Step 1: Set the working directory. You can right click on the file and click on button “property” to find the its location.
setwd("/Users/yerui/Documents/Research/MD Anderson/Rotations/Lin Lab/U01/R dataset")Step 2: Load the dataset.
drug_1hr <- read.csv ("1hr.csv", header=TRUE)## Dose X0nM X10000nM X1000nM X100nM X10nM X1nM X0.1nM
## 1 Alisertib 1 0.81 0.00 1.61 1.17 1.13 0.94
## 2 AMG 232 1 NA 6.06 0.99 0.70 0.90 0.74
## 3 AMG337 1 0.96 1.07 0.75 0.86 0.82 0.67
## 4 Azacytidine 1 0.45 1.39 1.30 1.15 1.24 1.03
## 5 AZD9291 1 1.99 0.91 0.76 0.64 0.82 0.69
## 6 Birinapant 1 0.91 0.78 0.69 0.83 0.75 0.81
## 7 Bortezomib 1 0.70 1.05 0.35 0.72 0.94 0.57
## 8 Cabozantinib 1 1.44 1.12 1.11 0.98 0.94 0.72
## 9 Dasatinib 1 NA 1.26 1.32 1.14 0.95 0.85
## 10 Erlotinib 1 1.84 1.41 0.81 0.85 0.75 0.76
## 11 FAU 1 0.82 1.10 1.13 0.78 1.15 0.79
## 12 Ibrutinib 1 1.59 1.13 0.93 0.84 1.02 0.90
## 13 INCB024360 1 0.97 1.10 1.01 0.91 1.21 1.13
## 14 Lapatinib 1 0.37 0.98 1.01 0.90 1.01 0.92
## 15 Lenalidomide 1 0.95 1.11 0.58 0.99 1.34 0.74
## 16 AZD1775 1 1.67 5.11 1.41 0.95 1.00 0.98
## 17 Pomalidomide 1 0.91 0.89 0.92 0.73 0.84 0.93
## 18 Rociletinib 1 NA 0.73 0.72 0.83 0.80 0.77
## 19 Selumetinib 1 4.01 2.88 1.10 0.79 0.80 0.79
## 20 Sorafenib 1 1.16 0.85 0.73 0.79 0.65 0.67
## 21 Sunitinib 1 0.96 0.92 0.94 0.84 0.88 0.86
## 22 Temsirolimus 1 1.32 1.33 1.35 0.93 0.90 0.83
## 23 Tivantinib 1 0.71 0.47 1.00 0.75 0.72 0.82
## 24 Trametinib 1 22.00 5.50 6.23 1.48 1.30 1.17
## 25 Vismodegib 1 0.71 0.94 0.60 0.85 0.82 0.89
## 26 VXc-984* 1 0.81 0.94 0.63 0.74 0.77 0.79
## 27 AZD8186 1 3.16 1.45 1.17 0.89 1.18 0.59
## 28 Osimertinib 1 0.31 0.81 0.82 0.72 0.86 0.88
## 29 Copanlisib 1 2.03 1.92 1.10 0.83 0.88 0.83
## 30 Belinostat 1 0.39 0.98 1.04 0.82 1.01 0.57
## 31 Pinometostat 1 0.65 0.87 0.70 0.70 0.81 0.50
## 32 Methoxyamine 1 0.92 1.07 1.20 1.03 1.11 1.03
## 33 Cediranib 1 2.05 1.21 0.71 0.97 0.99 1.10
## 34 Navitoclax 1 1.29 0.89 0.77 0.73 0.82 0.93
## 35 VX-970 1 0.34 0.68 3.57 0.84 0.82 0.82
## 36 Olaparib 1 2.81 1.88 0.93 0.80 0.73 0.44
## 37 Dabrafenib 1 1.20 3.33 1.22 0.83 0.92 0.88
## 38 Pazopanib 1 16.01 1.44 0.99 0.86 0.96 1.10
## 39 Veliparib 1 2.71 1.07 1.28 0.78 1.00 0.70
## 40 Tazemetostat 1 0.56 0.62 0.73 0.57 0.81 0.65
## 41 Entinostat 1 1.53 4.58 1.33 1.34 1.41 1.11
## 42 MLN0128 1 NA 0.35 0.88 1.10 0.87 0.97
## 43 Onalespib 1 0.73 0.48 0.97 0.75 0.96 1.25
## 44 Romidepsin 1 0.98 0.74 0.55 1.23 1.52 0.92
## 45 Talazoparib 1 1.36 0.54 0.68 2.95 1.65 1.00
## 46 Triapine 1 1.11 1.26 0.90 0.74 0.92 0.86
## 47 DMSO1 1 0.79 1.08 0.86 0.81 0.83 0.85
## 48 DMSO2 1 1.07 1.15 1.18 1.06 1.27 1.15Step 3: Oder the dataset by SRF value of 100nM concentration
drug_1hr <- drug_1hr[order(-drug_1hr$X100nM) , ]Step 4: Use the drug name as the row name for the R dataset
row.names(drug_1hr) <- drug_1hr$DoseStep 5: Remove the default rowname column, dose column, and the control column
drug_1hr <- drug_1hr [,3:8]## X10000nM X1000nM X100nM X10nM X1nM X0.1nM
## Trametinib 22.00 5.50 6.23 1.48 1.30 1.17
## VX-970 0.34 0.68 3.57 0.84 0.82 0.82
## Alisertib 0.81 0.00 1.61 1.17 1.13 0.94
## AZD1775 1.67 5.11 1.41 0.95 1.00 0.98
## Temsirolimus 1.32 1.33 1.35 0.93 0.90 0.83
## Entinostat 1.53 4.58 1.33 1.34 1.41 1.11
## Dasatinib NA 1.26 1.32 1.14 0.95 0.85
## Azacytidine 0.45 1.39 1.30 1.15 1.24 1.03
## Veliparib 2.71 1.07 1.28 0.78 1.00 0.70
## Dabrafenib 1.20 3.33 1.22 0.83 0.92 0.88
## Methoxyamine 0.92 1.07 1.20 1.03 1.11 1.03
## DMSO2 1.07 1.15 1.18 1.06 1.27 1.15
## AZD8186 3.16 1.45 1.17 0.89 1.18 0.59
## FAU 0.82 1.10 1.13 0.78 1.15 0.79
## Cabozantinib 1.44 1.12 1.11 0.98 0.94 0.72
## Selumetinib 4.01 2.88 1.10 0.79 0.80 0.79
## Copanlisib 2.03 1.92 1.10 0.83 0.88 0.83
## Belinostat 0.39 0.98 1.04 0.82 1.01 0.57
## INCB024360 0.97 1.10 1.01 0.91 1.21 1.13
## Lapatinib 0.37 0.98 1.01 0.90 1.01 0.92
## Tivantinib 0.71 0.47 1.00 0.75 0.72 0.82
## AMG 232 NA 6.06 0.99 0.70 0.90 0.74
## Pazopanib 16.01 1.44 0.99 0.86 0.96 1.10
## Onalespib 0.73 0.48 0.97 0.75 0.96 1.25
## Sunitinib 0.96 0.92 0.94 0.84 0.88 0.86
## Ibrutinib 1.59 1.13 0.93 0.84 1.02 0.90
## Olaparib 2.81 1.88 0.93 0.80 0.73 0.44
## Pomalidomide 0.91 0.89 0.92 0.73 0.84 0.93
## Triapine 1.11 1.26 0.90 0.74 0.92 0.86
## MLN0128 NA 0.35 0.88 1.10 0.87 0.97
## DMSO1 0.79 1.08 0.86 0.81 0.83 0.85
## Osimertinib 0.31 0.81 0.82 0.72 0.86 0.88
## Erlotinib 1.84 1.41 0.81 0.85 0.75 0.76
## Navitoclax 1.29 0.89 0.77 0.73 0.82 0.93
## AZD9291 1.99 0.91 0.76 0.64 0.82 0.69
## AMG337 0.96 1.07 0.75 0.86 0.82 0.67
## Sorafenib 1.16 0.85 0.73 0.79 0.65 0.67
## Tazemetostat 0.56 0.62 0.73 0.57 0.81 0.65
## Rociletinib NA 0.73 0.72 0.83 0.80 0.77
## Cediranib 2.05 1.21 0.71 0.97 0.99 1.10
## Pinometostat 0.65 0.87 0.70 0.70 0.81 0.50
## Birinapant 0.91 0.78 0.69 0.83 0.75 0.81
## Talazoparib 1.36 0.54 0.68 2.95 1.65 1.00
## VXc-984* 0.81 0.94 0.63 0.74 0.77 0.79
## Vismodegib 0.71 0.94 0.60 0.85 0.82 0.89
## Lenalidomide 0.95 1.11 0.58 0.99 1.34 0.74
## Romidepsin 0.98 0.74 0.55 1.23 1.52 0.92
## Bortezomib 0.70 1.05 0.35 0.72 0.94 0.57Step 6: Transform the dataset to data matrix
drug_1hr_matrix <- data.matrix(drug_1hr)Step 7: Install and load “gplot”" R package
install.packages("gplots")## Warning: unable to access index for repository <something sensible near you>/src/contrib:
## cannot open URL '<something sensible near you>/src/contrib/PACKAGES'## Warning: package 'gplots' is not available (for R version 3.4.3)## Warning: unable to access index for repository <something sensible near you>/bin/macosx/el-capitan/contrib/3.4:
## cannot open URL '<something sensible near you>/bin/macosx/el-capitan/contrib/3.4/PACKAGES'library(gplots)##
## Attaching package: 'gplots'## The following object is masked from 'package:stats':
##
## lowessStep 8: Install “RColorBrewer”" R oackage
install.packages("RColorBrewer", dependencies = TRUE)## Warning: unable to access index for repository <something sensible near you>/src/contrib:
## cannot open URL '<something sensible near you>/src/contrib/PACKAGES'## Warning: package 'RColorBrewer' is not available (for R version 3.4.3)## Warning: unable to access index for repository <something sensible near you>/bin/macosx/el-capitan/contrib/3.4:
## cannot open URL '<something sensible near you>/bin/macosx/el-capitan/contrib/3.4/PACKAGES'library(RColorBrewer)Step 9: Define color for heatmaps
my_palette <- colorRampPalette(c("blue","black","red")) (n=299)Step 10: Define breaks for colors
col_breaks = c(seq(0,0.99,length=100),seq(1,1.5, length=100), seq(1.51,2.5, length=100))Step 11: Generate the heatmap
heatmap.2(drug_1hr_matrix,dendrogram=“none”,scale=“none”,Colv=“NA”,Rowv=“NA”,main=“2GY after 2hr with Drug Only”,notecol=“black”, trace=“none”, col=my_palette, breaks=col_breaks, margin=c(6,6),key=TRUE,na.rm=TRUE,density.info=“none”,keysize=1)