Compositional map in R geology



I obtained compositional maps of my rock sample (thin-section) using micro-XRF (Bruker)

The image below is the obtained data. It is the compositional (intensity) map of one element. 


This map is very nice and good to identify the minerals. But I want to change the color scale because it is not very easy to see and the color is very strong. Better color scale help us to identify the compositional difference easily.

I try to change the color using r.



Library

library(dplyr)
library(tibble)
library(tidyr)
library(ggplot2)
library(tidyverse)
library(fields)
library(RColorBrewer)


read data (raw data of micro-XRF mapping, text file)

test1 <- read.table("test1.txt", sep =";") 
test2 <- read.table("test2.txt", sep =";")


read data

head(test1)
##     V1   V2   V3   V4   V5   V6   V7   V8   V9  V10  V11  V12  V13  V14  V15
## 1   38   76  164  260  635 1649 2686 3130 2970 2615 2578 3221 3296 3358 3316
## 2    0  285  512  469  586 1367 2384 2932 2603 2273 2429 2932 3178 3313 3115
## 3  210  611 1251 1493 1046  656 1363 2265 2678 2655 2487 2542 2858 3041 2979
## 4    0 2218 2504 1966 1042 1409 2379 2880 2992 2941 2514 2204 2311 2153 1478
## 5 1445 2348 2814 2610 1738 1287 2131 2880 3174 3166 2962 1957 1340 1136  877
## 6    0 2694 2270 1401  993 1800 2842 3187 3169 2984 1978  667  304  248  169
##    V16  V17  V18  V19 V20 V21 V22 V23 V24 V25 V26 V27 V28 V29 V30 V31 V32 V33
## 1 2905 2249 1246  877 571 349 248 191 187 163 136 113  58  33  18  13  11  10
## 2 2513 1490  969  828 472 248 235 241 160 164 147 141 105  59  19  14  14  12
## 3 2393 1304  794  944 974 492 268 246 186 147 132 179 210 172  88  15  12   6
## 4  757  501  803 1024 591 282 227 156  88  74 111 184 187 111  35  15  10   9
## 5  472  294  318  673 745 419 231 194  96  47  40  83 106 134  98  49   8  11
## 6  131  146  308  426 357 207 167  81  28  21  42  70 100 138  82  16  12  16
##   V34 V35 V36 V37 V38 V39 V40 V41 V42 V43 V44 V45 V46 V47 V48 V49 V50 V51 V52
## 1  11  11  13  18  11  12   7  15  20  17  10  14   7  14  13  11  14   5  11
## 2  16   8   9   8  14  10  12   9   5  14  14  11   8  12  10  13  12   8   6
## 3  12  10  15  15  11  12   6   7   9   9  23  22  14  16  10  13  10   6  11
## 4  10  10  10   9  13  11  17  12   8  18  18  21  17  17  14  15   7  11   6
## 5   9  11  17  18  11  11   5  11   8  10  15  16   8  15  10   9   7  17   9
## 6  10  16  18   9  14   7  13   8   9   4   9  15   8  14   6   4  11  11   9
......

Each cell shows the intensity of the element of each data point (pixel).


visualizing data

x <- as.matrix(test1)
image(x)
I want a scale bar.

visualizing data

x <- as.matrix(test1)
image.plot(x)


Plot is tilted 90 degrees from the original map....

data transformation

x <- as.matrix(test1)
(y <- t(x[nrow(x):1,ncol(x):1])[ncol(x):1,])
##      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
## V1      0  967    0  450    0 1002    0 2802    0   464     0  1446     0  3298
## V2   3343 2598 2906 1695 2522 1814 2330 2155 1258   511   134   962  1873  3172
## V3   3226 3146 2233 2632 1883 2805 1853 1764  806   422   146   492  1096  2945
## V4   2784 2686  944 1460 1325 1988 1218 1144  369   358   214   312   643  2096
## V5   1393 1460  429  930  874 1394  579  500  282   233   271   316   326  1031
## V6    650  438  252  517  332  608  312  285  278   231   258   250   260   355
## V7    452  348  267  250  549  329 1007  289  292   249   270   280   234   229
## V8    292  308  425  365 1688 1492 2605  751 1027   284   300   285   273   230
## V9    248  286 1066 1156 2905 2941 3305 2148 2702   669   644   253   242   231
## V10   269  376 1132 2423 3120 3394 3444 3295 3309  2096  1898   353   420   171
## V11   255  326  438 2160 2916 3466 3377 3432 3332  3114  3150  1544  1564   157


...... 
## V117      6     14
## V118      6      5
## V119     12     14
##  [ reached getOption("max.print") -- omitted 281 rows ]

visualizing data 2-1

image.plot(y)

Now I want to change the color palette


visualizing data 2-2 (changing color)

my_col    = brewer.pal(3, "RdYlBu")
pal <- colorRampPalette(my_col)
image.plot(y, col = pal(100))



visualizing data 2-3 (changing color)

my_col    = brewer.pal(7, "RdYlBu")
pal <- colorRampPalette(my_col)
image.plot(y, col = pal(100))

Compared to the original image, now it is easier to see the differences in intensity.


visualizing data 2-4 (changing color)

Using an original color palette
my_col    = colorRampPalette(c("hotpink", "grey99", "dodgerblue"))
image.plot(y,col = my_col(100))


visualizing data 2-5 (changing color)

my_col    = colorRampPalette(c("hotpink", "grey99", "dodgerblue"))
image.plot(y,col = my_col(5))

visualizing data 2-6 (changing color)

my_col    = colorRampPalette(c("royalblue2", "grey99", "tomato2"))
image.plot(y,col = my_col(100))

saving data (map)

jpeg("image.jpg")
image.plot(y,col = my_col(5))
dev.off()
the image will be saved in the same directory



Another element (test2)

x <- as.matrix(test2)
(y2 <- t(x[nrow(x):1,ncol(x):1])[ncol(x):1,])
##      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
## V1      0  775    0  894    0  480    0  228    0   881     0   740     0    66
## V2     24  318  113  424  159  329  211  395  649   931  1019   845   580   103
## V3     32   47  268  153  318  161  340  373  628   903   880   893   610   169
## V4    125  144  563  411  508  376  467  506  693   705   676   729   603   356
## V5    431  421  587  557  526  488  605  620  659   654   614   656   595   513
## V6    592  633  640  600  627  602  653  572  663   657   620   653   625   601
## V7    599  660  654  622  658  657  511  714  652   645   636   614   591   642
## V8    676  610  5

visualizing data (test2 data)

my_col    = brewer.pal(3, "RdYlBu")
pal <- colorRampPalette(my_col)
image.plot(y2, col = pal(100))