diff --git a/DESCRIPTION b/DESCRIPTION index 5b7daa3..be027e3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: ddh Type: Package Title: Utility Functions and Data Sets for Data-driven Hypothesis -Version: 0.3.33 +Version: 0.3.34 Authors@R: c( person(given = "Matthew", family = "Hirschey", diff --git a/R/plots.R b/R/plots.R index d70ec0b..5f80573 100644 --- a/R/plots.R +++ b/R/plots.R @@ -2676,7 +2676,7 @@ make_cellbar <- function(input = list(), } ## DENSITY PLOT ---------------------------------------------------------------- -#' Cell Dependencies Density Plot +#' Dependencies Density Plot #' #' Kernel density estimate of dependency scores. Dependency scores across all cell lines for queried genes, revealing overall influence of a gene on cellular fitness. The interval indicates the 95 percent quantile of the data, the dot indicates the median dependency score. The gray background highlights weak dependency values between -1 and 1. #' @@ -2852,7 +2852,7 @@ make_cellbins <- function(input = list(), ## LINEAGE LINERANGE PLOT ------------------------------------------------------ #' Dependency Lineage Plot #' -#' Each point shows the median dependency score for the gene query within a given cell lineage. The intervals show the 5 percent quantiles centered on the median, the interquartile ranges, and the 95 percent quantiles. The gray background highlights weak dependency values between -1 and 1. +#' Each point shows the median dependency score for the queried genes within a given cell lineage. The intervals show the 5 percent quantiles centered on the median, the interquartile ranges, and the 95 percent quantiles. #' #' @param input Expecting a list containing type and content variable. #' @param card A boolean that sets whether the plot should be scaled down to be a card @@ -3043,7 +3043,7 @@ make_lineage <- function(input = list(), ## SUB-LINEAGE LINE RANGE PLOT ------------------------------------------------------ #' Dependency Sub-lineage Plot #' -#' Each point shows the median dependency score for the gene query within a given cell sub-lineage. The intervals show the 5 percent quantiles centered on the median, the interquartile ranges, and the 95 percent quantiles. The gray background highlights weak dependency values between -1 and 1. +#' Each point shows the median dependency score for the queried genes within a given cell sub-lineage. The intervals show the 5 percent quantiles centered on the median, the interquartile ranges, and the 95 percent quantiles. #' #' @param input Expecting a list containing type and content variable. #' @param card A boolean that sets whether the plot should be scaled down to be a card @@ -3234,7 +3234,7 @@ make_sublineage <- function(input = list(), ## CORRELATION PLOT FOR CELL DEPS-------------------------------------------------------- #' Co-essentiality Correlation Plot #' -#' Each point shows the ranked correlation value ordered from high to low for each query. Correlation values outside the solid gray lines indicate the gene has a correlation value greater than the mean. +#' Each point shows the ranked correlation value ordered from high to low for each query. Correlation values above or below the dashed gray lines indicate the gene has a correlation value greater than the mean. #' #' @param input Expecting a list containing type and content variable. #' @param card A boolean that sets whether the plot should be scaled down to be a card @@ -3376,9 +3376,9 @@ make_correlation <- function(input = list(), } ## EXPvDEP PLOT -------------------------------------------------------- -#' Gene Dependency versus Expression +#' Gene Dependency vs Expression Plot #' -#' Each point shows the dependency value compared to the expression value for a gene within a given cell line. Gray area indicates dependency values that are between -1 and 1. +#' Each point shows the dependency value compared to the gene expression value for a gene within a given cell line. The Pearson correlation coefficient and the p-values are provided in the top-left corner of the plot. #' #' @param input Expecting a list containing type and content variable. #' @param card A boolean that sets whether the plot should be scaled down to be a card diff --git a/man/make_cellbins.Rd b/man/make_cellbins.Rd index 61af5c9..bddcefe 100644 --- a/man/make_cellbins.Rd +++ b/man/make_cellbins.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/plots.R \name{make_cellbins} \alias{make_cellbins} -\title{Cell Dependencies Density Plot} +\title{Dependencies Density Plot} \usage{ make_cellbins(input = list(), card = FALSE) } diff --git a/man/make_correlation.Rd b/man/make_correlation.Rd index 27e34d3..a9e7180 100644 --- a/man/make_correlation.Rd +++ b/man/make_correlation.Rd @@ -15,7 +15,7 @@ make_correlation(input = list(), card = FALSE, scale = NULL) If no error, then returns a correlation plot. If an error is thrown, then will return a bomb plot. } \description{ -Each point shows the ranked correlation value ordered from high to low for each query. Correlation values outside the solid gray lines indicate the gene has a correlation value greater than the mean. +Each point shows the ranked correlation value ordered from high to low for each query. Correlation values above or below the dashed gray lines indicate the gene has a correlation value greater than the mean. } \examples{ make_correlation(input = list(type = 'gene', query = 'ROCK1', content = 'ROCK1')) diff --git a/man/make_expdep.Rd b/man/make_expdep.Rd index 8d78be7..30a2e2a 100644 --- a/man/make_expdep.Rd +++ b/man/make_expdep.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/plots.R \name{make_expdep} \alias{make_expdep} -\title{Gene Dependency versus Expression} +\title{Gene Dependency vs Expression Plot} \usage{ make_expdep(input = list(), plot_se = FALSE, card = FALSE) } @@ -15,7 +15,7 @@ make_expdep(input = list(), plot_se = FALSE, card = FALSE) If no error, then returns a expdep plot. If an error is thrown, then will return a bomb plot. } \description{ -Each point shows the dependency value compared to the expression value for a gene within a given cell line. Gray area indicates dependency values that are between -1 and 1. +Each point shows the dependency value compared to the gene expression value for a gene within a given cell line. The Pearson correlation coefficient and the p-values are provided in the top-left corner of the plot. } \examples{ make_expdep(input = list(type = 'gene', query = 'ROCK1', content = 'ROCK1')) diff --git a/man/make_lineage.Rd b/man/make_lineage.Rd index 476d87a..10a9aaa 100644 --- a/man/make_lineage.Rd +++ b/man/make_lineage.Rd @@ -15,7 +15,7 @@ make_lineage(input = list(), card = FALSE, highlight = FALSE) If no error, then returns a lineage plot. If an error is thrown, then will return a bomb plot. } \description{ -Each point shows the median dependency score for the gene query within a given cell lineage. The intervals show the 5 percent quantiles centered on the median, the interquartile ranges, and the 95 percent quantiles. The gray background highlights weak dependency values between -1 and 1. +Each point shows the median dependency score for the queried genes within a given cell lineage. The intervals show the 5 percent quantiles centered on the median, the interquartile ranges, and the 95 percent quantiles. } \examples{ make_lineage(input = list(type = 'gene', query = 'ROCK1', content = 'ROCK1')) diff --git a/man/make_sublineage.Rd b/man/make_sublineage.Rd index 5d90833..9826014 100644 --- a/man/make_sublineage.Rd +++ b/man/make_sublineage.Rd @@ -15,7 +15,7 @@ make_sublineage(input = list(), card = FALSE, highlight = FALSE) If no error, then returns a lineage plot. If an error is thrown, then will return a bomb plot. } \description{ -Each point shows the median dependency score for the gene query within a given cell sub-lineage. The intervals show the 5 percent quantiles centered on the median, the interquartile ranges, and the 95 percent quantiles. The gray background highlights weak dependency values between -1 and 1. +Each point shows the median dependency score for the queried genes within a given cell sub-lineage. The intervals show the 5 percent quantiles centered on the median, the interquartile ranges, and the 95 percent quantiles. } \examples{ make_sublineage(input = list(type = 'gene', query = 'ROCK1', content = 'ROCK1'))