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Analysis Commands.txt
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Analysis Commands.txt
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# Molecular Analysis
# R Studio Required
# Biotechnology Dendrogram- Circular, Rectangular, Horizontal, Phylogenic Tree making from Binary Data (0,1)
# heatmaps, Distance matrix, Simirality matrix ...more gifts to be added soon..... so ----- ##### star ####
# run below commands in R environment now -------------------------------- -_-
# copy and paste below commands in R studio
# install below packages to work all commands properly
library(readxl)
library(ggplot2)
library(factoextra)
library(pheatmap)
library(RColorBrewer)
# import DATASET excel File
newraw <- rawdata[ ,-1]
# here (-1) to omit 1st column and Zero/space for none row to omit
# a (newraw) named file will be saved
analysisfile <- newraw
rownames(analysisfile) <- c(rawdata$Genotypes)
# here (Genotypes) is 1st Column head names of raw excel file
# ignore (Warning message : Setting row____deprecated.
View(analysisfile)
#
scale.af <- scale(analysisfile)
# check row names changed to Genotype names or not??
require(stats)
distance.af <- dist(x = scale.af,
method = "euclidean")
x <- as.matrix(distance.af)
# [1:6] for 1st six rows and next [1:6] to see 1st six columns
# may round up this DISTANCE MATRIX (eucledian)
round(x, digits = 2)
# optional cmd
View(x)
require(stats)
cluster.af <- hclust(d = distance.af,
method = "complete")
# this will plot a Dendrogram (simple rectangular without colours)
plot(x = cluster.af)
fviz_dend(cluster.af, cex = 0.6, lwd = 0.9, k = 5,
rect = TRUE,
k_colors = "jco",
rect_border = "jco",
rect_fill = TRUE)
# to plot this rectangular dendrogram- horizontally
fviz_dend(cluster.af, cex = 1.2, lwd = 0.9, k = 5,
rect = TRUE,
k_colors = "jco",
rect_border = "jco",
rect_fill = TRUE,
horiz = TRUE)
# type = "circular", "rectangle", "phylogenic"
fviz_dend(cluster.af, cex = 0.8, lwd = 0.9, k = 5,
rect = TRUE,
k_colors = "jco",
rect_border = "jco",
rect_fill = TRUE,
type = "circular")
# use (repel = TRUE) in the end when ploting "phylogenic"
# layouts for "phylogenic" (phylo_layout = "layout_as_tree", "layout_with_lgl", "layout_with_drl", "layout.gem", "layout.mds")
# example
fviz_dend(cluster.af, cex = 1.2, lwd = 10, k = 5,
rect = TRUE,
k_colors = "jco",
rect_border = "jco",
rect_fill = TRUE,
type = "phylogenic",
repel = TRUE,
phylo_layout = "layout_as_tree")
# #########################
# change names first - name for heatmap (heading)
pheatmap(analysisfile, scale = "row", cutree_row= 5, cluster_rows = TRUE,
kmeans_k = NA, main = "Change Name in Formula", show_colnames = FALSE,
show_rownames = TRUE,
color = colorRampPalette(rev(brewer.pal(n = 5, name ="Paired")))(255))
# more color combinations are (name) = YlOrRd,YlOrB,YlGnBu,Set3,Set2,RdYlBu,
# Reds,RdBu,Purples,PuOr, PuBuGn,PRGn,Pastel2,Pastel1,Paired,OrRd,Oranges,Greys,Greens,GnBu
# if error than view () file - find "NA/NaN" then edit (breaks = ?) ABOVE
# cutree_row= 5 (number of groups of Genotype) or cutree_cols = 2
# brewer.pal here n = mini 3 and max. depend upon data palette