| title: “LABS44_A” |
| author: “JESSICA PAOLA AGUILAR SERVIN” |
| date: “2023-03-09” |
| output: html_document |
LABORATORIO
ADICIONALES library(dplyr) library(seurat) library(patchwork) library(ggplot2) library(complexheatmap) library(seuratdata) library(hdWGCNA) library(WGCNA)
install.packages(gplots) library (gplot)
CARGAR LIBRERIA NECESARIA
library(stats)PAQUETES DE GPLOTS. Attaching package: ‘gplots’.lowess ANEXAMOS DATOS
h1 <- c(10,20,10,20,10,20,10,20)
h2 <- c(20,10,20,10,20,10,20,10)
l1 <- c(1,3,1,3,1,3,1,3)
l2 <- c(3,1,3,1,3,1,3,1)
mat <- rbind(h1,h2,l1,l2)CREAR GRÁFICO
par(mfrow =c(1,1), mar=c(4,4,1,1))
plot(1:8,rep(0,8), ylim=c(0,35), pch="", xlab="Time", ylab="Gene Expression")
for (i in 1:nrow(mat)) {lines(1:8,mat[i,], lwd=3, col=i)}
legend(1,35,rownames(mat), 1:4, cex=0.7)
CALCULAR DISTANCIA
dist(mat)## h1 h2 l1
## h2 28.284271
## l1 38.470768 40.496913
## l2 40.496913 38.470768 5.656854SACAR PLOT-use the default for linkage method: complete
plot(hclust(dist(mat)))
CALCULAR HEATMAP DE RENGLONES heatmap (mat, Colv=NA, col= greenred(10), scale = “row”) heatmap (mat, Colv=NA, col=greenred(10), scale = “none”)
mat.scaled<- t(scale(t(mat), center=TRUE, scale = TRUE))
mat.scaled## [,1] [,2] [,3] [,4] [,5] [,6] [,7]
## h1 -0.9354143 0.9354143 -0.9354143 0.9354143 -0.9354143 0.9354143 -0.9354143
## h2 0.9354143 -0.9354143 0.9354143 -0.9354143 0.9354143 -0.9354143 0.9354143
## l1 -0.9354143 0.9354143 -0.9354143 0.9354143 -0.9354143 0.9354143 -0.9354143
## l2 0.9354143 -0.9354143 0.9354143 -0.9354143 0.9354143 -0.9354143 0.9354143
## [,8]
## h1 0.9354143
## h2 -0.9354143
## l1 0.9354143
## l2 -0.9354143
## attr(,"scaled:center")
## h1 h2 l1 l2
## 15 15 2 2
## attr(,"scaled:scale")
## h1 h2 l1 l2
## 5.345225 5.345225 1.069045 1.069045DISTANCIA ENTRE GENES
dist(mat.scaled)## h1 h2 l1
## h2 5.291503
## l1 0.000000 5.291503
## l2 5.291503 0.000000 5.291503NUEVO GRAFICO
plot(hclust(dist(mat.scaled)))
heatmap(mat.scaled, Colv = NA, scale = “none”)
CORRELACION ENTRE GENES
cor(t(mat))## h1 h2 l1 l2
## h1 1 -1 1 -1
## h2 -1 1 -1 1
## l1 1 -1 1 -1
## l2 -1 1 -1 1DISTANCIA EN LAS CORRELACIONES
1- cor(t(mat))## h1 h2 l1 l2
## h1 0 2 0 2
## h2 2 0 2 0
## l1 0 2 0 2
## l2 2 0 2 0GRAFICAS
hc <- hclust(as.dist(1-cor(t(mat))))
plot(hc)
PRIMERA ADECUACION HEATMAPS
heatmap(mat, Colv = NA, Rowv=as.dendrogram(hc), scale = "none")
SEGUNDA oPCION DE HEATMAPS
heatmap(mat, trace = "none", Colv= NA, dendrogram = "row", scale = "none")## Warning in plot.window(...): "trace" is not a graphical parameter## Warning in plot.window(...): "dendrogram" is not a graphical parameter## Warning in plot.xy(xy, type, ...): "trace" is not a graphical parameter## Warning in plot.xy(xy, type, ...): "dendrogram" is not a graphical parameter## Warning in title(...): "trace" is not a graphical parameter## Warning in title(...): "dendrogram" is not a graphical parameter
TERCERA OPCION HEATMAPS
heatmap(mat, trace = "none", Colv= NA, dendrogram = "row", scale = "row")## Warning in plot.window(...): "trace" is not a graphical parameter## Warning in plot.window(...): "dendrogram" is not a graphical parameter## Warning in plot.xy(xy, type, ...): "trace" is not a graphical parameter## Warning in plot.xy(xy, type, ...): "dendrogram" is not a graphical parameter## Warning in title(...): "trace" is not a graphical parameter## Warning in title(...): "dendrogram" is not a graphical parameter
CUARTA OPCION HEATMAPS USANDO DISTANCIA ECLUDIANA
heatmap (t(scale(t(mat), center=TRUE, scale=TRUE)), trace = "none", Colv= NA, dendrogram = "row")## Warning in plot.window(...): "trace" is not a graphical parameter## Warning in plot.window(...): "dendrogram" is not a graphical parameter## Warning in plot.xy(xy, type, ...): "trace" is not a graphical parameter## Warning in plot.xy(xy, type, ...): "dendrogram" is not a graphical parameter## Warning in title(...): "trace" is not a graphical parameter## Warning in title(...): "dendrogram" is not a graphical parameter
USO 1-COR (x) DE CORRELACION EN HEAT
heatmap (mat, trace = "none",
Colv= NA, dendrogram = "row",
scale = "none",
hclust=function(x) hclust(x, method="complete"), distfun=function(x) as.dist(1-cor(t(x))))## Warning in plot.window(...): "trace" is not a graphical parameter## Warning in plot.window(...): "dendrogram" is not a graphical parameter## Warning in plot.xy(xy, type, ...): "trace" is not a graphical parameter## Warning in plot.xy(xy, type, ...): "dendrogram" is not a graphical parameter## Warning in title(...): "trace" is not a graphical parameter## Warning in title(...): "dendrogram" is not a graphical parameter
OTRA ESCALA REPRESENTADA POR LOS COLORES
heatmap(mat, trace = "none",
Colv= NA, dendrogram = "row",
scale = "row",
hclust=function(x) hclust(x, method='complete'), distfun=function(x) as.dist(1-cor(t(x))))## Warning in plot.window(...): "trace" is not a graphical parameter## Warning in plot.window(...): "dendrogram" is not a graphical parameter## Warning in plot.xy(xy, type, ...): "trace" is not a graphical parameter## Warning in plot.xy(xy, type, ...): "dendrogram" is not a graphical parameter## Warning in title(...): "trace" is not a graphical parameter## Warning in title(...): "dendrogram" is not a graphical parameter
ULTIMA COLORACION DE CLUSTERS
heatmap(t(scale(t(mat), center=TRUE, scale=TRUE)), trace = "none",
Colv= NA, dendrogram = "row",
hclust=function(x) hclust(x, method='complete'), distfun=function(x) as.dist(1-cor(t(x))))## Warning in plot.window(...): "trace" is not a graphical parameter## Warning in plot.window(...): "dendrogram" is not a graphical parameter## Warning in plot.xy(xy, type, ...): "trace" is not a graphical parameter## Warning in plot.xy(xy, type, ...): "dendrogram" is not a graphical parameter## Warning in title(...): "trace" is not a graphical parameter## Warning in title(...): "dendrogram" is not a graphical parameter