slanted_reorder.RdGiven a matrix expressing the cross-similarity between two (possibly different) sets of entities,
this uses slanted_orders to compute the "best" order for visualizing the matrix, then
returns the reordered data. Commonly used in pheatmap(slanted_reorder(data), ...), and of
course sheatmap does this internally for you.
slanted_reorder( data, order_data = NULL, order_rows = TRUE, order_cols = TRUE, squared_order = TRUE, same_order = FALSE, discount_outliers = TRUE )
| data | A rectangular matrix to reorder, of non-negative values (unless |
|---|---|
| order_data | An optional matrix of non-negative values of the same size to use for computing the orders. |
| order_rows | Whether to reorder the rows. |
| order_cols | Whether to reorder the columns. |
| squared_order | Whether to reorder to minimize the l2 norm (otherwise minimizes the l1 norm). |
| same_order | Whether to apply the same order to both rows and columns. |
| discount_outliers | Whether to do a final order phase discounting outlier values far from the diagonal. |
A matrix of the same shape whose rows and columns are a permutation of the input.
#> Cadillac Fleetwood Pontiac Firebird Hornet 4 Drive #> Cadillac Fleetwood 1.0000000 0.9996817 0.9978952 #> Pontiac Firebird 0.9996817 1.0000000 0.9990297 #> Hornet 4 Drive 0.9978952 0.9990297 1.0000000 #> Lincoln Continental 0.9995539 0.9992724 0.9970348 #> Merc 240D 0.9881256 0.9911454 0.9959252 #> Dodge Challenger 0.9991617 0.9995087 0.9982656 #> Valiant 0.9975630 0.9986500 0.9992580 #> Hornet Sportabout 0.9986132 0.9990524 0.9975793 #> AMC Javelin 0.9983419 0.9987290 0.9972864 #> Chrysler Imperial 0.9969115 0.9969150 0.9942116 #> Merc 450SLC 0.9828425 0.9833994 0.9800784 #> Merc 450SE 0.9827991 0.9834429 0.9801772 #> Merc 450SL 0.9827183 0.9834394 0.9802828 #> Duster 360 0.9787143 0.9789599 0.9744818 #> Camaro Z28 0.9756237 0.9758341 0.9710662 #> Mazda RX4 0.9747543 0.9768412 0.9755949 #> Mazda RX4 Wag 0.9747020 0.9767863 0.9756154 #> Merc 230 0.9713151 0.9741785 0.9754758 #> Ford Pantera L 0.9664936 0.9668629 0.9615811 #> Merc 280C 0.9681688 0.9697178 0.9674808 #> Merc 280 0.9679019 0.9696245 0.9675175 #> Porsche 914-2 0.9545629 0.9584635 0.9592908 #> Honda Civic 0.9241250 0.9320459 0.9409279 #> Toyota Corona 0.9471343 0.9503172 0.9503239 #> Datsun 710 0.9339623 0.9376925 0.9377512 #> Volvo 142E 0.9297053 0.9326570 0.9309608 #> Fiat X1-9 0.9158350 0.9223159 0.9273347 #> Fiat 128 0.9012275 0.9089942 0.9157302 #> Maserati Bora 0.8880549 0.8885687 0.8802035 #> Toyota Corolla 0.8718034 0.8805717 0.8882435 #> Ferrari Dino 0.8635937 0.8654714 0.8588699 #> Lotus Europa 0.8515095 0.8566400 0.8552800 #> Lincoln Continental Merc 240D Dodge Challenger Valiant #> Cadillac Fleetwood 0.9995539 0.9881256 0.9991617 0.9975630 #> Pontiac Firebird 0.9992724 0.9911454 0.9995087 0.9986500 #> Hornet 4 Drive 0.9970348 0.9959252 0.9982656 0.9992580 #> Lincoln Continental 1.0000000 0.9868169 0.9996470 0.9977794 #> Merc 240D 0.9868169 1.0000000 0.9902099 0.9948513 #> Dodge Challenger 0.9996470 0.9902099 1.0000000 0.9990828 #> Valiant 0.9977794 0.9948513 0.9990828 1.0000000 #> Hornet Sportabout 0.9994983 0.9893532 0.9998857 0.9987885 #> AMC Javelin 0.9993949 0.9891081 0.9998142 0.9988216 #> Chrysler Imperial 0.9987959 0.9839211 0.9987105 0.9966330 #> Merc 450SLC 0.9878395 0.9702379 0.9884685 0.9864103 #> Merc 450SE 0.9877938 0.9705086 0.9884838 0.9864589 #> Merc 450SL 0.9877098 0.9708627 0.9884775 0.9865508 #> Duster 360 0.9843942 0.9626936 0.9845757 0.9814781 #> Camaro Z28 0.9817339 0.9589152 0.9818811 0.9785863 #> Mazda RX4 0.9803858 0.9709778 0.9826427 0.9826444 #> Mazda RX4 Wag 0.9803290 0.9711244 0.9826074 0.9826990 #> Merc 230 0.9765449 0.9756630 0.9799370 0.9825497 #> Ford Pantera L 0.9737102 0.9491148 0.9739763 0.9703559 #> Merc 280C 0.9748547 0.9610683 0.9766813 0.9760419 #> Merc 280 0.9745835 0.9614781 0.9765418 0.9759904 #> Porsche 914-2 0.9615637 0.9603211 0.9656933 0.9679007 #> Honda Civic 0.9290026 0.9585105 0.9375444 0.9470811 #> Toyota Corona 0.9552364 0.9495368 0.9589193 0.9607729 #> Datsun 710 0.9430615 0.9379252 0.9472385 0.9492576 #> Volvo 142E 0.9396044 0.9278683 0.9429176 0.9433944 #> Fiat X1-9 0.9241089 0.9381059 0.9312529 0.9378364 #> Fiat 128 0.9094065 0.9305930 0.9177615 0.9258627 #> Maserati Bora 0.9013784 0.8651658 0.9018176 0.8963508 #> Toyota Corolla 0.8812198 0.9061161 0.8906478 0.8998474 #> Ferrari Dino 0.8781242 0.8486224 0.8801175 0.8765768 #> Lotus Europa 0.8656163 0.8564798 0.8709701 0.8722962 #> Hornet Sportabout AMC Javelin Chrysler Imperial Merc 450SLC #> Cadillac Fleetwood 0.9986132 0.9983419 0.9969115 0.9828425 #> Pontiac Firebird 0.9990524 0.9987290 0.9969150 0.9833994 #> Hornet 4 Drive 0.9975793 0.9972864 0.9942116 0.9800784 #> Lincoln Continental 0.9994983 0.9993949 0.9987959 0.9878395 #> Merc 240D 0.9893532 0.9891081 0.9839211 0.9702379 #> Dodge Challenger 0.9998857 0.9998142 0.9987105 0.9884685 #> Valiant 0.9987885 0.9988216 0.9966330 0.9864103 #> Hornet Sportabout 1.0000000 0.9999405 0.9992468 0.9903498 #> AMC Javelin 0.9999405 1.0000000 0.9993749 0.9911796 #> Chrysler Imperial 0.9992468 0.9993749 1.0000000 0.9942034 #> Merc 450SLC 0.9903498 0.9911796 0.9942034 1.0000000 #> Merc 450SE 0.9903899 0.9911872 0.9941905 0.9999895 #> Merc 450SL 0.9903916 0.9911818 0.9941296 0.9999749 #> Duster 360 0.9868227 0.9876712 0.9917758 0.9995091 #> Camaro Z28 0.9843162 0.9852514 0.9897951 0.9990266 #> Mazda RX4 0.9849219 0.9858452 0.9883171 0.9976821 #> Mazda RX4 Wag 0.9848669 0.9858144 0.9882470 0.9976410 #> Merc 230 0.9818801 0.9830387 0.9840321 0.9933019 #> Ford Pantera L 0.9769543 0.9780454 0.9836189 0.9968131 #> Merc 280C 0.9792976 0.9805742 0.9842639 0.9971749 #> Merc 280 0.9792033 0.9804235 0.9840579 0.9969982 #> Porsche 914-2 0.9687526 0.9698631 0.9723443 0.9880709 #> Honda Civic 0.9398642 0.9406541 0.9378112 0.9501861 #> Toyota Corona 0.9622047 0.9638558 0.9674682 0.9870962 #> Datsun 710 0.9510709 0.9528131 0.9571134 0.9806200 #> Volvo 142E 0.9470799 0.9489501 0.9546893 0.9803080 #> Fiat X1-9 0.9348882 0.9364749 0.9378163 0.9610464 #> Fiat 128 0.9215490 0.9229437 0.9234681 0.9473084 #> Maserati Bora 0.9075443 0.9098086 0.9212426 0.9566258 #> Toyota Corolla 0.8950651 0.8966876 0.8976567 0.9269695 #> Ferrari Dino 0.8864176 0.8889901 0.9004177 0.9415899 #> Lotus Europa 0.8773760 0.8797277 0.8883790 0.9307268 #> Merc 450SE Merc 450SL Duster 360 Camaro Z28 Mazda RX4 #> Cadillac Fleetwood 0.9827991 0.9827183 0.9787143 0.9756237 0.9747543 #> Pontiac Firebird 0.9834429 0.9834394 0.9789599 0.9758341 0.9768412 #> Hornet 4 Drive 0.9801772 0.9802828 0.9744818 0.9710662 0.9755949 #> Lincoln Continental 0.9877938 0.9877098 0.9843942 0.9817339 0.9803858 #> Merc 240D 0.9705086 0.9708627 0.9626936 0.9589152 0.9709778 #> Dodge Challenger 0.9884838 0.9884775 0.9845757 0.9818811 0.9826427 #> Valiant 0.9864589 0.9865508 0.9814781 0.9785863 0.9826444 #> Hornet Sportabout 0.9903899 0.9903916 0.9868227 0.9843162 0.9849219 #> AMC Javelin 0.9911872 0.9911818 0.9876712 0.9852514 0.9858452 #> Chrysler Imperial 0.9941905 0.9941296 0.9917758 0.9897951 0.9883171 #> Merc 450SLC 0.9999895 0.9999749 0.9995091 0.9990266 0.9976821 #> Merc 450SE 1.0000000 0.9999947 0.9994897 0.9989992 0.9978407 #> Merc 450SL 0.9999947 1.0000000 0.9994309 0.9989318 0.9980218 #> Duster 360 0.9994897 0.9994309 1.0000000 0.9998887 0.9966708 #> Camaro Z28 0.9989992 0.9989318 0.9998887 1.0000000 0.9963801 #> Mazda RX4 0.9978407 0.9980218 0.9966708 0.9963801 1.0000000 #> Mazda RX4 Wag 0.9977928 0.9979733 0.9965779 0.9962848 0.9999946 #> Merc 230 0.9934467 0.9937331 0.9908191 0.9902667 0.9979862 #> Ford Pantera L 0.9968069 0.9967513 0.9985815 0.9992412 0.9952363 #> Merc 280C 0.9972201 0.9973257 0.9971237 0.9974082 0.9989810 #> Merc 280 0.9970806 0.9972066 0.9969199 0.9971885 0.9991635 #> Porsche 914-2 0.9884321 0.9888285 0.9870457 0.9873208 0.9960446 #> Honda Civic 0.9509727 0.9519069 0.9445592 0.9435349 0.9679038 #> Toyota Corona 0.9872684 0.9875682 0.9868730 0.9877597 0.9942831 #> Datsun 710 0.9808700 0.9812300 0.9810345 0.9823933 0.9897806 #> Volvo 142E 0.9804773 0.9807341 0.9819685 0.9837963 0.9879852 #> Fiat X1-9 0.9616029 0.9623204 0.9589004 0.9596667 0.9771175 #> Fiat 128 0.9480671 0.9489426 0.9445163 0.9451632 0.9665339 #> Maserati Bora 0.9565886 0.9565090 0.9634194 0.9672440 0.9598113 #> Toyota Corolla 0.9278273 0.9288236 0.9245797 0.9258214 0.9497922 #> Ferrari Dino 0.9416717 0.9417605 0.9483130 0.9526674 0.9495308 #> Lotus Europa 0.9311976 0.9316971 0.9350718 0.9389672 0.9467139 #> Mazda RX4 Wag Merc 230 Ford Pantera L Merc 280C Merc 280 #> Cadillac Fleetwood 0.9747020 0.9713151 0.9664936 0.9681688 0.9679019 #> Pontiac Firebird 0.9767863 0.9741785 0.9668629 0.9697178 0.9696245 #> Hornet 4 Drive 0.9756154 0.9754758 0.9615811 0.9674808 0.9675175 #> Lincoln Continental 0.9803290 0.9765449 0.9737102 0.9748547 0.9745835 #> Merc 240D 0.9711244 0.9756630 0.9491148 0.9610683 0.9614781 #> Dodge Challenger 0.9826074 0.9799370 0.9739763 0.9766813 0.9765418 #> Valiant 0.9826990 0.9825497 0.9703559 0.9760419 0.9759904 #> Hornet Sportabout 0.9848669 0.9818801 0.9769543 0.9792976 0.9792033 #> AMC Javelin 0.9858144 0.9830387 0.9780454 0.9805742 0.9804235 #> Chrysler Imperial 0.9882470 0.9840321 0.9836189 0.9842639 0.9840579 #> Merc 450SLC 0.9976410 0.9933019 0.9968131 0.9971749 0.9969982 #> Merc 450SE 0.9977928 0.9934467 0.9968069 0.9972201 0.9970806 #> Merc 450SL 0.9979733 0.9937331 0.9967513 0.9973257 0.9972066 #> Duster 360 0.9965779 0.9908191 0.9985815 0.9971237 0.9969199 #> Camaro Z28 0.9962848 0.9902667 0.9992412 0.9974082 0.9971885 #> Mazda RX4 0.9999946 0.9979862 0.9952363 0.9989810 0.9991635 #> Mazda RX4 Wag 1.0000000 0.9981426 0.9951176 0.9990100 0.9991795 #> Merc 230 0.9981426 1.0000000 0.9885613 0.9964616 0.9966519 #> Ford Pantera L 0.9951176 0.9885613 1.0000000 0.9974507 0.9972767 #> Merc 280C 0.9990100 0.9964616 0.9974507 1.0000000 0.9999656 #> Merc 280 0.9991795 0.9966519 0.9972767 0.9999656 1.0000000 #> Porsche 914-2 0.9960766 0.9966691 0.9883380 0.9953131 0.9959150 #> Honda Civic 0.9681143 0.9778126 0.9425926 0.9617182 0.9632309 #> Toyota Corona 0.9944076 0.9950507 0.9898566 0.9960771 0.9963272 #> Datsun 710 0.9898806 0.9905132 0.9859917 0.9922630 0.9926709 #> Volvo 142E 0.9880478 0.9867305 0.9883243 0.9920354 0.9922724 #> Fiat X1-9 0.9773155 0.9834791 0.9627322 0.9765082 0.9775593 #> Fiat 128 0.9667258 0.9744802 0.9484588 0.9646508 0.9660922 #> Maserati Bora 0.9596644 0.9504740 0.9761991 0.9697838 0.9695713 #> Toyota Corolla 0.9500043 0.9589877 0.9310236 0.9487738 0.9504343 #> Ferrari Dino 0.9494473 0.9425465 0.9634519 0.9600815 0.9601352 #> Lotus Europa 0.9467045 0.9456460 0.9498219 0.9541565 0.9550090 #> Porsche 914-2 Honda Civic Toyota Corona Datsun 710 #> Cadillac Fleetwood 0.9545629 0.9241250 0.9471343 0.9339623 #> Pontiac Firebird 0.9584635 0.9320459 0.9503172 0.9376925 #> Hornet 4 Drive 0.9592908 0.9409279 0.9503239 0.9377512 #> Lincoln Continental 0.9615637 0.9290026 0.9552364 0.9430615 #> Merc 240D 0.9603211 0.9585105 0.9495368 0.9379252 #> Dodge Challenger 0.9656933 0.9375444 0.9589193 0.9472385 #> Valiant 0.9679007 0.9470811 0.9607729 0.9492576 #> Hornet Sportabout 0.9687526 0.9398642 0.9622047 0.9510709 #> AMC Javelin 0.9698631 0.9406541 0.9638558 0.9528131 #> Chrysler Imperial 0.9723443 0.9378112 0.9674682 0.9571134 #> Merc 450SLC 0.9880709 0.9501861 0.9870962 0.9806200 #> Merc 450SE 0.9884321 0.9509727 0.9872684 0.9808700 #> Merc 450SL 0.9888285 0.9519069 0.9875682 0.9812300 #> Duster 360 0.9870457 0.9445592 0.9868730 0.9810345 #> Camaro Z28 0.9873208 0.9435349 0.9877597 0.9823933 #> Mazda RX4 0.9960446 0.9679038 0.9942831 0.9897806 #> Mazda RX4 Wag 0.9960766 0.9681143 0.9944076 0.9898806 #> Merc 230 0.9966691 0.9778126 0.9950507 0.9905132 #> Ford Pantera L 0.9883380 0.9425926 0.9898566 0.9859917 #> Merc 280C 0.9953131 0.9617182 0.9960771 0.9922630 #> Merc 280 0.9959150 0.9632309 0.9963272 0.9926709 #> Porsche 914-2 1.0000000 0.9815847 0.9981955 0.9968802 #> Honda Civic 0.9815847 1.0000000 0.9740879 0.9736937 #> Toyota Corona 0.9981955 0.9740879 1.0000000 0.9991120 #> Datsun 710 0.9968802 0.9736937 0.9991120 1.0000000 #> Volvo 142E 0.9939359 0.9630656 0.9978030 0.9990375 #> Fiat X1-9 0.9916326 0.9913067 0.9904406 0.9926894 #> Fiat 128 0.9847491 0.9934268 0.9818228 0.9851826 #> Maserati Bora 0.9633905 0.9048621 0.9730680 0.9768834 #> Toyota Corolla 0.9732722 0.9867701 0.9711836 0.9769965 #> Ferrari Dino 0.9594920 0.9089867 0.9697639 0.9761739 #> Lotus Europa 0.9660054 0.9397725 0.9725778 0.9811911 #> Volvo 142E Fiat X1-9 Fiat 128 Maserati Bora Toyota Corolla #> Cadillac Fleetwood 0.9297053 0.9158350 0.9012275 0.8880549 0.8718034 #> Pontiac Firebird 0.9326570 0.9223159 0.9089942 0.8885687 0.8805717 #> Hornet 4 Drive 0.9309608 0.9273347 0.9157302 0.8802035 0.8882435 #> Lincoln Continental 0.9396044 0.9241089 0.9094065 0.9013784 0.8812198 #> Merc 240D 0.9278683 0.9381059 0.9305930 0.8651658 0.9061161 #> Dodge Challenger 0.9429176 0.9312529 0.9177615 0.9018176 0.8906478 #> Valiant 0.9433944 0.9378364 0.9258627 0.8963508 0.8998474 #> Hornet Sportabout 0.9470799 0.9348882 0.9215490 0.9075443 0.8950651 #> AMC Javelin 0.9489501 0.9364749 0.9229437 0.9098086 0.8966876 #> Chrysler Imperial 0.9546893 0.9378163 0.9234681 0.9212426 0.8976567 #> Merc 450SLC 0.9803080 0.9610464 0.9473084 0.9566258 0.9269695 #> Merc 450SE 0.9804773 0.9616029 0.9480671 0.9565886 0.9278273 #> Merc 450SL 0.9807341 0.9623204 0.9489426 0.9565090 0.9288236 #> Duster 360 0.9819685 0.9589004 0.9445163 0.9634194 0.9245797 #> Camaro Z28 0.9837963 0.9596667 0.9451632 0.9672440 0.9258214 #> Mazda RX4 0.9879852 0.9771175 0.9665339 0.9598113 0.9497922 #> Mazda RX4 Wag 0.9880478 0.9773155 0.9667258 0.9596644 0.9500043 #> Merc 230 0.9867305 0.9834791 0.9744802 0.9504740 0.9589877 #> Ford Pantera L 0.9883243 0.9627322 0.9484588 0.9761991 0.9310236 #> Merc 280C 0.9920354 0.9765082 0.9646508 0.9697838 0.9487738 #> Merc 280 0.9922724 0.9775593 0.9660922 0.9695713 0.9504343 #> Porsche 914-2 0.9939359 0.9916326 0.9847491 0.9633905 0.9732722 #> Honda Civic 0.9630656 0.9913067 0.9934268 0.9048621 0.9867701 #> Toyota Corona 0.9978030 0.9904406 0.9818228 0.9730680 0.9711836 #> Datsun 710 0.9990375 0.9926894 0.9851826 0.9768834 0.9769965 #> Volvo 142E 1.0000000 0.9871267 0.9780049 0.9851604 0.9697187 #> Fiat X1-9 0.9871267 1.0000000 0.9985037 0.9489268 0.9942616 #> Fiat 128 0.9780049 0.9985037 1.0000000 0.9349039 0.9979526 #> Maserati Bora 0.9851604 0.9489268 0.9349039 1.0000000 0.9279730 #> Toyota Corolla 0.9697187 0.9942616 0.9979526 0.9279730 1.0000000 #> Ferrari Dino 0.9836829 0.9542644 0.9431153 0.9971614 0.9408047 #> Lotus Europa 0.9838514 0.9752213 0.9709341 0.9809147 0.9735639 #> Ferrari Dino Lotus Europa #> Cadillac Fleetwood 0.8635937 0.8515095 #> Pontiac Firebird 0.8654714 0.8566400 #> Hornet 4 Drive 0.8588699 0.8552800 #> Lincoln Continental 0.8781242 0.8656163 #> Merc 240D 0.8486224 0.8564798 #> Dodge Challenger 0.8801175 0.8709701 #> Valiant 0.8765768 0.8722962 #> Hornet Sportabout 0.8864176 0.8773760 #> AMC Javelin 0.8889901 0.8797277 #> Chrysler Imperial 0.9004177 0.8883790 #> Merc 450SLC 0.9415899 0.9307268 #> Merc 450SE 0.9416717 0.9311976 #> Merc 450SL 0.9417605 0.9316971 #> Duster 360 0.9483130 0.9350718 #> Camaro Z28 0.9526674 0.9389672 #> Mazda RX4 0.9495308 0.9467139 #> Mazda RX4 Wag 0.9494473 0.9467045 #> Merc 230 0.9425465 0.9456460 #> Ford Pantera L 0.9634519 0.9498219 #> Merc 280C 0.9600815 0.9541565 #> Merc 280 0.9601352 0.9550090 #> Porsche 914-2 0.9594920 0.9660054 #> Honda Civic 0.9089867 0.9397725 #> Toyota Corona 0.9697639 0.9725778 #> Datsun 710 0.9761739 0.9811911 #> Volvo 142E 0.9836829 0.9838514 #> Fiat X1-9 0.9542644 0.9752213 #> Fiat 128 0.9431153 0.9709341 #> Maserati Bora 0.9971614 0.9809147 #> Toyota Corolla 0.9408047 0.9735639 #> Ferrari Dino 1.0000000 0.9908847 #> Lotus Europa 0.9908847 1.0000000