## ----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()