| cor.test {opmextra} | R Documentation |
This calculates all-against-all correlations between selected parameters inferred from the contained wells or correlations between all wells and selected wells of interest.
## S4 method for signature 'MOPMX'
cor.test(x, ...)
## S4 method for signature 'OPMS'
cor.test(x, y = NULL, method = "pearson",
use = "everything", subset = opm_opt("curve.param"), ...)
x |
|
y |
Optional vector with names or indexes of columns
to correlate with the full extracted matrix. Note that
the names must refer to this generated matrix, not to the
well names in |
method |
Character scalar passed to |
use |
Character scalar also passed to |
subset |
Character scalar passed to
|
... |
Optional arguments passed to
|
The resulting matrix can be plotted, e.g., using the
corrplot function from the corrplot package.
For the OPMS method, a squared matrix of
correlations if y is empty, another matrix with
correlations otherwise. The MOPMX method
returns a list of such matrices.
stats::cor stats::cor.test corrplot::corrplot
Other res: opm_dbclear,
opm_dbfind, opm_dbget,
opm_dbnext, opm_dbput
(x <- cor.test(vaas_4[, , 1:20]))
## A01 (Negative Control) A02 (Dextrin)
## A01 (Negative Control) 1.0000000 0.9343689
## A02 (Dextrin) 0.9343689 1.0000000
## A03 (D-Maltose) 0.9864752 0.9384444
## A04 (D-Trehalose) 0.9980328 0.9318611
## A05 (D-Cellobiose) 0.9824109 0.8876293
## A06 (b-Gentiobiose) 0.9853181 0.9060785
## A07 (Sucrose) 0.9745074 0.8890715
## A08 (Turanose) 0.9730569 0.8819663
## A09 (Stachyose) 0.9595438 0.8669180
## A10 (Positive Control) 0.7617319 0.9424511
## A11 (pH 6) 0.7355035 0.9277478
## A12 (pH 5) 0.6749599 0.3800228
## B01 (D-Raffinose) 0.9761730 0.8905174
## B02 (a-D-Lactose) 0.9888151 0.9447480
## B03 (D-Melibiose) 0.9851289 0.9252868
## B04 (b-Methyl-D-Glucoside) 0.9933638 0.9230296
## B05 (D-Salicin) 0.9919382 0.8912754
## B06 (N-Acetyl-D-Glucosamine) 0.5681506 0.3214127
## B07 (N-Acetyl-b-D-Mannosamine) 0.9881198 0.9291654
## B08 (N-Acetyl-D-Galactosamine) 0.9878884 0.9164698
## A03 (D-Maltose) A04 (D-Trehalose)
## A01 (Negative Control) 0.9864752 0.9980328
## A02 (Dextrin) 0.9384444 0.9318611
## A03 (D-Maltose) 1.0000000 0.9942885
## A04 (D-Trehalose) 0.9942885 1.0000000
## A05 (D-Cellobiose) 0.9912431 0.9910556
## A06 (b-Gentiobiose) 0.9961068 0.9938440
## A07 (Sucrose) 0.9924407 0.9862461
## A08 (Turanose) 0.9904771 0.9849182
## A09 (Stachyose) 0.9849081 0.9746685
## A10 (Positive Control) 0.7852956 0.7604106
## A11 (pH 6) 0.7480932 0.7291470
## A12 (pH 5) 0.6678176 0.6889118
## B01 (D-Raffinose) 0.9928532 0.9874238
## B02 (a-D-Lactose) 0.9997336 0.9953585
## B03 (D-Melibiose) 0.9993402 0.9938993
## B04 (b-Methyl-D-Glucoside) 0.9971734 0.9985873
## B05 (D-Salicin) 0.9861054 0.9950679
## B06 (N-Acetyl-D-Glucosamine) 0.6233418 0.6042267
## B07 (N-Acetyl-b-D-Mannosamine) 0.9995288 0.9957197
## B08 (N-Acetyl-D-Galactosamine) 0.9978573 0.9956342
## A05 (D-Cellobiose) A06 (b-Gentiobiose)
## A01 (Negative Control) 0.9824109 0.9853181
## A02 (Dextrin) 0.8876293 0.9060785
## A03 (D-Maltose) 0.9912431 0.9961068
## A04 (D-Trehalose) 0.9910556 0.9938440
## A05 (D-Cellobiose) 1.0000000 0.9990208
## A06 (b-Gentiobiose) 0.9990208 1.0000000
## A07 (Sucrose) 0.9984185 0.9984863
## A08 (Turanose) 0.9986033 0.9979537
## A09 (Stachyose) 0.9944587 0.9934449
## A10 (Positive Control) 0.6969598 0.7277545
## A11 (pH 6) 0.6554954 0.6874673
## A12 (pH 5) 0.7599432 0.7307384
## B01 (D-Raffinose) 0.9987940 0.9988567
## B02 (a-D-Lactose) 0.9892602 0.9946504
## B03 (D-Melibiose) 0.9951265 0.9985047
## B04 (b-Methyl-D-Glucoside) 0.9960869 0.9982833
## B05 (D-Salicin) 0.9959607 0.9944002
## B06 (N-Acetyl-D-Glucosamine) 0.7038895 0.6793092
## B07 (N-Acetyl-b-D-Mannosamine) 0.9947317 0.9982619
## B08 (N-Acetyl-D-Galactosamine) 0.9976945 0.9996769
## A07 (Sucrose) A08 (Turanose)
## A01 (Negative Control) 0.9745074 0.9730569
## A02 (Dextrin) 0.8890715 0.8819663
## A03 (D-Maltose) 0.9924407 0.9904771
## A04 (D-Trehalose) 0.9862461 0.9849182
## A05 (D-Cellobiose) 0.9984185 0.9986033
## A06 (b-Gentiobiose) 0.9984863 0.9979537
## A07 (Sucrose) 1.0000000 0.9998677
## A08 (Turanose) 0.9998677 1.0000000
## A09 (Stachyose) 0.9982271 0.9985621
## A10 (Positive Control) 0.7080902 0.6965678
## A11 (pH 6) 0.6635078 0.6514647
## A12 (pH 5) 0.7482893 0.7589800
## B01 (D-Raffinose) 0.9999686 0.9998278
## B02 (a-D-Lactose) 0.9897359 0.9875541
## B03 (D-Melibiose) 0.9962169 0.9948145
## B04 (b-Methyl-D-Glucoside) 0.9935689 0.9925237
## B05 (D-Salicin) 0.9895426 0.9898259
## B06 (N-Acetyl-D-Glucosamine) 0.7135556 0.7230397
## B07 (N-Acetyl-b-D-Mannosamine) 0.9949516 0.9934694
## B08 (N-Acetyl-D-Galactosamine) 0.9971119 0.9961971
## A09 (Stachyose) A10 (Positive Control)
## A01 (Negative Control) 0.9595438 0.76173186
## A02 (Dextrin) 0.8669180 0.94245106
## A03 (D-Maltose) 0.9849081 0.78529564
## A04 (D-Trehalose) 0.9746685 0.76041065
## A05 (D-Cellobiose) 0.9944587 0.69695981
## A06 (b-Gentiobiose) 0.9934449 0.72775446
## A07 (Sucrose) 0.9982271 0.70809016
## A08 (Turanose) 0.9985621 0.69656775
## A09 (Stachyose) 1.0000000 0.68301753
## A10 (Positive Control) 0.6830175 1.00000000
## A11 (pH 6) 0.6339480 0.99604945
## A12 (pH 5) 0.7661000 0.06361297
## B01 (D-Raffinose) 0.9977685 0.70898600
## B02 (a-D-Lactose) 0.9808541 0.79411858
## B03 (D-Melibiose) 0.9902228 0.76296153
## B04 (b-Methyl-D-Glucoside) 0.9850689 0.74987729
## B05 (D-Salicin) 0.9811177 0.69270433
## B06 (N-Acetyl-D-Glucosamine) 0.7489869 0.06496288
## B07 (N-Acetyl-b-D-Mannosamine) 0.9878652 0.76679838
## B08 (N-Acetyl-D-Galactosamine) 0.9908995 0.74397185
## A11 (pH 6) A12 (pH 5) B01 (D-Raffinose)
## A01 (Negative Control) 0.735503506 0.674959854 0.9761730
## A02 (Dextrin) 0.927747836 0.380022817 0.8905174
## A03 (D-Maltose) 0.748093174 0.667817572 0.9928532
## A04 (D-Trehalose) 0.729146990 0.688911786 0.9874238
## A05 (D-Cellobiose) 0.655495423 0.759943174 0.9987940
## A06 (b-Gentiobiose) 0.687467283 0.730738438 0.9988567
## A07 (Sucrose) 0.663507758 0.748289292 0.9999686
## A08 (Turanose) 0.651464698 0.758979968 0.9998278
## A09 (Stachyose) 0.633948012 0.766099994 0.9977685
## A10 (Positive Control) 0.996049447 0.063612973 0.7089860
## A11 (pH 6) 1.000000000 0.008658569 0.6649735
## A12 (pH 5) 0.008658569 1.000000000 0.7479069
## B01 (D-Raffinose) 0.664973523 0.747906945 1.0000000
## B02 (a-D-Lactose) 0.758767180 0.656848699 0.9903024
## B03 (D-Melibiose) 0.723732131 0.693571052 0.9965273
## B04 (b-Methyl-D-Glucoside) 0.714257682 0.706040728 0.9943444
## B05 (D-Salicin) 0.657666923 0.757116664 0.9906211
## B06 (N-Acetyl-D-Glucosamine) -0.012386116 0.925251604 0.7102250
## B07 (N-Acetyl-b-D-Mannosamine) 0.729060175 0.689330569 0.9954093
## B08 (N-Acetyl-D-Galactosamine) 0.705173940 0.714094621 0.9975703
## B02 (a-D-Lactose) B03 (D-Melibiose)
## A01 (Negative Control) 0.9888151 0.9851289
## A02 (Dextrin) 0.9447480 0.9252868
## A03 (D-Maltose) 0.9997336 0.9993402
## A04 (D-Trehalose) 0.9953585 0.9938993
## A05 (D-Cellobiose) 0.9892602 0.9951265
## A06 (b-Gentiobiose) 0.9946504 0.9985047
## A07 (Sucrose) 0.9897359 0.9962169
## A08 (Turanose) 0.9875541 0.9948145
## A09 (Stachyose) 0.9808541 0.9902228
## A10 (Positive Control) 0.7941186 0.7629615
## A11 (pH 6) 0.7587672 0.7237321
## A12 (pH 5) 0.6568487 0.6935711
## B01 (D-Raffinose) 0.9903024 0.9965273
## B02 (a-D-Lactose) 1.0000000 0.9984023
## B03 (D-Melibiose) 0.9984023 1.0000000
## B04 (b-Methyl-D-Glucoside) 0.9970668 0.9979414
## B05 (D-Salicin) 0.9857236 0.9892142
## B06 (N-Acetyl-D-Glucosamine) 0.6064504 0.6504035
## B07 (N-Acetyl-b-D-Mannosamine) 0.9990002 0.9998199
## B08 (N-Acetyl-D-Galactosamine) 0.9968982 0.9993365
## B04 (b-Methyl-D-Glucoside) B05 (D-Salicin)
## A01 (Negative Control) 0.9933638 0.9919382
## A02 (Dextrin) 0.9230296 0.8912754
## A03 (D-Maltose) 0.9971734 0.9861054
## A04 (D-Trehalose) 0.9985873 0.9950679
## A05 (D-Cellobiose) 0.9960869 0.9959607
## A06 (b-Gentiobiose) 0.9982833 0.9944002
## A07 (Sucrose) 0.9935689 0.9895426
## A08 (Turanose) 0.9925237 0.9898259
## A09 (Stachyose) 0.9850689 0.9811177
## A10 (Positive Control) 0.7498773 0.6927043
## A11 (pH 6) 0.7142577 0.6576669
## A12 (pH 5) 0.7060407 0.7571167
## B01 (D-Raffinose) 0.9943444 0.9906211
## B02 (a-D-Lactose) 0.9970668 0.9857236
## B03 (D-Melibiose) 0.9979414 0.9892142
## B04 (b-Methyl-D-Glucoside) 1.0000000 0.9957053
## B05 (D-Salicin) 0.9957053 1.0000000
## B06 (N-Acetyl-D-Glucosamine) 0.6385717 0.6672093
## B07 (N-Acetyl-b-D-Mannosamine) 0.9987583 0.9904332
## B08 (N-Acetyl-D-Galactosamine) 0.9991786 0.9937985
## B06 (N-Acetyl-D-Glucosamine)
## A01 (Negative Control) 0.56815059
## A02 (Dextrin) 0.32141269
## A03 (D-Maltose) 0.62334176
## A04 (D-Trehalose) 0.60422668
## A05 (D-Cellobiose) 0.70388954
## A06 (b-Gentiobiose) 0.67930921
## A07 (Sucrose) 0.71355556
## A08 (Turanose) 0.72303968
## A09 (Stachyose) 0.74898688
## A10 (Positive Control) 0.06496288
## A11 (pH 6) -0.01238612
## A12 (pH 5) 0.92525160
## B01 (D-Raffinose) 0.71022502
## B02 (a-D-Lactose) 0.60645035
## B03 (D-Melibiose) 0.65040355
## B04 (b-Methyl-D-Glucoside) 0.63857165
## B05 (D-Salicin) 0.66720926
## B06 (N-Acetyl-D-Glucosamine) 1.00000000
## B07 (N-Acetyl-b-D-Mannosamine) 0.63966422
## B08 (N-Acetyl-D-Galactosamine) 0.66085286
## B07 (N-Acetyl-b-D-Mannosamine)
## A01 (Negative Control) 0.9881198
## A02 (Dextrin) 0.9291654
## A03 (D-Maltose) 0.9995288
## A04 (D-Trehalose) 0.9957197
## A05 (D-Cellobiose) 0.9947317
## A06 (b-Gentiobiose) 0.9982619
## A07 (Sucrose) 0.9949516
## A08 (Turanose) 0.9934694
## A09 (Stachyose) 0.9878652
## A10 (Positive Control) 0.7667984
## A11 (pH 6) 0.7290602
## A12 (pH 5) 0.6893306
## B01 (D-Raffinose) 0.9954093
## B02 (a-D-Lactose) 0.9990002
## B03 (D-Melibiose) 0.9998199
## B04 (b-Methyl-D-Glucoside) 0.9987583
## B05 (D-Salicin) 0.9904332
## B06 (N-Acetyl-D-Glucosamine) 0.6396642
## B07 (N-Acetyl-b-D-Mannosamine) 1.0000000
## B08 (N-Acetyl-D-Galactosamine) 0.9993858
## B08 (N-Acetyl-D-Galactosamine)
## A01 (Negative Control) 0.9878884
## A02 (Dextrin) 0.9164698
## A03 (D-Maltose) 0.9978573
## A04 (D-Trehalose) 0.9956342
## A05 (D-Cellobiose) 0.9976945
## A06 (b-Gentiobiose) 0.9996769
## A07 (Sucrose) 0.9971119
## A08 (Turanose) 0.9961971
## A09 (Stachyose) 0.9908995
## A10 (Positive Control) 0.7439719
## A11 (pH 6) 0.7051739
## A12 (pH 5) 0.7140946
## B01 (D-Raffinose) 0.9975703
## B02 (a-D-Lactose) 0.9968982
## B03 (D-Melibiose) 0.9993365
## B04 (b-Methyl-D-Glucoside) 0.9991786
## B05 (D-Salicin) 0.9937985
## B06 (N-Acetyl-D-Glucosamine) 0.6608529
## B07 (N-Acetyl-b-D-Mannosamine) 0.9993858
## B08 (N-Acetyl-D-Galactosamine) 1.0000000
stopifnot(is.matrix(x), dim(x) == 20)
# adapt default text size to a full 96-well plate
my_corrplot <- function(corr, tl.col = "grey30", tl.cex = 0.4,
mar = c(2, 2, 2, 2), ...) {
corrplot::corrplot(corr = corr, tl.col = tl.col,
tl.cex = tl.cex, mar = mar, ...)
}
my_corrplot(x)