>>> Best,
>>>>>
>>>>> Manuel
>>>>>
>>>>>
>>>>> On 07/11/2010 04:00 a.m., Paul Hiemstra wrote:
>>>>>> Hi Manuel,
>>>>>>
>>>>>> Please do not respond to me alone, include the mailing list in the
>>>>>> cc. You waste the option of someone else answering your question
>>>>>> and the answers are not stored in the archives for other people.
>>>>>>
>>>>>> But back to your question. The tiff file has 3 bands, rgb bands.
>>>>>> Probably the contents in those bands is a number between 0 and
>>>>>> 255, but you do not specify this in your mail. In this case the
>>>>>> tiff file does not contain the 'real' values but is a picture. So
>>>>>> drawing individual bands does not make sense. What you could try
>>>>>> is to construct a new column in the dataset with the color and try
>>>>>> to use in the aes() argument (col = col, where col is the name of
>>>>>> the column with the color).
>>>>>>
>>>>>> cheers,
>>>>>> Paul
>>>>>>
>>>>>>
>>>>>> On 11/06/2010 03:03 PM, Paul Hiemstra wrote:
>>>>>>> Gpplot cannot plot SpatialPixelsDataFrame's in one go. You need to
>>>>>>> convert the grid to a data frame.
>>>>>>>
>>>>>>> An example using the meuse dataset:
>>>>>>>
>>>>>>> library(sp)
>>>>>>> library(ggplot2)
>>>>>>> data(meuse.grid)
>>>>>>> gridded(meuse.grid) = ~x+y
>>>>>>> summary(meuse.grid)
>>>>>>>
>>>>>>> meuse.grid_df = as(meuse.grid, "data.frame")
>>>>>>>
>>>>>>> # Now make a plot with ggplot
>>>>>>> p = ggplot(aes(x = x, y = y, fill = dist), data = meuse.grid_df) +
>>>>>>> geom_tile()
>>>>>>> print(p)
>>>>>>>
>>>>>>> # Add some tricks specially suitable for
>>>>>>> # spatial plots
>>>>>>> print(p +
>>>>>>> scale_x_continuous('', labels = NA, breaks = NA) +
>>>>>>> scale_y_continuous('', labels = NA, breaks = NA) +
>>>>>>> opts(aspect.ratio = 1, alpha = 0.5))
>>>>>>>
>>>>>>> cheers,
>>>>>>> Paul
>>>>>>>
>>>>>>> On 11/06/2010 02:28 PM, Manuel Spínola wrote:
>>>>>>>
>>>>>>>> Thank you very much Paul.
>>>>>>>>
>>>>>>>> With plot I got a black polygon and with spplpot I got:
>>>>>>>>
>>>>>>>>
>>>>>>>>> spplot(riquezakrig)
>>>>>>>>>
>>>>>>>> Error: cannot allocate vector of size 22.6 Mb
>>>>>>>>
>>>>>>>> with image show me what I want but no legend.
>>>>>>>>
>>>>>>>> Any specific geom to plot with ggplot?
>>>>>>>>
>>>>>>>> Best,
>>>>>>>>
>>>>>>>> Manuel
>>>>>>>>
>>>>>>>> On 06/11/2010 06:46 a.m., Paul Hiemstra wrote:
>>>>>>>>
>>>>>>>>> On 11/06/2010 11:15 AM, Manuel Spínola wrote:
>>>>>>>>>
>>>>>>>>>> Dear list members,
>>>>>>>>>>
>>>>>>>>>> I read a .tif file with readGDAL.
>>>>>>>>>> What is the best way to display it?.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> spplot or ggplot
>>>>>>>>>
>>>>>>>>>> I tried function image but there is no legend.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> true
>>>>>>>>>
>>>>>>>>>> I tried plot and spplot but I couldn't get them to work.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> why not? What error? What version of R and sp? You're not giving
>>>>>>>>> us
>>>>>>>>> any information that could give us a clue to what's going wrong.
>>>>>>>>>
>>>>>>>>> cheers,
>>>>>>>>> Paul
>>>>>>>>>
>>>>>>>>>> Any help will be appreciated.
>>>>>>>>>>
>>>>>>>>>> Best,
>>>>>>>>>>
>>>>>>>>>> Manuel
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> R-sig-Geo mailing list
>>>>>>>>>> R-sig-Geo at stat.math.ethz.ch
>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Drs. Paul Hiemstra
>>>>>>>>> Department of Physical Geography
>>>>>>>>> Faculty of Geosciences
>>>>>>>>> University of Utrecht
>>>>>>>>> Heidelberglaan 2
>>>>>>>>> P.O. Box 80.115
>>>>>>>>> 3508 TC Utrecht
>>>>>>>>> Phone: +3130 253 5773
>>>>>>>>> http://intamap.geo.uu.nl/~paul
>>>>>>>>> http://nl.linkedin.com/pub/paul-hiemstra/20/30b/770
>>>>>>>>>
>>>>>>>> --
>>>>>>>> *Manuel Spínola, Ph.D.*
>>>>>>>> Instituto Internacional en Conservación y Manejo de Vida Silvestre
>>>>>>>> Universidad Nacional
>>>>>>>> Apartado 1350-3000
>>>>>>>> Heredia
>>>>>>>> COSTA RICA
>>>>>>>> mspinola at una.ac.cr
>>>>>>>> mspinola10 at gmail.com
>>>>>>>> Teléfono: (506) 2277-3598
>>>>>>>> Fax: (506) 2237-7036
>>>>>>>> Personal website: Lobito de río
>>>>>>>> <https://sites.google.com/site/lobitoderio/>
>>>>>>>> Institutional website: ICOMVIS<http://www.icomvis.una.ac.cr/>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> R-sig-Geo mailing list
>>>>>>> R-sig-Geo at stat.math.ethz.ch
>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Drs. Paul Hiemstra
>>>>>> Department of Physical Geography
>>>>>> Faculty of Geosciences
>>>>>> University of Utrecht
>>>>>> Heidelberglaan 2
>>>>>> P.O. Box 80.115
>>>>>> 3508 TC Utrecht
>>>>>> Phone: +3130 253 5773
>>>>>> http://intamap.geo.uu.nl/~paul
>>>>>> http://nl.linkedin.com/pub/paul-hiemstra/20/30b/770
>>>>>
>>>>>
>>>>> --
>>>>> *Manuel Spínola, Ph.D.*
>>>>> Instituto Internacional en Conservación y Manejo de Vida Silvestre
>>>>> Universidad Nacional
>>>>> Apartado 1350-3000
>>>>> Heredia
>>>>> COSTA RICA
>>>>> mspinola at una.ac.cr
>>>>> mspinola10 at gmail.com
>>>>> Teléfono: (506) 2277-3598
>>>>> Fax: (506) 2237-7036
>>>>> Personal website: Lobito de río
>>>>> <https://sites.google.com/site/lobitoderio/>
>>>>> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
>>>>
>>>>
>>>> --
>>>> Drs. Paul Hiemstra
>>>> Department of Physical Geography
>>>> Faculty of Geosciences
>>>> University of Utrecht
>>>> Heidelberglaan 2
>>>> P.O. Box 80.115
>>>> 3508 TC Utrecht
>>>> Phone: +3130 253 5773
>>>> http://intamap.geo.uu.nl/~paul
>>>> http://nl.linkedin.com/pub/paul-hiemstra/20/30b/770
>>>
>>>
>>> --
>>> *Manuel Spínola, Ph.D.*
>>> Instituto Internacional en Conservación y Manejo de Vida Silvestre
>>> Universidad Nacional
>>> Apartado 1350-3000
>>> Heredia
>>> COSTA RICA
>>> mspinola at una.ac.cr
>>> mspinola10 at gmail.com
>>> Teléfono: (506) 2277-3598
>>> Fax: (506) 2237-7036
>>> Personal website: Lobito de río
>>> <https://sites.google.com/site/lobitoderio/>
>>> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
>>
>>
>> --
>> Drs. Paul Hiemstra
>> Department of Physical Geography
>> Faculty of Geosciences
>> University of Utrecht
>> Heidelberglaan 2
>> P.O. Box 80.115
>> 3508 TC Utrecht
>> Phone: +3130 253 5773
>> http://intamap.geo.uu.nl/~paul
>> http://nl.linkedin.com/pub/paul-hiemstra/20/30b/770
>
>
> --
> *Manuel Spínola, Ph.D.*
> Instituto Internacional en Conservación y Manejo de Vida Silvestre
> Universidad Nacional
> Apartado 1350-3000
> Heredia
> COSTA RICA
> mspinola at una.ac.cr
> mspinola10 at gmail.com
> Teléfono: (506) 2277-3598
> Fax: (506) 2237-7036
> Personal website: Lobito de río
> <https://sites.google.com/site/lobitoderio/>
> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
>
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