Matt:LabNotes/2015-12-11: Difference between revisions
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>Mzcai (Created page with " load.packages("gplots") library(gplots) tileA <- read.table("C:\\Users\\Matt\\Dropbox\\GradZhangLab\\SpatialSearching\\20151029_20XDecoding\\DARTFISH_BA8_suppv2_20151029_Ti...") |
>Mzcai mNo edit summary |
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(One intermediate revision by the same user not shown) | |||
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=20X DARTFISH Differential Expression & Subpopulation Analysis= | |||
==Heatmap== | |||
*http://sebastianraschka.com/Articles/heatmaps_in_r.html | |||
load.packages("gplots") | load.packages("gplots") | ||
library(gplots) | library(gplots) | ||
tileA <- read.table("C:\\Users\\Matt\\Dropbox\\GradZhangLab\\SpatialSearching\\20151029_20XDecoding\\DARTFISH_BA8_suppv2_20151029_TileA_240genes21bins.txt",header=TRUE,sep="\t",row.names=1) | tileA <- read.table("C:\\Users\\Matt\\Dropbox\\GradZhangLab\\SpatialSearching\\20151029_20XDecoding\\DARTFISH_BA8_suppv2_20151029_TileA_240genes21bins.txt",header=TRUE,sep="\t",row.names=1) | ||
tileB <- read.table("C:\\Users\\Matt\\Dropbox\\GradZhangLab\\SpatialSearching\\20151029_20XDecoding\\DARTFISH_BA8_suppv2_20151029_TileB_240genes21bins.txt",header=TRUE,sep="\t",row.names=1) | tileB <- read.table("C:\\Users\\Matt\\Dropbox\\GradZhangLab\\SpatialSearching\\20151029_20XDecoding\\DARTFISH_BA8_suppv2_20151029_TileB_240genes21bins.txt",header=TRUE,sep="\t",row.names=1) | ||
y <- as.matrix(tileA) | y <- as.matrix(tileA) | ||
z <- as.matrix(tileB) | z <- as.matrix(tileB) | ||
my_palette <- colorRampPalette(c("turquoise","yellow","red"))(n=299) | |||
col_breaks=c(seq(-4,-1,length=100),seq(-1,1,length=100),seq(1,4,length=100)) | |||
heatmap.2(y,density.info="none",trace="none",col=my_palette,breaks=col_breaks) | |||
==PCA== | |||
==tSNE== |
Latest revision as of 03:55, 15 December 2015
20X DARTFISH Differential Expression & Subpopulation Analysis[edit]
Heatmap[edit]
load.packages("gplots") library(gplots)
tileA <- read.table("C:\\Users\\Matt\\Dropbox\\GradZhangLab\\SpatialSearching\\20151029_20XDecoding\\DARTFISH_BA8_suppv2_20151029_TileA_240genes21bins.txt",header=TRUE,sep="\t",row.names=1) tileB <- read.table("C:\\Users\\Matt\\Dropbox\\GradZhangLab\\SpatialSearching\\20151029_20XDecoding\\DARTFISH_BA8_suppv2_20151029_TileB_240genes21bins.txt",header=TRUE,sep="\t",row.names=1) y <- as.matrix(tileA) z <- as.matrix(tileB)
my_palette <- colorRampPalette(c("turquoise","yellow","red"))(n=299) col_breaks=c(seq(-4,-1,length=100),seq(-1,1,length=100),seq(1,4,length=100))
heatmap.2(y,density.info="none",trace="none",col=my_palette,breaks=col_breaks)