PCA dimensional reduction analysis for RNA-Seq.
Arguments
- sample_gene
Dataframe: All genes in all samples expression dataframe of RNA-Seq (1st-col: Genes, 2nd-col~: Samples).
- group_sample
Dataframe: Samples and groups for gene expression (1st-col: Samples, 2nd-col: Groups).
Examples
# 1. Library package TOmicsVis
library(TOmicsVis)
# 2. Load example datasets
data(gene_expression)
head(gene_expression)
#> Genes CT_1 CT_2 CT_3 LT20_1 LT20_2 LT20_3 LT15_1 LT15_2
#> 1 transcript_0 655.78 631.08 669.89 654.21 402.56 447.09 510.08 442.22
#> 2 transcript_1 92.72 112.26 150.30 88.35 76.35 94.55 120.24 80.89
#> 3 transcript_10 21.74 31.11 22.58 15.09 13.67 13.24 12.48 7.53
#> 4 transcript_100 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> 5 transcript_1000 0.00 14.15 36.01 0.00 0.00 193.59 208.45 0.00
#> 6 transcript_10000 89.18 158.04 86.28 82.97 117.78 102.24 129.61 112.73
#> LT15_3 LT12_1 LT12_2 LT12_3 LT12_6_1 LT12_6_2 LT12_6_3
#> 1 399.82 483.30 437.89 444.06 405.43 416.63 464.75
#> 2 73.94 96.25 82.62 85.48 65.12 61.94 73.44
#> 3 13.35 11.16 11.36 6.96 7.82 4.01 10.02
#> 4 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> 5 232.40 148.58 0.00 181.61 0.02 12.18 0.00
#> 6 85.70 80.89 124.11 115.25 113.87 107.69 119.83
data(samples_groups)
head(samples_groups)
#> Samples Groups
#> 1 CT_1 CT
#> 2 CT_2 CT
#> 3 CT_3 CT
#> 4 LT20_1 LT20
#> 5 LT20_2 LT20
#> 6 LT20_3 LT20
# 3. Default parameters
res <- pca_analysis(gene_expression, samples_groups)
head(res)
#> PC1 PC2 PC3 PC4 PC5 PC6
#> CT_1 -27010.536 -18328.2803 5955.2569 46547.7319 11394.1043 -7197.285
#> CT_2 16248.651 29132.9251 -824.1857 20747.9618 -18798.8755 21096.088
#> CT_3 22421.017 -26832.3964 6789.4490 5864.1171 -15375.3418 17424.861
#> LT20_1 -18587.073 -472.9036 -21638.7836 7765.9575 114.1225 -3943.968
#> LT20_2 33275.933 -9874.9959 -14991.3942 -7443.9250 -4600.8302 -8072.298
#> LT20_3 -1596.255 11683.5426 -10892.8493 381.0795 11080.3560 -8994.187
#> PC7 PC8 PC9 PC10 PC11 PC12
#> CT_1 2150.6739 4850.320 4051.745 7666.9445 -3141.9327 -2487.939
#> CT_2 -12329.1138 -3353.734 4805.659 1503.8533 11184.0296 -4865.436
#> CT_3 12744.2255 -10037.516 -11468.842 202.4016 -11001.6260 -3847.291
#> LT20_1 8864.7482 -14171.127 -1968.082 -3562.1899 7446.2105 14831.486
#> LT20_2 -941.3943 -5072.401 5345.106 6494.1383 -3954.2153 9351.346
#> LT20_3 7263.9321 -7774.725 -1853.546 -21427.2641 -46.1503 -12507.011
#> PC13 PC14 PC15
#> CT_1 -2704.613 2396.7383 2.528517e-11
#> CT_2 -2633.057 -1375.3352 6.825657e-11
#> CT_3 5193.978 188.5601 2.255671e-11
#> LT20_1 3937.457 -7871.8062 4.864246e-11
#> LT20_2 -12904.673 6071.6618 -2.020696e-10
#> LT20_3 -5369.380 2606.1762 1.903509e-11