#v1.7.3, 06/18/2020: Library path was changed to ~/R_version/ODA. PCA labels and ellipses were added (not officially enabled yet).
#v1.7.3, 08/04/2020: R 4.0.2 was tested. Data template was changed to .xlsx. Macro was no longer needed. Library path was changed to ~/R/4.0.2-gccmkl for BioHPC. PCA labels and ellipses were added. Heatmap colors were added.
#v1.7.2, 03/26/2020: A bug regarding empty feature IDs was fixed.
#v1.7.1, 12/04/2019: Figures were saved as both .ps and .png files. Euler plot was disabled for >6 samples. Samples / features can be clustered or not on the heatmaps.
#v1.7.0, 10/22/2019: Figures were saved as .ps files in a Figure folder. Correlation plot was genrated with the old method for better speed. Euler plot was disabled for >10 samples. Y axis of volcano plot could be raw or adjusted p-values. DESeq was renamed RLE as I would implement the DESeq differential expression analysis in the future. RLE is the same method used by DESeq but I slightly modified it to allow for zeros, missing values and / or values below the value filter. Due to this reason I couldn't use the DESeq normalization directly.
#This script was developed by zhiyu.zhao@utsouthwestern.edu .
#v1.7.3, 08/04/2020: R 4.0.2 was tested. Data template was changed to .xlsx. Macro was no longer needed. Library path was changed to ~/R/ODA. PCA labels and ellipses were added. Heatmap colors were added.
#v1.7.3, 08/04/2020: R 4.0.2 was tested. Data template was changed to .xlsx. Macro was no longer needed. Library path was changed to ~/R/4.0.2-gccmkl for BioHPC. PCA labels and ellipses were added. Heatmap colors were added.
#v1.7.2, 03/26/2020: A bug regarding empty feature IDs was fixed.
#v1.7.1, 12/04/2019: Figures were saved as both .ps and .png files. Euler plot was disabled for >6 samples. Samples / features can be clustered or not on the heatmaps.
#v1.7.0, 10/22/2019: Figures were saved as .ps files in a Figure folder. Correlation plot was generated with the old method for better speed. Euler plot was disabled for >10 samples. Y axis of volcano plot could be raw or adjusted p-values. DESeq was renamed RLE as I would implement the DESeq differential expression analysis in the future. RLE is the same method used by DESeq but I slightly modified it to allow for zeros, missing values and / or values below the value filter. Due to this reason I couldn't use the DESeq normalization directly.
