update readme

sulab-wmu · Nov 21, 2023 · 569ed1a · 569ed1a
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diff --git a/.Rhistory b/.Rhistory
@@ -1,4 +1,3 @@
-legend.key = element_rect(colour = NA, fill = NA), axis.ticks = element_blank(),
 plot.margin = unit(c(0, 0, 0, 0), "points")
 )
 p <- p + coord_cartesian(xlim = xlims, ylim = ylims, expand = FALSE, default = T)
@@ -510,3 +509,4 @@ head(block_annotation_hg37)
 block_annotation_hg37[1:10,]
 block_annotation_hg37[1:20,]
 dim(block_annotation_hg37)
+library(scPagwas)
diff --git a/R/.Rhistory b/R/.Rhistory
diff --git a/README.Rmd b/README.Rmd
@@ -43,7 +43,6 @@ install.packages("ggpubr")
 if (!require("BiocManager", quietly = TRUE))
     install.packages("BiocManager")
 BiocManager::install("GenomicRanges")
-BiocManager::install("IRanges")
 
 devtools::install_github("sulab-wmu/scPagwas")
 ```
@@ -54,11 +53,6 @@ In many cases, installing packages using `devtools::install_github` may fail.
 library(devtools)
 install_git("https://github.com/sulab-wmu/scPagwas.git", ref = "main")
 ```
-Or, download the package file from [here](https://api.github.com/repos/sulab-wmu/scPagwas/tarball/HEAD)
-Then install it locally.
-```r
-devtools::install_local("sulab-wmu-scPagwas-****.tar.gz")
-```
 
 
 ## Usage 

diff --git a/README.md b/README.md
@@ -36,7 +36,6 @@ install.packages("ggpubr")
 if (!require("BiocManager", quietly = TRUE))
     install.packages("BiocManager")
 BiocManager::install("GenomicRanges")
-BiocManager::install("IRanges")
 
 devtools::install_github("sulab-wmu/scPagwas")
 ```
@@ -49,14 +48,6 @@ library(devtools)
 install_git("https://github.com/sulab-wmu/scPagwas.git", ref = "main")
 ```
 
-Or, download the package file from
-[here](https://api.github.com/repos/sulab-wmu/scPagwas/tarball/HEAD)
-Then install it locally.
-
-``` r
-devtools::install_local("sulab-wmu-scPagwas-****.tar.gz")
-```
-
 ## Usage
 
 quick-start example:

diff --git a/inst/extdata/plot_scpathway_contri_dot.R b/inst/extdata/plot_scpathway_contri_dot.R
@@ -125,6 +125,7 @@ plot_scpathway_dot <- function(Pagwas,
   spe <- unique(spe2$path)
 
   ######### 合并产生画图函数
+  spe<-intersect(rownames(proportion_df),spe)
   scPathrankP <- scPathrankP[spe, celltypes]
   proportion_df <- proportion_df[spe, celltypes]
   proportion_df <- as.data.frame(proportion_df)