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inst/doc/chromoMap.R
In chromoMap: Interactive Genomic Visualization of Biological Data
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
#knitr::opts_chunk$set(widgetframe_widgetsdir = 'widgets')
## ---- eval=FALSE--------------------------------------------------------------
# install.packages("chromoMap")
#
## -----------------------------------------------------------------------------
# chromosome files
chr_file_1 = "chr_file_without_centromere.txt"
chr_file_2 = "chr_file_with_centromere.txt"
# annotation files
anno_file_1 = "annotation_pos.txt"
anno_file_2 = "annotation_pos_and_neg.txt"
## ----echo=F-------------------------------------------------------------------
library(chromoMap)
#my_path <- "C:/Users/laksh/Documents/PROJECTS/chromoMap_v3_production/chromoMap/vignettes/data/"
my_path = "data/"
chr_file_1 <- paste0(my_path,chr_file_1)
chr_file_2 <- paste0(my_path,chr_file_2)
anno_file_1 <-paste0(my_path,anno_file_1)
anno_file_2 <-paste0(my_path,anno_file_2)
anno_file_cate <- paste0(my_path,"discrete_colormap.txt")
## -----------------------------------------------------------------------------
head(read.table(chr_file_1,sep = "\t"))
## -----------------------------------------------------------------------------
head(read.table(chr_file_2,sep = "\t"))
## -----------------------------------------------------------------------------
head(read.table(anno_file_1,sep = "\t"))
## -----------------------------------------------------------------------------
head(read.table(anno_file_2,sep = "\t"))
## ----eval=F-------------------------------------------------------------------
# # passing data.frames directly instead of files
# chromoMap(list(chr.data),list(anno.data))
# # for polyploidy
# chromoMap(list(chr.data1,chr.data2),
# list(anno.data1,anno.data2),ploidy = 2)
#
## ---- eval=F------------------------------------------------------------------
# library(chromoMap)
# chromoMap(chr_file_1,anno_file_1)
#
## ---- echo=F, fig.height=2----------------------------------------------------
chromoMap(chr_file_1,anno_file_1,canvas_height = 200,id="cmap1")
## ---- eval=F------------------------------------------------------------------
# library(chromoMap)
# chromoMap(chr_file_2,anno_file_1)
#
## ---- echo=F, fig.height=2----------------------------------------------------
chromoMap(chr_file_2,anno_file_1,canvas_height = 200,id="cmap189564")
## ---- eval=F------------------------------------------------------------------
# library(chromoMap)
# chromoMap(c(chr_file_1,chr_file_1),c(anno_file_1,anno_file_2),
# ploidy = 2)
#
## ---- echo=F, fig.height=2----------------------------------------------------
chromoMap(c(chr_file_1,chr_file_1),c(anno_file_1,anno_file_2),
ploidy = 2,canvas_height = 300,id="cmap2")
## ----eval=F-------------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",segment_annotation = T)
#
## ---- eval=F------------------------------------------------------------------
# # default value
# library(chromoMap)
# chromoMap(chr_file_1,anno_file_1,
# n_win.factor = 1,
# win.summary.display=T)
#
## ---- echo=F, fig.height=2----------------------------------------------------
chromoMap(chr_file_1,anno_file_1,canvas_height = 200,
id="cmapRR1",n_win.factor = 1,
win.summary.display=T)
## ---- eval=F------------------------------------------------------------------
# library(chromoMap)
# chromoMap(chr_file_1,anno_file_1,
# n_win.factor = 3,
# win.summary.display = T)
#
## ---- echo=F, fig.height=2,fig.width=1----------------------------------------
chromoMap(chr_file_1,anno_file_1,canvas_height = 200,id="cmapRR2",
n_win.factor = 3,win.summary.display = T)
## ---- eval=F------------------------------------------------------------------
# library(chromoMap)
# chromoMap(chr_file_1,anno_file_1,
# fixed.window = T,
# window.size = 5,
# win.summary.display = T)
#
## ---- echo=F, fig.height=2,fig.width=1----------------------------------------
chromoMap(chr_file_1,anno_file_1,canvas_height = 200,id="cmapRRu2",
fixed.window = T,window.size = 5,win.summary.display = T)
## ----eval=F-------------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# data_based_color_map = T,
# data_type = "categorical",
# data_colors = list(c("orange","yellow")))
#
## ---- echo=F, fig.height=3----------------------------------------------------
chromoMap(chr_file_1,"data/discrete_colormap.txt",data_based_color_map = T,data_type = "categorical",legend = T,canvas_height = 250,id="cmap310",data_colors = list(c("orange","yellow")),
lg_x = 15)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric")
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_2,data_based_color_map = T,data_type = "numeric",legend = T,canvas_height = 300,id="cmap4",lg_y = 50)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# data_based_color_map = T,
# data_type = "numeric",
# aggregate_func = "sum")
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(c("chromosome_file_set_1.txt","chromosome_file_set_2.txt")
# ,c("annotation_file_set_1.txt","annotation_file_set_2.txt"),
# ploidy = 2, data_based_color_map = T,data_type = "numeric"
# ,aggregate_func = c("avg","sum"))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_1,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "bar")
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_1,data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="cmap5",lg_y = 50,
plots = "bar",plot_ticks = 3)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_1,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "bar",
# heat_map = F)
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_1,data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="cmap51",lg_y = 50,
plots = "bar",heat_map = F,plot_ticks = 3)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "scatter")
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_2,data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="cmap6",lg_y = 50,
plots = "scatter",left_margin = 60,plot_height = 40)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "tags")
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_2,data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="cmap7",
plots = "tags")
## ----echo=F-------------------------------------------------------------------
library(knitr)
OPERATION_TYPE_LABEL = c("eq","lt","gt","lte","gte","gtalt","gtolt","gtealte","gteolte")
DESCRIPTION = c("equal","less than","greater than","less than equal","greater than equal","greater than AND less than","greater than OR less than","greater than equal AND less than equal","greater than equal OR less than equal")
USAGE_EXAMPLE = c('list(c("eq",5))','list(c("lt",-5))','list(c("gt",6))','list(c("lte",6))','list(c("gte",6))','list(c("gtalt",5,-5))','list(c("gtolt",5,-5))','list(c("gtealte",5,-5))','list(c("gteolte",5,-5))')
gggg = data.frame(OPERATION_TYPE_LABEL,DESCRIPTION,USAGE_EXAMPLE)
colnames(gggg)=c("operation type label","description","usage example")
kable(gggg)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "tags",
# tag_filter = list(c("lt",0)))
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_2,data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="cmap8",
plots = "tags",tag_filter = list(c("lt",0)))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_1,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "bar",
# plot_filter = list(c("gte",50,"green")))
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_1,data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="cmap9",
plots = "bar",plot_filter = list(c("gte",50,"green")),plot_ticks = 3)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "scatter",
# plot_filter = list(c("lt",0,"red")))
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_2,data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="cmap10",lg_y = 50,
plots = "scatter",left_margin = 60,plot_filter = list(c("lt",0,"red")),plot_height = 40)
## ----echo=F-------------------------------------------------------------------
anno_file_3 <- read.table("data/ANNO_DATA_FOR_CATSCATTER.txt")
## -----------------------------------------------------------------------------
head(anno_file_3)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_3,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "scatter",
# plot_filter = list(c("col","byCategory")),
# ch2D.colors = c("pink3","orange3","purple","blue2"))
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,"data/ANNO_DATA_FOR_CATSCATTER.txt",data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="cmapnew10",lg_y = 50,
plots = "scatter",left_margin = 60,plot_filter = list(c("col","byCategory")),plot_height = 40,
ch2D.colors = c("pink3","orange3","purple","blue2"),canvas_width = 600,
ch2D.lg_y = 100)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# chr.2D.plot = T)
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_2,chr.2D.plot = T,canvas_height = 300,id="cmaphyd10")
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# chr.2D.plot = T,
# plot_filter = list(c("col","byNumber")))
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_2,chr.2D.plot = T,canvas_height = 300,id="cmaphiygd10",plot_filter = list(c("col","byNumber")),
lg_x = 10)
## -----------------------------------------------------------------------------
head(read.table(anno_file_cate))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_cate,
# chr.2D.plot = T,
# plot_filter = list(c("col","byCategory")),
# ch2D.colors = c("red","blue"))
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_cate,chr.2D.plot = T,canvas_height = 300,id="cmtrphiygd10",plot_filter = list(c("col","byCategory")),
ch2D.colors = c("red","blue"),ch2D.lg_x = 15
)
## ----echo=F-------------------------------------------------------------------
chr_file <- "data/SLINK_chr.txt"
anno_file <- "data/SLINK_anno.txt"
link_data <- read.csv("data/SLINK22.csv",header = T)
## -----------------------------------------------------------------------------
head(link_data)
## ----eval=F-------------------------------------------------------------------
# chromoMap(chr_file, anno_file,
# # main arguments
# show.links = T,
# loci_links = link_data[,c(1:4)],
# links.colors = "red2",
# #plot adjustments
# ch_gap = 50,
# y_chr_scale = 100,
# top_margin = 100,
# )
## ----echo=F,fig.height=4.0----------------------------------------------------
chromoMap(chr_file, anno_file,
show.links = T,
loci_links = link_data[,c(1:4)],
#plot adjustments
links.colors = "red2",
ch_gap = 50,
y_chr_scale = 100,
top_margin = 100,
id="cnew1"
)
## ----eval=F-------------------------------------------------------------------
# chromoMap(chr_file, anno_file,
# # main arguments
# show.links = T,
# loci_links = link_data,
# links.colors = c("red2","blue2"),
# #plot adjustments
# ch_gap = 50,
# y_chr_scale = 100,
# top_margin = 100,
# links.lg_y = 300
# )
## ----echo=F,fig.height=4.0----------------------------------------------------
chromoMap(chr_file, anno_file,
show.links = T,
loci_links = link_data,
#plot adjustments
links.colors = c("red2","blue2"),
ch_gap = 50,
y_chr_scale = 100,
top_margin = 100,
id="cnew2",
canvas_width = 600,
links.lg_y = 30
)
## ----echo=F-------------------------------------------------------------------
link_data <- read.csv("data/SLINK_link2.csv",header = F)
## ----eval=F-------------------------------------------------------------------
# chromoMap(chr_file, anno_file,
# # main arguments
# show.links = T,
# loci_links = link_data,
# links.colors = c("red2","blue2","orange3","purple"),
# #plot adjustments
# ch_gap = 50,
# y_chr_scale = 100,
# top_margin = 100,
# )
## ----echo=F,fig.height=4.0----------------------------------------------------
chromoMap(chr_file, anno_file,
show.links = T,
loci_links = link_data,
#plot adjustments
links.colors = c("red2","blue2","orange3","purple"),
ch_gap = 50,
y_chr_scale = 100,
top_margin = 100,
id="cnew3",
canvas_width = 600,
links.lg_y = 30
)
## ----eval=F-------------------------------------------------------------------
# chromoMap(chr_file, anno_file,
# # main arguments
# show.links = T,
# loci_links = link_data,
# links.colors = c("red2","blue2","orange3","purple"),
# directed.edges = T,
# #plot adjustments
# ch_gap = 50,
# y_chr_scale = 100,
# top_margin = 100,
# )
## ----echo=F,fig.height=4.0----------------------------------------------------
chromoMap(chr_file, anno_file,
show.links = T,
loci_links = link_data,
#plot adjustments
links.colors = c("red2","blue2","orange3","purple"),
ch_gap = 50,
y_chr_scale = 100,
top_margin = 100,
id="cnew33",
canvas_width = 600,
links.lg_y = 30,
directed.edges = T
)
## ----echo=F-------------------------------------------------------------------
chr_file <- "data/TEST_chr.txt"
anno_file <- "data/TEST_anno.txt"
link_data <- read.csv("data/TEST_LINKSSS.csv",header = T)
## ----eval=F-------------------------------------------------------------------
# chromoMap(chr_file, anno_file,
# # main arguments
# segment_annotation = T,
# show.links = T,
# loci_links = link_data,
# links.colors = c("orange3","purple","green2"),
# #plot adjustments
# ch_gap = 50,
# y_chr_scale = 100,
# top_margin = 100,
# )
## ----echo=F,fig.height=4.0----------------------------------------------------
chromoMap(chr_file, anno_file,
show.links = T,
loci_links = link_data,
segment_annotation = T,
#plot adjustments
links.colors = c("orange3","purple","green2"),
ch_gap = 50,
y_chr_scale = 100,
top_margin = 100,
id="cnew4",
canvas_width = 600,
links.lg_y = 30
)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# canvas_width = 600,
# canvas_height = 700)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# title = "my first chromoMap plot")
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# title = "my first chromoMap plot",
# title_font_size = 12)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# top_margin = 25,
# left_margin = 15)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# chr_color = c("orange"))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(c("chromosome_file_set_1.txt","chromosome_file_set_2.txt")
# ,c("annotation_file_set_1.txt","annotation_file_set_2.txt"),
# ploidy = 2,
# chr_color = c("pink","blue"))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# anno_col = c("orange"))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(c("chromosome_file_set_1.txt","chromosome_file_set_2.txt")
# ,c("annotation_file_set_1.txt","annotation_file_set_2.txt"),
# ploidy = 2,
# anno_col = c("pink","blue"))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# chr_width = 4,
# chr_length = 5)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# ch_gap = 6)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# chr_curve = 5)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# chr_text = F)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(c("chromosome_file_set_1.txt","chromosome_file_set_2.txt")
# ,c("annotation_file_set_1.txt","annotation_file_set_2.txt"),
# ploidy = 2,
# chr_text = c(T,F))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# interactivity = F)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# scale.suffix = "cM")
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# display.chr = c(F))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# guides = T,
# guides_color = "black")
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# id="my_plot_1")
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_1,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "bar",
# ref_line = T,
# refl_pos = 15)
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_1,data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="cmap21",
plots = "bar",plot_ticks = 3,ref_line = T,
refl_pos = 15)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "scatter",
# ref_line = T,
# refl_pos = 20)
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_2,data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="cmap22",lg_y = 50,
plots = "scatter",left_margin = 60,plot_height = 40,ref_line = T,refl_pos = 20)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "scatter",
# plot_height = 50)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "scatter",
# plot_color = "orange")
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "tags",
# tagColor = "orange")
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "scatter",
# plot_ticks = 3,
# plot_y_domain = list(c(-5,5)))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(c(chr_file_1,chr_file_1),c(anno_file_1,anno_file_2),
# ploidy = 2
# data_based_color_map = T,
# data_type = "numeric",
# plots = c("bar","scatter"),
# plot_height = 40,
# plot_color = c("green","red"),
# ref_line = T,
# refl_pos = 20,
# #gridline arguments
# vertical_grid = T,
# grid_array = c(1,54,100,420,621))
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(c(chr_file_1,chr_file_1),c(anno_file_1,anno_file_2),data_based_color_map = T,data_type = "numeric",canvas_height = 400,id="cmap23",ploidy = 2,
plots = c("bar","scatter"),
plot_height = 40,
plot_color = c("green","red"),
ref_line = T,
refl_pos = 20,
vertical_grid = T,
grid_array = c(1,54,100,420,621),left_margin = 60)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(c(chr_file_1,chr_file_1),c(anno_file_1,anno_file_2),
# ploidy = 2
# data_based_color_map = T,
# data_type = "numeric",
# plots = c("bar","scatter"),
# plot_height = 40,
# plot_color = c("green","red"),
# ref_line = T,
# refl_pos = 20,
# #gridline arguments
# vertical_grid = T,
# grid_array = c(1,54,100,420,621),
# grid_text = c("","","mark 1","region 1",""))
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(c(chr_file_1,chr_file_1),c(anno_file_1,anno_file_2),data_based_color_map = T,data_type = "numeric",canvas_height = 400,id="cnew4125",ploidy = 2,
plots = c("bar","scatter"),
plot_height = 40,
plot_color = c("green","red"),
ref_line = T,
refl_pos = 20,
vertical_grid = T,
grid_array = c(1,54,100,420,621),left_margin = 60
,grid_text = c("","","mark 1","region 1",""))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "scatter",
# #highlighting a region on chr1
# vertical_grid = T,
# grid_array = c(550,754))
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_2,data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="new7777",lg_y = 50,
plots = "scatter",left_margin = 60,plot_height = 40,
vertical_grid = T,
grid_array = c(550,754))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "scatter",
# #zoom in
# region = c("chr1:1:550:754"))
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_2,data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="new77894",lg_y = 50,
plots = "scatter",left_margin = 60,plot_height = 40,
region = c("chr1:1:550:754"))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "scatter",
# #zoom in
# region = c("chr1:1:550:754","chr2:1:221:450"))
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_2,data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="newh745994",lg_y = 50,
plots = "scatter",left_margin = 60,plot_height = 40,
region = c("chr1:1:550:754","chr2:1:221:450"))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# data_based_color_map = T,
# data_type = "categorical",
# legend = T)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(c("chromosome_file_set_1.txt","chromosome_file_set_2.txt")
# ,c("annotation_file_set_1.txt","annotation_file_set_2.txt"),
# ploidy = 2,
# data_based_color_map = T,
# data_type = "numeric",
# legend = c(F,T))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# data_based_color_map = T,
# data_type = "categorical",
# legend = T, lg_x = 100,
# lg_y = 250)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# labels=T)
## ---- echo=F, fig.height=3----------------------------------------------------
chromoMap(chr_file_1,"data/discrete_colormap.txt",
canvas_height = 250,id="cmap1254",labels = T)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# labels=T,
# label_font = 12,
# label_angle = -65)
## ---- echo=F, fig.height=3----------------------------------------------------
chromoMap(chr_file_1,"data/discrete_colormap.txt",
canvas_height = 250,id="cmap1925",labels = T,
label_font = 10,
label_angle = -65)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# labels=T,
# label_angle = -65,
# chr_length = 6,
# chr_width = 25,
# canvas_width = 800)
## ---- echo=F, fig.height=3----------------------------------------------------
chromoMap(chr_file_1,"data/discrete_colormap.txt",
canvas_height = 250,id="cmap17445",labels = T,
chr_length = 7,
chr_width = 25,
canvas_width = 900,label_font = 10,label_angle = -65)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# hlinks=T)
## ----eval=FALSE---------------------------------------------------------------
# library(shiny)
# library(chromoMap)
#
# # Define UI for application that draws chromoMap
# ui <- fluidPage(
#
# # Application title
# titlePanel("An example of chromoMap in Shiny"),
#
# # you can use GUI controls for your chromoMap
# sidebarLayout(
# sidebarPanel(
# #some code
# ),
#
# # Show a plot of the generated distribution
# mainPanel(
# chromoMapOutput("myChromoMap")
# )
# )
# )
#
# # Define server logic required to draw chromoMap
# server <- function(input, output) {
#
# output$myChromoMap <- renderChromoMap({
# chromoMap("chromosome_file.txt","annotation_file.txt")
# })
# }
#
# # Run the application
# shinyApp(ui = ui, server = server)
#
## -----------------------------------------------------------------------------
sessionInfo()
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## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
#knitr::opts_chunk$set(widgetframe_widgetsdir = 'widgets')
## ---- eval=FALSE--------------------------------------------------------------
# install.packages("chromoMap")
#
## -----------------------------------------------------------------------------
# chromosome files
chr_file_1 = "chr_file_without_centromere.txt"
chr_file_2 = "chr_file_with_centromere.txt"
# annotation files
anno_file_1 = "annotation_pos.txt"
anno_file_2 = "annotation_pos_and_neg.txt"
## ----echo=F-------------------------------------------------------------------
library(chromoMap)
#my_path <- "C:/Users/laksh/Documents/PROJECTS/chromoMap_v3_production/chromoMap/vignettes/data/"
my_path = "data/"
chr_file_1 <- paste0(my_path,chr_file_1)
chr_file_2 <- paste0(my_path,chr_file_2)
anno_file_1 <-paste0(my_path,anno_file_1)
anno_file_2 <-paste0(my_path,anno_file_2)
anno_file_cate <- paste0(my_path,"discrete_colormap.txt")
## -----------------------------------------------------------------------------
head(read.table(chr_file_1,sep = "\t"))
## -----------------------------------------------------------------------------
head(read.table(chr_file_2,sep = "\t"))
## -----------------------------------------------------------------------------
head(read.table(anno_file_1,sep = "\t"))
## -----------------------------------------------------------------------------
head(read.table(anno_file_2,sep = "\t"))
## ----eval=F-------------------------------------------------------------------
# # passing data.frames directly instead of files
# chromoMap(list(chr.data),list(anno.data))
# # for polyploidy
# chromoMap(list(chr.data1,chr.data2),
# list(anno.data1,anno.data2),ploidy = 2)
#
## ---- eval=F------------------------------------------------------------------
# library(chromoMap)
# chromoMap(chr_file_1,anno_file_1)
#
## ---- echo=F, fig.height=2----------------------------------------------------
chromoMap(chr_file_1,anno_file_1,canvas_height = 200,id="cmap1")
## ---- eval=F------------------------------------------------------------------
# library(chromoMap)
# chromoMap(chr_file_2,anno_file_1)
#
## ---- echo=F, fig.height=2----------------------------------------------------
chromoMap(chr_file_2,anno_file_1,canvas_height = 200,id="cmap189564")
## ---- eval=F------------------------------------------------------------------
# library(chromoMap)
# chromoMap(c(chr_file_1,chr_file_1),c(anno_file_1,anno_file_2),
# ploidy = 2)
#
## ---- echo=F, fig.height=2----------------------------------------------------
chromoMap(c(chr_file_1,chr_file_1),c(anno_file_1,anno_file_2),
ploidy = 2,canvas_height = 300,id="cmap2")
## ----eval=F-------------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",segment_annotation = T)
#
## ---- eval=F------------------------------------------------------------------
# # default value
# library(chromoMap)
# chromoMap(chr_file_1,anno_file_1,
# n_win.factor = 1,
# win.summary.display=T)
#
## ---- echo=F, fig.height=2----------------------------------------------------
chromoMap(chr_file_1,anno_file_1,canvas_height = 200,
id="cmapRR1",n_win.factor = 1,
win.summary.display=T)
## ---- eval=F------------------------------------------------------------------
# library(chromoMap)
# chromoMap(chr_file_1,anno_file_1,
# n_win.factor = 3,
# win.summary.display = T)
#
## ---- echo=F, fig.height=2,fig.width=1----------------------------------------
chromoMap(chr_file_1,anno_file_1,canvas_height = 200,id="cmapRR2",
n_win.factor = 3,win.summary.display = T)
## ---- eval=F------------------------------------------------------------------
# library(chromoMap)
# chromoMap(chr_file_1,anno_file_1,
# fixed.window = T,
# window.size = 5,
# win.summary.display = T)
#
## ---- echo=F, fig.height=2,fig.width=1----------------------------------------
chromoMap(chr_file_1,anno_file_1,canvas_height = 200,id="cmapRRu2",
fixed.window = T,window.size = 5,win.summary.display = T)
## ----eval=F-------------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# data_based_color_map = T,
# data_type = "categorical",
# data_colors = list(c("orange","yellow")))
#
## ---- echo=F, fig.height=3----------------------------------------------------
chromoMap(chr_file_1,"data/discrete_colormap.txt",data_based_color_map = T,data_type = "categorical",legend = T,canvas_height = 250,id="cmap310",data_colors = list(c("orange","yellow")),
lg_x = 15)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric")
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_2,data_based_color_map = T,data_type = "numeric",legend = T,canvas_height = 300,id="cmap4",lg_y = 50)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# data_based_color_map = T,
# data_type = "numeric",
# aggregate_func = "sum")
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(c("chromosome_file_set_1.txt","chromosome_file_set_2.txt")
# ,c("annotation_file_set_1.txt","annotation_file_set_2.txt"),
# ploidy = 2, data_based_color_map = T,data_type = "numeric"
# ,aggregate_func = c("avg","sum"))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_1,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "bar")
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_1,data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="cmap5",lg_y = 50,
plots = "bar",plot_ticks = 3)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_1,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "bar",
# heat_map = F)
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_1,data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="cmap51",lg_y = 50,
plots = "bar",heat_map = F,plot_ticks = 3)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "scatter")
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_2,data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="cmap6",lg_y = 50,
plots = "scatter",left_margin = 60,plot_height = 40)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "tags")
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_2,data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="cmap7",
plots = "tags")
## ----echo=F-------------------------------------------------------------------
library(knitr)
OPERATION_TYPE_LABEL = c("eq","lt","gt","lte","gte","gtalt","gtolt","gtealte","gteolte")
DESCRIPTION = c("equal","less than","greater than","less than equal","greater than equal","greater than AND less than","greater than OR less than","greater than equal AND less than equal","greater than equal OR less than equal")
USAGE_EXAMPLE = c('list(c("eq",5))','list(c("lt",-5))','list(c("gt",6))','list(c("lte",6))','list(c("gte",6))','list(c("gtalt",5,-5))','list(c("gtolt",5,-5))','list(c("gtealte",5,-5))','list(c("gteolte",5,-5))')
gggg = data.frame(OPERATION_TYPE_LABEL,DESCRIPTION,USAGE_EXAMPLE)
colnames(gggg)=c("operation type label","description","usage example")
kable(gggg)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "tags",
# tag_filter = list(c("lt",0)))
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_2,data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="cmap8",
plots = "tags",tag_filter = list(c("lt",0)))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_1,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "bar",
# plot_filter = list(c("gte",50,"green")))
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_1,data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="cmap9",
plots = "bar",plot_filter = list(c("gte",50,"green")),plot_ticks = 3)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "scatter",
# plot_filter = list(c("lt",0,"red")))
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_2,data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="cmap10",lg_y = 50,
plots = "scatter",left_margin = 60,plot_filter = list(c("lt",0,"red")),plot_height = 40)
## ----echo=F-------------------------------------------------------------------
anno_file_3 <- read.table("data/ANNO_DATA_FOR_CATSCATTER.txt")
## -----------------------------------------------------------------------------
head(anno_file_3)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_3,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "scatter",
# plot_filter = list(c("col","byCategory")),
# ch2D.colors = c("pink3","orange3","purple","blue2"))
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,"data/ANNO_DATA_FOR_CATSCATTER.txt",data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="cmapnew10",lg_y = 50,
plots = "scatter",left_margin = 60,plot_filter = list(c("col","byCategory")),plot_height = 40,
ch2D.colors = c("pink3","orange3","purple","blue2"),canvas_width = 600,
ch2D.lg_y = 100)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# chr.2D.plot = T)
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_2,chr.2D.plot = T,canvas_height = 300,id="cmaphyd10")
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# chr.2D.plot = T,
# plot_filter = list(c("col","byNumber")))
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_2,chr.2D.plot = T,canvas_height = 300,id="cmaphiygd10",plot_filter = list(c("col","byNumber")),
lg_x = 10)
## -----------------------------------------------------------------------------
head(read.table(anno_file_cate))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_cate,
# chr.2D.plot = T,
# plot_filter = list(c("col","byCategory")),
# ch2D.colors = c("red","blue"))
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_cate,chr.2D.plot = T,canvas_height = 300,id="cmtrphiygd10",plot_filter = list(c("col","byCategory")),
ch2D.colors = c("red","blue"),ch2D.lg_x = 15
)
## ----echo=F-------------------------------------------------------------------
chr_file <- "data/SLINK_chr.txt"
anno_file <- "data/SLINK_anno.txt"
link_data <- read.csv("data/SLINK22.csv",header = T)
## -----------------------------------------------------------------------------
head(link_data)
## ----eval=F-------------------------------------------------------------------
# chromoMap(chr_file, anno_file,
# # main arguments
# show.links = T,
# loci_links = link_data[,c(1:4)],
# links.colors = "red2",
# #plot adjustments
# ch_gap = 50,
# y_chr_scale = 100,
# top_margin = 100,
# )
## ----echo=F,fig.height=4.0----------------------------------------------------
chromoMap(chr_file, anno_file,
show.links = T,
loci_links = link_data[,c(1:4)],
#plot adjustments
links.colors = "red2",
ch_gap = 50,
y_chr_scale = 100,
top_margin = 100,
id="cnew1"
)
## ----eval=F-------------------------------------------------------------------
# chromoMap(chr_file, anno_file,
# # main arguments
# show.links = T,
# loci_links = link_data,
# links.colors = c("red2","blue2"),
# #plot adjustments
# ch_gap = 50,
# y_chr_scale = 100,
# top_margin = 100,
# links.lg_y = 300
# )
## ----echo=F,fig.height=4.0----------------------------------------------------
chromoMap(chr_file, anno_file,
show.links = T,
loci_links = link_data,
#plot adjustments
links.colors = c("red2","blue2"),
ch_gap = 50,
y_chr_scale = 100,
top_margin = 100,
id="cnew2",
canvas_width = 600,
links.lg_y = 30
)
## ----echo=F-------------------------------------------------------------------
link_data <- read.csv("data/SLINK_link2.csv",header = F)
## ----eval=F-------------------------------------------------------------------
# chromoMap(chr_file, anno_file,
# # main arguments
# show.links = T,
# loci_links = link_data,
# links.colors = c("red2","blue2","orange3","purple"),
# #plot adjustments
# ch_gap = 50,
# y_chr_scale = 100,
# top_margin = 100,
# )
## ----echo=F,fig.height=4.0----------------------------------------------------
chromoMap(chr_file, anno_file,
show.links = T,
loci_links = link_data,
#plot adjustments
links.colors = c("red2","blue2","orange3","purple"),
ch_gap = 50,
y_chr_scale = 100,
top_margin = 100,
id="cnew3",
canvas_width = 600,
links.lg_y = 30
)
## ----eval=F-------------------------------------------------------------------
# chromoMap(chr_file, anno_file,
# # main arguments
# show.links = T,
# loci_links = link_data,
# links.colors = c("red2","blue2","orange3","purple"),
# directed.edges = T,
# #plot adjustments
# ch_gap = 50,
# y_chr_scale = 100,
# top_margin = 100,
# )
## ----echo=F,fig.height=4.0----------------------------------------------------
chromoMap(chr_file, anno_file,
show.links = T,
loci_links = link_data,
#plot adjustments
links.colors = c("red2","blue2","orange3","purple"),
ch_gap = 50,
y_chr_scale = 100,
top_margin = 100,
id="cnew33",
canvas_width = 600,
links.lg_y = 30,
directed.edges = T
)
## ----echo=F-------------------------------------------------------------------
chr_file <- "data/TEST_chr.txt"
anno_file <- "data/TEST_anno.txt"
link_data <- read.csv("data/TEST_LINKSSS.csv",header = T)
## ----eval=F-------------------------------------------------------------------
# chromoMap(chr_file, anno_file,
# # main arguments
# segment_annotation = T,
# show.links = T,
# loci_links = link_data,
# links.colors = c("orange3","purple","green2"),
# #plot adjustments
# ch_gap = 50,
# y_chr_scale = 100,
# top_margin = 100,
# )
## ----echo=F,fig.height=4.0----------------------------------------------------
chromoMap(chr_file, anno_file,
show.links = T,
loci_links = link_data,
segment_annotation = T,
#plot adjustments
links.colors = c("orange3","purple","green2"),
ch_gap = 50,
y_chr_scale = 100,
top_margin = 100,
id="cnew4",
canvas_width = 600,
links.lg_y = 30
)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# canvas_width = 600,
# canvas_height = 700)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# title = "my first chromoMap plot")
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# title = "my first chromoMap plot",
# title_font_size = 12)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# top_margin = 25,
# left_margin = 15)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# chr_color = c("orange"))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(c("chromosome_file_set_1.txt","chromosome_file_set_2.txt")
# ,c("annotation_file_set_1.txt","annotation_file_set_2.txt"),
# ploidy = 2,
# chr_color = c("pink","blue"))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# anno_col = c("orange"))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(c("chromosome_file_set_1.txt","chromosome_file_set_2.txt")
# ,c("annotation_file_set_1.txt","annotation_file_set_2.txt"),
# ploidy = 2,
# anno_col = c("pink","blue"))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# chr_width = 4,
# chr_length = 5)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# ch_gap = 6)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# chr_curve = 5)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# chr_text = F)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(c("chromosome_file_set_1.txt","chromosome_file_set_2.txt")
# ,c("annotation_file_set_1.txt","annotation_file_set_2.txt"),
# ploidy = 2,
# chr_text = c(T,F))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# interactivity = F)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# scale.suffix = "cM")
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# display.chr = c(F))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# guides = T,
# guides_color = "black")
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# id="my_plot_1")
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_1,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "bar",
# ref_line = T,
# refl_pos = 15)
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_1,data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="cmap21",
plots = "bar",plot_ticks = 3,ref_line = T,
refl_pos = 15)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "scatter",
# ref_line = T,
# refl_pos = 20)
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_2,data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="cmap22",lg_y = 50,
plots = "scatter",left_margin = 60,plot_height = 40,ref_line = T,refl_pos = 20)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "scatter",
# plot_height = 50)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "scatter",
# plot_color = "orange")
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "tags",
# tagColor = "orange")
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "scatter",
# plot_ticks = 3,
# plot_y_domain = list(c(-5,5)))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(c(chr_file_1,chr_file_1),c(anno_file_1,anno_file_2),
# ploidy = 2
# data_based_color_map = T,
# data_type = "numeric",
# plots = c("bar","scatter"),
# plot_height = 40,
# plot_color = c("green","red"),
# ref_line = T,
# refl_pos = 20,
# #gridline arguments
# vertical_grid = T,
# grid_array = c(1,54,100,420,621))
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(c(chr_file_1,chr_file_1),c(anno_file_1,anno_file_2),data_based_color_map = T,data_type = "numeric",canvas_height = 400,id="cmap23",ploidy = 2,
plots = c("bar","scatter"),
plot_height = 40,
plot_color = c("green","red"),
ref_line = T,
refl_pos = 20,
vertical_grid = T,
grid_array = c(1,54,100,420,621),left_margin = 60)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(c(chr_file_1,chr_file_1),c(anno_file_1,anno_file_2),
# ploidy = 2
# data_based_color_map = T,
# data_type = "numeric",
# plots = c("bar","scatter"),
# plot_height = 40,
# plot_color = c("green","red"),
# ref_line = T,
# refl_pos = 20,
# #gridline arguments
# vertical_grid = T,
# grid_array = c(1,54,100,420,621),
# grid_text = c("","","mark 1","region 1",""))
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(c(chr_file_1,chr_file_1),c(anno_file_1,anno_file_2),data_based_color_map = T,data_type = "numeric",canvas_height = 400,id="cnew4125",ploidy = 2,
plots = c("bar","scatter"),
plot_height = 40,
plot_color = c("green","red"),
ref_line = T,
refl_pos = 20,
vertical_grid = T,
grid_array = c(1,54,100,420,621),left_margin = 60
,grid_text = c("","","mark 1","region 1",""))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "scatter",
# #highlighting a region on chr1
# vertical_grid = T,
# grid_array = c(550,754))
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_2,data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="new7777",lg_y = 50,
plots = "scatter",left_margin = 60,plot_height = 40,
vertical_grid = T,
grid_array = c(550,754))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "scatter",
# #zoom in
# region = c("chr1:1:550:754"))
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_2,data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="new77894",lg_y = 50,
plots = "scatter",left_margin = 60,plot_height = 40,
region = c("chr1:1:550:754"))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(chr_file_1,anno_file_2,
# data_based_color_map = T,
# data_type = "numeric",
# plots = "scatter",
# #zoom in
# region = c("chr1:1:550:754","chr2:1:221:450"))
## ---- echo=F, fig.height=3.5--------------------------------------------------
chromoMap(chr_file_1,anno_file_2,data_based_color_map = T,data_type = "numeric",canvas_height = 300,id="newh745994",lg_y = 50,
plots = "scatter",left_margin = 60,plot_height = 40,
region = c("chr1:1:550:754","chr2:1:221:450"))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# data_based_color_map = T,
# data_type = "categorical",
# legend = T)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap(c("chromosome_file_set_1.txt","chromosome_file_set_2.txt")
# ,c("annotation_file_set_1.txt","annotation_file_set_2.txt"),
# ploidy = 2,
# data_based_color_map = T,
# data_type = "numeric",
# legend = c(F,T))
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# data_based_color_map = T,
# data_type = "categorical",
# legend = T, lg_x = 100,
# lg_y = 250)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# labels=T)
## ---- echo=F, fig.height=3----------------------------------------------------
chromoMap(chr_file_1,"data/discrete_colormap.txt",
canvas_height = 250,id="cmap1254",labels = T)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# labels=T,
# label_font = 12,
# label_angle = -65)
## ---- echo=F, fig.height=3----------------------------------------------------
chromoMap(chr_file_1,"data/discrete_colormap.txt",
canvas_height = 250,id="cmap1925",labels = T,
label_font = 10,
label_angle = -65)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# labels=T,
# label_angle = -65,
# chr_length = 6,
# chr_width = 25,
# canvas_width = 800)
## ---- echo=F, fig.height=3----------------------------------------------------
chromoMap(chr_file_1,"data/discrete_colormap.txt",
canvas_height = 250,id="cmap17445",labels = T,
chr_length = 7,
chr_width = 25,
canvas_width = 900,label_font = 10,label_angle = -65)
## ----eval=FALSE---------------------------------------------------------------
# chromoMap("chromosome_file.txt","annotation_file.txt",
# hlinks=T)
## ----eval=FALSE---------------------------------------------------------------
# library(shiny)
# library(chromoMap)
#
# # Define UI for application that draws chromoMap
# ui <- fluidPage(
#
# # Application title
# titlePanel("An example of chromoMap in Shiny"),
#
# # you can use GUI controls for your chromoMap
# sidebarLayout(
# sidebarPanel(
# #some code
# ),
#
# # Show a plot of the generated distribution
# mainPanel(
# chromoMapOutput("myChromoMap")
# )
# )
# )
#
# # Define server logic required to draw chromoMap
# server <- function(input, output) {
#
# output$myChromoMap <- renderChromoMap({
# chromoMap("chromosome_file.txt","annotation_file.txt")
# })
# }
#
# # Run the application
# shinyApp(ui = ui, server = server)
#
## -----------------------------------------------------------------------------
sessionInfo()
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