[{"path":"/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. 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END TERMS CONDITIONS","code":""},{"path":"/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see <http://www.gnu.org/licenses/>. GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read <http://www.gnu.org/philosophy/--lgpl.html>.","code":"<one line to give the program's name and a brief idea of what it does.> Copyright (C) <year>  <name of author>  This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>. <program>  Copyright (C) <year>  <name of author> This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"/articles/surv-corr-connection.html","id":"univariable-cox-analysis","dir":"Articles","previous_headings":"","what":"Univariable Cox analysis","title":"Polar plot for survival and correlation connection","text":"","code":"df_cox = ezcox(data, vars) df_cox #> # A tibble: 7 × 12 #>   Variable  is_control contrast_level ref_level n_contrast n_ref      beta    HR #>   <chr>     <lgl>      <chr>          <chr>          <int> <int>     <dbl> <dbl> #> 1 age       FALSE      age            age              228   228  0.0187   1.02  #> 2 sex       FALSE      sex            sex              228   228 -0.531    0.588 #> 3 ph.ecog   FALSE      ph.ecog        ph.ecog          227   227  0.476    1.61  #> 4 ph.karno  FALSE      ph.karno       ph.karno         227   227 -0.0164   0.984 #> 5 pat.karno FALSE      pat.karno      pat.karno        225   225 -0.0199   0.98  #> 6 meal.cal  FALSE      meal.cal       meal.cal         181   181 -0.000124 1     #> 7 wt.loss   FALSE      wt.loss        wt.loss          214   214  0.00132  1     #> # … with 4 more variables: lower_95 <dbl>, upper_95 <dbl>, p.value <dbl>, #> #   global.pval <dbl>"},{"path":"/articles/surv-corr-connection.html","id":"correlation-analysis","dir":"Articles","previous_headings":"","what":"Correlation analysis","title":"Polar plot for survival and correlation connection","text":"","code":"vars_comb = combn(vars, 2, simplify = FALSE) cor_value = sapply(vars_comb, function(x) {   cor(data[[x[1]]], data[[x[2]]], use = \"pairwise\") })  df_cor = cbind(as.data.frame(t(sapply(vars_comb, function(x) x))), cor_value) colnames(df_cor) = c(\"var1\", \"var2\", \"correlation\") df_cor$size = abs(df_cor$correlation) df_cor$way = ifelse(df_cor$correlation > 0, \"positive\", \"negative\") df_cor #>         var1      var2 correlation       size      way #> 1        age       sex -0.12216709 0.12216709 negative #> 2        age   ph.ecog  0.19323604 0.19323604 positive #> 3        age  ph.karno -0.20318207 0.20318207 negative #> 4        age pat.karno -0.12616688 0.12616688 negative #> 5        age  meal.cal -0.23141071 0.23141071 negative #> 6        age   wt.loss  0.03814787 0.03814787 positive #> 7        sex   ph.ecog -0.02060379 0.02060379 negative #> 8        sex  ph.karno  0.01138505 0.01138505 positive #> 9        sex pat.karno  0.04607145 0.04607145 positive #> 10       sex  meal.cal -0.16835976 0.16835976 negative #> 11       sex   wt.loss -0.12907708 0.12907708 negative #> 12   ph.ecog  ph.karno -0.80726666 0.80726666 negative #> 13   ph.ecog pat.karno -0.51122086 0.51122086 negative #> 14   ph.ecog  meal.cal -0.09851018 0.09851018 negative #> 15   ph.ecog   wt.loss  0.18758944 0.18758944 positive #> 16  ph.karno pat.karno  0.52029737 0.52029737 positive #> 17  ph.karno  meal.cal  0.04223324 0.04223324 positive #> 18  ph.karno   wt.loss -0.17543452 0.17543452 negative #> 19 pat.karno  meal.cal  0.16575874 0.16575874 positive #> 20 pat.karno   wt.loss -0.17199064 0.17199064 negative #> 21  meal.cal   wt.loss -0.10257242 0.10257242 negative"},{"path":"/articles/surv-corr-connection.html","id":"visualization","dir":"Articles","previous_headings":"","what":"Visualization","title":"Polar plot for survival and correlation connection","text":"","code":"df_cox$role = ifelse(   df_cox$p.value > 0.05, \"non-signf\",   ifelse(df_cox$HR < 1, \"protector\", \"risker\") ) df_cox$`-log10(p)` = -log10(df_cox$p.value) p = polar_init(df_cox, x = Variable, aes(color = role, size = `-log10(p)`)) p p +    ggnewscale::new_scale(\"color\") +   polar_connect(df_cor, x1 = var1, x2= var2, size = size, color = way, alpha = 0.3) +    scale_size(range = c(0.1, 4)) #> Scale for 'size' is already present. Adding another scale for 'size', which #> will replace the existing scale."},{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors","text":"Shixiang Wang. Author, maintainer.","code":""},{"path":"/index.html","id":"ggpolar-dots-and-their-connections-in-polar-coordinate-system","dir":"","previous_headings":"","what":"Dots and Their Connections in Polar Coordinate System","title":"Dots and Their Connections in Polar Coordinate System","text":"ggpolar provides flexible way create dots coordinate system event list connect dots segments based {ggplot2}.","code":""},{"path":"/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Dots and Their Connections in Polar Coordinate System","text":"can install released version ggpolar CRAN : can install development version ggpolar GitHub :","code":"install.packages(\"ggpolar\") remotes::install_github(\"ShixiangWang/polar\")"},{"path":[]},{"path":"/index.html","id":"init-a-polar-plot","dir":"","previous_headings":"Example","what":"Init a polar plot","title":"Dots and Their Connections in Polar Coordinate System","text":"","code":"library(ggpolar) #> Loading required package: ggplot2  data <- data.frame(x = LETTERS[1:7])  p1 <- polar_init(data, x = x) p1 # Set aes value p2 <- polar_init(data, x = x, size = 3, color = \"red\", alpha = 0.5) p2 # Set aes mapping set.seed(123L) data1 <- data.frame(   x = LETTERS[1:7],   shape = c(\"r\", \"r\", \"r\", \"b\", \"b\", \"b\", \"b\"),   color = c(\"r\", \"r\", \"r\", \"b\", \"b\", \"b\", \"b\"),   size = abs(rnorm(7)) ) # Check https://ggplot2.tidyverse.org/reference/geom_point.html # for how to use both stroke and color p3 <- polar_init(data1, x = x, aes(size = size, color = color, shape = shape), alpha = 0.5) p3"},{"path":"/index.html","id":"connect-polar-dots","dir":"","previous_headings":"Example","what":"Connect polar dots","title":"Dots and Their Connections in Polar Coordinate System","text":"","code":"data2 <- data.frame(   x1 = LETTERS[1:7],   x2 = c(\"B\", \"C\", \"D\", \"E\", \"C\", \"A\", \"C\"),   color = c(\"r\", \"r\", \"r\", \"b\", \"b\", \"b\", \"b\") ) p4 <- p3 + polar_connect(data2, x1, x2) p4 # Unlike polar_init, mappings don't need to be included in aes() p5 <- p3 + polar_connect(data2, x1, x2, color = color, alpha = 0.8, linetype = 2) p5 # Use two different color scales if (requireNamespace(\"ggnewscale\")) {   library(ggnewscale)   p6 = p3 +     new_scale(\"color\") +     polar_connect(data2, x1, x2, color = color, alpha = 0.8, linetype = 2)   print(p6 + scale_color_brewer())   print(p6 + scale_color_manual(values = c(\"darkgreen\", \"magenta\"))) } #> Loading required namespace: ggnewscale"},{"path":"/index.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Dots and Their Connections in Polar Coordinate System","text":"use ggpolar academic research, please cite following paper along GitHub repo. Antigen presentation tumor immunogenicity cancer immunotherapy response prediction, eLife. https://doi.org/10.7554/eLife.49020.","code":""},{"path":"/reference/polar_connect.html","id":null,"dir":"Reference","previous_headings":"","what":"Connects dots — polar_connect","title":"Connects dots — polar_connect","text":"Check polar_init() examples.","code":""},{"path":"/reference/polar_connect.html","id":null,"dir":"Reference","previous_headings":"","what":"Usage","title":"Connects dots — polar_connect","text":"","code":"polar_connect(data, x1, x2, ...)"},{"path":"/reference/polar_connect.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Connects dots — polar_connect","text":"data data.frame contains connections events. x1, x2 column names (without quote) storing connected events. ... parameters passing ggplot2::geom_segment, expect c(x, xend, y, yend) 4 mapping parameters.","code":""},{"path":"/reference/polar_connect.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Connects dots — polar_connect","text":"ggplot object.","code":""},{"path":"/reference/polar_init.html","id":null,"dir":"Reference","previous_headings":"","what":"Init a dot plot in polar system — polar_init","title":"Init a dot plot in polar system — polar_init","text":"Init dot plot polar system","code":""},{"path":"/reference/polar_init.html","id":null,"dir":"Reference","previous_headings":"","what":"Usage","title":"Init a dot plot in polar system — polar_init","text":"","code":"polar_init(data, x, ...)"},{"path":"/reference/polar_init.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Init a dot plot in polar system — polar_init","text":"data data.frame contains events, e.g., genes. x column name (without quote) storing event list. ... parameters passing ggplot2::geom_point.","code":""},{"path":"/reference/polar_init.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Init a dot plot in polar system — polar_init","text":"ggplot object.","code":""}]
