Hi, I have a dataset showing gene expression of 25 genes. I wanted to show their expression patterns in comparison with one another (so on the same graph- although if someone has a better idea, please say).
I feel like I've gone about it in the worst way. Any help would be greatly appreciated. I am a newbie.
Data:
Gene_ID Name
1 KfGene001686-RA KgGene003950
2 KfGene003305-RA KgGene005761
3 KfGene013436-RA KgGene007054
4 KfGene010817-RA KgGene008773
5 KfGene021651-RA KgGene009113
6 KfGene017462-RA KgGene009699
7 KfGene023407-RA KgGene013521
8 KfGene020112-RA KgGene014989
9 KfGene047087-RA KgGene016113
10 KfGene021800-RA KgGene016131
11 KfGene027372-RA KgGene019586
12 KfGene010608-RA KgGene021134
13 KfGene009235-RA KgGene022206
14 KfGene038923-RA KgGene022959
15 KfGene038671-RA KgGene023146
16 KfGene042277-RA KgGene025874
17 KfGene046061-RA KgGene028203
18 KfGene017802-RA KgGene029754
19 KfGene044330-RA KgGene031775
20 KfGene049262-RA KgGene032770
21 KfGene051908-RA KgGene036270
22 KfGene006149-RA KgGene038284
23 KfGene007051-RA KgGene039081
24 KfGene007231-RA KgGene039169
25 KfGene007581-RA KgGene039437
Description LP1.2.L LP1.6.L
1 "Similar to AGPS1 Glucose-1-phosphate adenylyltransferase large subunit 1 (Fragment) (Solanum tuberosum)" 0.4264431 0.52143121
2 "Similar to RPT2 Root phototropism protein 2 (Arabidopsis thaliana)" 0.4122265 0.06219286
3 "Similar to OFP2 Transcription repressor OFP2 (Arabidopsis thaliana)" 14.6008091 7.43314649
4 "Similar to TT12 Protein TRANSPARENT TESTA 12 (Arabidopsis thaliana)" 6.1392649 4.39425790
5 "Similar to AGT1 Serine--glyoxylate aminotransferase (Arabidopsis thaliana)" 17.2920840 9.19213274
6 "Similar to MBR1 E3 ubiquitin-protein ligase MBR1 (Arabidopsis thaliana)" 145.1126882 55.77949721
7 "Similar to Os01g0794400 Probable nucleoredoxin 2 (Oryza sativa subsp. japonica)" 10.2413639 3.75089988
8 "Similar to NADP-dependent malic enzyme (Vitis vinifera)" 6.8751455 4.48627072
9 "Similar to FAF1 Protein FANTASTIC FOUR 1 (Arabidopsis thaliana)" 84.0142386 10.89528380
10 "Similar to PSK6 Putative phytosulfokines 6 (Arabidopsis thaliana)" 4.2818285 4.30661445
11 "Similar to BBX32 B-box zinc finger protein 32 (Arabidopsis thaliana)" 183.7225775 12.61997616
12 "Similar to HAB1 Protein phosphatase 2C 16 (Arabidopsis thaliana)" 4.0473340 3.06663315
13 "Similar to SS Sucrose synthase (Glycine max)" 23.1440493 8.32848959
14 "Similar to NUDT18 Nudix hydrolase 18, mitochondrial (Arabidopsis thaliana)" 8.6286346 4.01706307
15 "Similar to ogdh 2-oxoglutarate dehydrogenase, mitochondrial (Dictyostelium discoideum)" 2.3051120 1.29359867
16 "Similar to lip Lipase (Staphylococcus hyicus)" 62.1337068 3.64342613
17 "Similar to At3g62260 Probable protein phosphatase 2C 49 (Arabidopsis thaliana)" 20.9940935 22.67153910
18 "Similar to HEMH Ferrochelatase-2, chloroplastic (Cucumis sativus)" 2.2201068 0.85731305
19 "Similar to Os02g0814900 Nicotinamide mononucleotide adenylyltransferase (Oryza sativa subsp. japonica)" 25.4562517 24.63512532
20 "Similar to PPCK2 Phosphoenolpyruvate carboxylase kinase 2 (Arabidopsis thaliana)" 8.6620994 10.51275726
21 "Similar to PDK [Pyruvate dehydrogenase (acetyl-transferring)] kinase, mitochondrial (Arabidopsis thaliana)" 8.9156566 9.26763727
22 "Similar to BBX19 B-box zinc finger protein 19 (Arabidopsis thaliana)" 0.6648074 0.48156551
23 "Similar to PPD Pyruvate, phosphate dikinase, chloroplastic (Mesembryanthemum crystallinum)" 0.1533274 0.00000000
24 "Similar to BAM9 Inactive beta-amylase 9 (Arabidopsis thaliana)" 149.8861201 74.87488653
25 "Similar to CIPK1 CBL-interacting serine/threonine-protein kinase 1 (Arabidopsis thaliana)" 30.6399281 18.11187192
LP1.10.L LP1.14.D LP1.18.D LP1.22.D C3.total LP6.2.L LP6.6.L LP6.10.L LP6.14.D LP6.18.D LP6.22.D
1 0.2133601 0.8430212 0.7502430 0.6900248 3.4445234 16.4185549 0.9023816 5.0930956 3.533190e+01 94.5372414 65.357835
2 0.0000000 0.2314601 0.2112554 0.1759484 1.0930833 1.0715797 0.4990551 0.4400818 9.105903e+00 24.6161083 24.558166
3 5.6703519 6.5570740 7.4213166 4.3975597 46.0802578 178.5743192 35.6985223 19.7006657 1.845690e+01 98.7268478 77.700972
4 0.9894706 5.8041184 7.7542889 5.5395039 30.6209045 38.0232572 11.8685914 2.7966816 9.887390e+00 85.9265634 141.972271
5 5.1030608 8.7821537 14.5675635 18.7647394 73.7017341 66.2603485 28.7889093 20.0530542 3.413571e+01 116.5450726 143.497169
6 30.4775395 45.5083921 52.0346459 71.7194843 400.6322472 1683.1774372 116.3847484 16.9971875 1.636875e+01 480.4353430 1042.550910
7 3.2513178 6.0309224 10.1626182 16.5206598 49.9577820 23.2564900 1.7205024 1.0586824 1.753363e+00 81.8385515 157.374504
8 4.6819403 9.3798388 12.5621347 13.6957459 51.6810758 32.4721477 8.6237208 11.5575678 7.698440e+01 118.1234515 122.325626
9 1.8752927 10.0032708 68.3018929 160.4874927 335.5774715 64.3020702 3.6529963 1.5641389 4.775783e+01 168.9211836 206.577497
10 3.5059520 6.5283774 7.3376091 4.5004226 30.4608041 5.3354962 5.4467062 5.5730065 3.141412e+01 67.3558547 52.908843
11 1.0746035 4.5619287 38.9165085 140.4976982 381.3932925 194.9908373 3.4146946 0.6486074 2.093917e+01 617.0983014 1036.509991
12 1.0671272 3.2177405 2.6652127 2.3904046 16.4544522 20.2769351 29.3950827 29.1545026 7.418605e+01 24.7283871 14.204890
13 8.4937532 11.4508221 23.9412844 30.8763938 106.2347924 19.7241650 3.7174692 10.6390067 2.184707e+02 493.6432298 487.438332
14 5.1304012 8.5577109 10.7234438 7.6325103 44.6897639 11.2776385 7.7268876 10.8347496 2.064168e+01 22.3713699 23.189719
15 1.4791686 2.1793645 2.2186922 1.8218322 11.2977682 2.7895203 2.1835422 1.4211416 4.954620e+00 7.2629566 10.143671
16 0.8155321 2.2422061 35.8281281 103.4660691 208.1290683 108.1908398 2.2502554 1.1120553 3.692218e+01 126.2838044 151.804979
17 20.1524642 30.9555731 26.8051761 26.7001286 148.2789746 44.9949385 28.6532563 24.9735806 3.579121e+01 37.0084131 48.436210
18 0.3688430 1.0930002 1.1246729 0.4485652 6.1125011 24.6796498 9.2094505 7.6399414 4.885953e+00 6.9089508 3.802639
19 9.4196101 37.4498270 66.1139217 31.7732991 194.8480349 3.8704895 1.2314163 11.0040589 2.905534e+01 102.1121242 142.733987
20 10.9093432 5.9254095 9.2788614 5.1360626 50.4245334 1.1282758 1.9296688 17.4202551 1.700417e+01 14.4149598 11.686084
21 10.6847013 11.6519048 10.4166068 7.4762513 58.4127582 7.8784681 4.6695005 7.6456648 1.184245e+01 13.1081761 8.948890
22 0.6567177 0.9066858 1.7365522 1.0848326 5.5311612 0.5245827 0.1556234 1.1510490 4.056261e+01 63.0262119 30.987811
23 0.0000000 0.0000000 0.0000000 0.0000000 0.1533274 14.5173036 4.8905799 0.8349723 4.146681e-02 0.2261183 0.000000
24 42.0272983 113.7850115 206.4108905 146.2144952 733.1987020 2610.5584795 1753.7868931 1509.1986928 2.113935e+03 2664.0804869 2652.695872
25 19.3076360 35.0680821 53.8591586 104.0636253 261.0503021 19.1370432 30.9437906 73.3727939 8.113122e+02 1525.3676310 1683.824735
Time <- c(2,6,10,14,18,22)
KF.1 <- c(KF$LP6.2.L[1],
KF$LP6.6.L[1],
KF$LP6.10.L[1],
KF$LP6.14.D[1],
KF$LP6.18.D[1],
KF$LP6.22.D[1])
KF.2 <- c(KF$LP6.2.L[2],
KF$LP6.6.L[2],
KF$LP6.10.L[2],
KF$LP6.14.D[2],
KF$LP6.18.D[2],
KF$LP6.22.D[2])
KF.3 <- c(KF$LP6.2.L[3],
KF$LP6.6.L[3],
KF$LP6.10.L[3],
KF$LP6.14.D[3],
KF$LP6.18.D[3],
KF$LP6.22.D[3])
KF.4 <- c(KF$LP6.2.L[4],
KF$LP6.6.L[4],
KF$LP6.10.L[4],
KF$LP6.14.D[4],
KF$LP6.18.D[4],
KF$LP6.22.D[4])
KF.5 <- c(KF$LP6.2.L[5],
KF$LP6.6.L[5],
KF$LP6.10.L[5],
KF$LP6.14.D[5],
KF$LP6.18.D[5],
KF$LP6.22.D[5])
KF.6 <- c(KF$LP6.2.L[6],
KF$LP6.6.L[6],
KF$LP6.10.L[6],
KF$LP6.14.D[6],
KF$LP6.18.D[6],
KF$LP6.22.D[6])
KF.7 <- c(KF$LP6.2.L[7],
KF$LP6.6.L[7],
KF$LP6.10.L[7],
KF$LP6.14.D[7],
KF$LP6.18.D[7],
KF$LP6.22.D[7])
KF.8 <- c(KF$LP6.2.L[8],
KF$LP6.6.L[8],
KF$LP6.10.L[8],
KF$LP6.14.D[8],
KF$LP6.18.D[8],
KF$LP6.22.D[8])
KF.9 <- c(KF$LP6.2.L[9],
KF$LP6.6.L[9],
KF$LP6.10.L[9],
KF$LP6.14.D[9],
KF$LP6.18.D[9],
KF$LP6.22.D[9])
KF.10 <- c(KF$LP6.2.L[10],
KF$LP6.6.L[10],
KF$LP6.10.L[10],
KF$LP6.14.D[10],
KF$LP6.18.D[10],
KF$LP6.22.D[10])
KF.11 <- c(KF$LP6.2.L[11],
KF$LP6.6.L[11],
KF$LP6.10.L[11],
KF$LP6.14.D[11],
KF$LP6.18.D[11],
KF$LP6.22.D[11]
KF.12 <- c(KF$LP6.2.L[12],
KF$LP6.6.L[12],
KF$LP6.10.L[12],
KF$LP6.14.D[12],
KF$LP6.18.D[12],
KF$LP6.22.D[12])
KF.13 <- c(KF$LP6.2.L[13],
KF$LP6.6.L[13],
KF$LP6.10.L[13],
KF$LP6.14.D[13],
KF$LP6.18.D[13],
KF$LP6.22.D[13])
KF.14 <- c(KF$LP6.2.L[14],
KF$LP6.6.L[14],
KF$LP6.10.L[14],
KF$LP6.14.D[14],
KF$LP6.18.D[14],
KF$LP6.22.D[14])
KF.15 <- c(KF$LP6.2.L[15],
KF$LP6.6.L[15],
KF$LP6.10.L[15],
KF$LP6.14.D[15],
KF$LP6.18.D[15],
KF$LP6.22.D[15])
KF.16 <- c(KF$LP6.2.L[16],
KF$LP6.6.L[16],
KF$LP6.10.L[16],
KF$LP6.14.D[16],
KF$LP6.18.D[16],
KF$LP6.22.D[16])
KF.17 <- c(KF$LP6.2.L[17],
KF$LP6.6.L[17],
KF$LP6.10.L[17],
KF$LP6.14.D[17],
KF$LP6.18.D[17],
KF$LP6.22.D[17])
KF.18 <- c(KF$LP6.2.L[18],
KF$LP6.6.L[18],
KF$LP6.10.L[18],
KF$LP6.14.D[18],
KF$LP6.18.D[18],
KF$LP6.22.D[18])
KF.19 <- c(KF$LP6.2.L[19],
KF$LP6.6.L[19],
KF$LP6.10.L[19],
KF$LP6.14.D[19],
KF$LP6.18.D[19],
KF$LP6.22.D[19])
KF.20 <- c(KF$LP6.2.L[20],
KF$LP6.6.L[20],
KF$LP6.10.L[20],
KF$LP6.14.D[20],
KF$LP6.18.D[20],
KF$LP6.22.D[20])
KF.21 <- c(KF$LP6.2.L[21],
KF$LP6.6.L[21],
KF$LP6.10.L[21],
KF$LP6.14.D[21],
KF$LP6.18.D[21],
KF$LP6.22.D[21])
KF.22 <- c(KF$LP6.2.L[22],
KF$LP6.6.L[22],
KF$LP6.10.L[22],
KF$LP6.14.D[22],
KF$LP6.18.D[22],
KF$LP6.22.D[22])
KF.23 <- c(KF$LP6.2.L[23],
KF$LP6.6.L[23],
KF$LP6.10.L[23],
KF$LP6.14.D[23],
KF$LP6.18.D[23],
KF$LP6.22.D[23])
KF.24 <- c(KF$LP6.2.L[24],
KF$LP6.6.L[24],
KF$LP6.10.L[24],
KF$LP6.14.D[24],
KF$LP6.18.D[24],
KF$LP6.22.D[24])
KF.25 <- c(KF$LP6.2.L[25],
KF$LP6.6.L[25],
KF$LP6.10.L[25],
KF$LP6.14.D[25],
KF$LP6.18.D[25],
KF$LP6.22.D[25])
#Combine vectors into a matrix to plot the gene expression####
GraphingMatrix<-cbind(Time, KF.1, KF.2, KF.3, KF.4, KF.5, KF.6, KF.7, KF.8, KF.9, KF.10,
KF.11, KF.12, KF.13, KF.14, KF.15, KF.16, KF.17, KF.18, KF.19,
KF.20, KF.21, KF.22, KF.23, KF.24, KF.25)
jpeg(paste("PPCK-like Expression", ".jpeg", sep="")) #name of jpeg file
#Set plot layout
layout(mat = matrix(c(1, 2),
nrow = 1,
ncol = 1),
heights = c(2, 2), # Heights of the two rows
widths = c(2)) # Widths of the two columns
#par(mfrow=c(2,1))
min_value = min(GraphingMatrix[,2:ncol(GraphingMatrix)])
max_value = max(GraphingMatrix[,2:ncol(GraphingMatrix)])
#plot1
print(plot(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.1'], type='b',
xlim=c(0, 25), ylim=c(min_value, max_value), main="PPCK-like Expression")),
col = "blue", xlab = "Time (h)", ylab = "Expression")),
lines(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.2'], type='b', col='red')
lines(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.3'], type='b', col='turquoise4')
lines(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.4'], type='b', col='green')
lines(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.5'], type='b', col='yellow')
lines(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.6'], type='b', col='orange')
lines(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.7'], type='b', col='cyan')
lines(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.8'], type='b', col='dimgrey')
lines(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.9'], type='b', col='deeppink')
lines(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.10'], type='b', col='darkslategray')
lines(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.11'], type='b', col='goldenrod')
lines(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.12'], type='b', col='firebrick')
lines(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.13'], type='b', col='forestgreen')
lines(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.14'], type='b', col='hotpink')
lines(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.15'], type='b', col='lightblue')
lines(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.16'], type='b', col='lightsalmon')
lines(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.17'], type='b', col='magenta')
lines(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.18'], type='b', col='maroon')
lines(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.19'], type='b', col='olivedrab')
lines(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.20'], type='b', col='mediumorchid')
lines(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.21'], type='b', col='pink')
lines(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.22'], type='b', col='plum4')
lines(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.23'], type='b', col='royalblue')
lines(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.24'], type='b', col='sienna1')
lines(x=GraphingMatrix[,'Time'], y=GraphingMatrix[,'KF.25'], type='b', col='tomato4')
legend(x="topleft",
legend=c('AGPS1', 'RPT2', 'OFP2', 'TT12', 'AGT1', 'MBR1', 'Nucleoredoxin 2', 'NADP-ME', 'FAF1',
'PSK6', 'BBX32', 'HAB1', 'SS', 'NUDT18', 'ogdh', 'Lip', 'PP2C', 'HEMH', 'Nicotinamide',
'PPCK', 'PDK', 'BBX19', 'PPD', 'BAM9', 'CIPK1'),
col=c('blue', 'red', 'tuquoise4', 'green', 'yellow', 'orange', 'cyan','dimgrey',
'deeppink', 'darkslategray', 'goldenrod', 'firebrick', 'forestgreen', 'hotpink',
'lightblue', 'lightsalmon', 'magenta', 'maroon', 'olivedrab', 'mediumorchid',
'pink', 'plum4', 'royalblue', 'sienna1', 'tomato4'),
lty = 1, lwd = 2, cex=0.55)